st general meeting june 22-24, 2015 ipk gatersleben,...

COST FA1306 The quest for tolerant varieties - Phenotyping at

plant and cellular level

1st General Meeting June 22-24, 2015

IPK Gatersleben, Germany

1st General Meeting June 22-24, 2015 COST FA1306 The quest for tolerant varieties - Phenotyping at plant and cellular level

Table of Contents WELCOME ............................................................................................................................. I

General Information ............................................................................................................... II

Internet access ..................................................................................................................... IV

Organizing Committee ........................................................................................................... V

Local Organizers and support................................................................................................ V

General Information about COST FA1306 ............................................................................ VI

Program .............................................................................................................................. VII

Abstracts for oral presentations ............................................................................................. 1

Session 1: Novel sensors and sensor integration: from low tech to high tech .................... 2

Session 2: Phenotyping the metabolome ..........................................................................20

Session 3: From gene to phene: screening natural diversity .............................................35

Poster Abstracts ...................................................................................................................49

Session 1: Novel sensors and sensor integration: from low tech to high tech ...................50

Session 2: Phenotyping the metabolome ..........................................................................62

Session 3: From gene to phene: screening natural diversity .............................................71

Map of IPK ...........................................................................................................................96

List of participants ................................................................................................................97


I

WELCOME

Dear participants of the 1st General Meeting of the COST Action FA 1306 – The quest for tolerant varieties – Phenotyping at the plant and cellular level,

On behalf of the meeting organizers and the Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), we would like to extend to you a warm welcome to Gatersleben. It is a great pleasure to have you around for the next three days and to have the opportunity to exchange our ideas, experiences, and results in the scientific area covered by this COST Action, which is of common interest to all of us.

We hope that we were able to put together an attractive program with four excellent key note lectures of colleagues leading their fields of research, 40 further oral presentations, and 45 posters. With 128 registered participants, this meeting shall serve as a platform not only to listen and discuss the presentations given in the three plenary sessions and the two poster sessions, but shall also give all of us a forum to talk in person, learn from each other, and get to know new colleagues. We hope that this is not only supported by the environment here at the Gatersleben campus, but also by our gathering in the historic city of Quedlinburg, where you also are accommodated.

The topic addressed in the COST Action FA 1306 is of particular interest to IPK, whose vision is to conduct modern plant research as a contribution to meet future societal challenges and whose aims are to develop approaches and to gain knowledge to support the efficient and sustainable supply of food, feed, raw materials, and energy through knowledge-based preservation, expansion, and utilization of crop plant biodiversity. We are therefore particularly pleased to host you here and to give you also some insight into the research conducted here and an impression of the facilities and resources we have available and we are pleased to share with our co-operation partners in research projects of mutual interest. It is our sincere hope that this meeting will not only strengthen the already existing links to many of you but will furthermore lead to many new contacts, interactions, and future collaborations.

We would like to thank the COST Organisation and all of our further supporters for the financial and kind contributions to this meeting, without which we would not be able to conduct the conference and many of the participants would not be able to attend.

We wish all of us an inspiring and enjoyable conference!

Astrid Junker & Thomas Altmann

On behalf of the Organizing Committee


II

General Information

Shuttle busses

For all three meeting days we organized bus transfers from Hotel Acron and Hotel

Schlossmühle to the institute in Gatersleben. Please consult the city map of Quedlinburg

(next page) for checking the pick-up sites.

Acron Hotel

Gartenstraße 44 A, 06484 Quedlinburg

Pick up times:

Monday, 22.06.2015 8:00am

Tuesday and Wednesday, 23./24.06.2015 7:45am

Hotel Schlossmühle

Kaiser Otto Straße 28, 06484 Quedlinburg

Pick up times:

Monday, 22.06.2015 8:00am

Tuesday and Wednesday, 23./24.06.2015 7:45am

Please check the program for times of the transfer back to Quedlinburg.


III


IV

Internet access at IPK

EDUROAM

Eduroam Account – SSID = eduroam

Employees from other scientific institutions with eduroam participation can login with their home-login name (username@homedomain)

For connection please choose the WLAN with the SSID „eduroam“ and when a input mask appears, type your home-username (username@homedomain) with the respective password.

If a certificate warning message is shown, check it thoroughly and accept it if the server is reliable.

For this connection please do not configure a proxy server!

GUEST

WLAN (free of charge) - SSID = guest

Vouchers are available at the reception desk.

For connection please choose the WLAN with the SSID „guest“ and type the WPA/WPA2 encryption key as shown on the voucher. Open a browser and you’ll be redirected to a login page. Type the username and password from the Voucher.

Please enable automatic proxy configuration for this connection:


V

Organizing Committee

Astrid Junker, IPK Gatersleben, Germany

Thomas Altmann, IPK Gatersleben, Germany

Sebastien Carpentier, KU Leuven, Belgium (Chair of the COST Action FA1306)

Ulrich Schurr, Forschungszentrum Juelich, Germany (Co-Chair of the COST Action FA1306)

Andreas Voloudakis, Agricultural University of Athens, Greece

Estelle Goulas, UMR 8576 CNRS/Université Lille 1, France

Carla Pinheiro, ITQB, Portugal

Dyonisia Fasoula, Agricultural Research Institute, Cyprus

Diego Rubiales, Institute for Sustainable Agriculture, CSIC, Spain

Rick van de Zedde, Wageningen UR, The Netherlands

Carl-Otto Ottosen, Aarhus University, Denmark

Eva Rosenqvist, University of Copenhagen, Denmark

Local Organizers and support IPK Gatersleben

Astrid Junker

Thomas Altmann

Uwe Scholz

Daniel Arend

Sibille Bettermann

Karin Lipfert

Beate Scheer

Katrin Menzel


VI

General Information about COST FA1306

Mission of FA1306

Phenotyping is an emerging science that characterizes plant behaviour and quantifies features such as growth and stress tolerance in a precise and reproducible manner that allows linking to genetic control. As a highly interdisciplinary research area, phenotyping covers a wide range of methodological approaches from imaging based whole plant phenotyping (characterization of morphological and physiological plant features), over molecular phenotyping approaches on a cellular level (transcriptomics, proteomics, metabolomics) up to computational methods for image analysis, plant growth modeling and statistical data analysis and data integration. The FA1306 work plan is divided into 3 work groups (WG):

Work Group 1 Phenotyping at the plant level

This WG will collect information and novel developments in: - sensors & image analysis - plant physiology/pathology - modelling plant growth and real time monitoring - data management & statistics - Screening the biodiversity of European gene bank collections - Screening the parents and the offspring of breeding programs and different genetically modified plants

Work Group 2 Phenotyping at the cell level

This WG will collect information and novel developments in: - Metabolomics and flux analysis - Proteomics - Transcriptomics - Genomics

Work Group 3 Integration of phenotyping at both levels and translation into good practices for applied end use

This WG will follow up the developments made in systems biology by integrating phenotyping on different levels and will collect the developments in translational research. - Phenotyping in practice (greenhouse/field) - Integration of different omics technologies


VII

Program Monday, 22.6.2015 Session 1: Novel sensors and sensor integration: from low tech to

high tech

08:00 Registration 09:00 Opening (Altmann/Junker/Carpentier) 09:30 Keynote Lecture Malcolm Bennett (University of Nottingham, UK)

Root Phenotyping: uncovering novel traits using tomographic tools 10:30 Coffee break

Chair: Diego Rubiales 10:50 Ralf C. Sammler (IPK Gatersleben, Germany)

Estimating the nutrient status of plants by hyperspectral imaging 11:10 Ethan Stewart (ETH Zurich, Switzerland)

Elucidating the quantitative nature of virulence in an important wheat pathogen using high throughput automated image analysis

11:30 Reinhard Töpfer (Julius Kühn-Institut, Germany) High-throughput phenotyping in vineyards

11:50 Nicolas Rispail (Institute for Sustainable Agriculture – CSIC, Spain)

Infra-red thermography as new tool for screening Fusarium wilt resistance in pea

12:10 Lunch at IPK Casino Chair: Dionysia Fasoula

13:00 David Rousseau (Université Lyon, France) Image denoising techniques for computational imaging in plant sciences

13:20 Marie Neal (Aberystwyth University, United Kingdom) Micro-climate Monitoring for Crop Phenotyping

13:40 Eva Rosenqvist (University of Copenhagen, Denmark) Chlorophyll fluorescence – protocols for medium throughput phenotyping

14:00 Paulo Sergio de Paula Herrmann (Forschungszentrum Jülich, Germany)

A non-invasive method, using microstrip patch antennas, to measure the volumetric soil moisture content in the profile of a rhizobox

14:20 Onno Müller (Forschungszentrum Jülich, Germany)

Field Phenotyping: Combining low-tech with high-tech paving the road to high throughput field phenotyping

14:40 Coffee Break Chair: Andreas Voloudakis

15:00 Stefan Gerth (Fraunhofer IIS, Development Center X-Ray Technology EZRT, Germany)

Tuber growth analysis using x-ray computed tomography 15:20 Ralf Metzner (Forschungszentrum Jülich , Germany)

Imaging belowground dynamics with MRI and PET 15:40 Grégoire Hummel (PHENOSPEX, The Netherlands)

LeasyScan – a novel semi-field platform to phenotype traits controlling plant water budget


VIII

Monday, 22.6.2015 Session 1: Novel sensors and sensor integration: from low tech to high tech

16:00 Rick van de Zedde (Wageningen UR, The Netherlands) Reproducibility of phenotyping platforms

16:20 Beat Keller (Forschungszentrum Jülich , Germany)

The Light Induced Fluorescence Transient (LIFT) method for active leaf fluorescence measurements from field to lab

16:40 Ulrich Schurr (Forschungszentrum Jülich , Germany)

EMPHASIS - European Multi-environment Plant pHenotyping And Simulation InfraStructure

17:00 Astrid Junker (IPK Gatersleben, Germany)

Plant Phenomics at IPK: multi-sensor setups for a comprehensive and integrated analysis of plant phenotypes

17:20 Guided tours through IPK Phenomics facilities 19:00 Dinner at IPK Casino 20:00 Poster Session (parallel session: MC meeting) 22:00 Transport to QLB

Tuesday, 23.6.2015 Session 2: Phenotyping the metabolome

Chair: Sebastien Carpentier 08:30 Keynote Lecture: Yves Gibon (INRA Bordeaux, France)

Investigating plant performance using metabolic phenotyping 09:30 Gerrit Beemster (University of Antwerp, Belgium)

Kinematic analysis of cell division in maize leaves: a basis for sampling for "omics" to gain an integrated understanding of the growth response to drought

09:50 Giles Nicholas Johnson (University of Manchester, United Kingdom)

Metabolic Signalling in Temperture and Light Acclimation of Arabidopsis

10:10 Pinheiro, Carla (ITQB, Portugal)

Discriminating between good quality and bad quality cork by means of polyphenol profiling

10:30 Coffee break Chair: Estelle Goulas

11:00 Marta Wilton Vasconcelo (Universidade católica Portuguesa, Portugal)

Meta(l)bolomics: metabolomics analysis of iron (Fe) deficiency responses in soybean

11:20 Chrystalla Antoniou (Cyprus University of Technology, Cyprus)

Cross-talk between spermine homeostasis and reactive oxygen/nitrogen species increases tolerance to nitro-oxidative stress in Arabidopsis thaliana via modifications in root system architecture and RFO-related metabolites


IX

Tuesday, 23.6.2015 Session 2: Phenotyping the metabolome

11:40 Eliana Alves (University of Aveiro, Portugal)

A valuable “omics” platform for plant fingerprinting: the lipidome of marine macroalgae as a case study

12:00 Michal Janiak (KU Leuven, Belgium)

Phenotyping translates the gobbledygook of the speaking plant: the story of the sucrose feedback in nutrient sensing and the role of trehalase in transpiration efficiency

12:20 Lunch at IPK Casino 13:15 Guided tour through IPK proteomics/metabolomics facilities

Chair: Sebastien Carpentier

15:00 Radomira Vankova (Institute of Experimental Botany AS CR, Czech Republic)

The comparison of phytohormone functions in salt and phosphate deficiency stress responses

15:20 Stefanie Wienkoop (University of Vienna, Austria)

Impact of plant nutrition towards enhance drought tolerance – a different perspective

15:40 Coffee break Chair: Carla Pinhiero

16:00 Elisabete Maciel (University of Aveiro, Portugal)

Plant lipidomics based on HILIC-MS to valorisation of autochthonous halophyte plants

16:20 Leonor Guerra-Guimarães (Instituto de Investigação Cientifica Tropical, Portugal)

The role of phenolic compounds, salicylic acid and PR-proteins in the Coffea arabica-Hemileia vastatrix interactions

16:40 Monika Wimmer (University of Bonn, Germany)

Early detection of drought stress in young sugar beet plants (Beta vulgaris L.) by metabolite analysis and thermography

17:00 Thomas Altmann (IPK Gatersleben, Germany)

Plant phenotyping for analysis of genetic variation and heterosis of growth and metabolism

17:20 Poster Session 18:00 Transport to Quedlinburg 18:30 Short walk to the castle, presentation of QLB history 19:30 Dinner Schlossmühle Quedlinburg


X

Wednesday, 24.6.2014 Session 3: From gene to phene: screening natural diversity

Chair: Rick van de Zedde 08:30 Keynote Lecture: Andreas Graner (IPK Gatersleben, Germany)

Trait discovery and trait mapping in ex situ collections: challenges and opportunities

09:30 Keynote Lecture: Peter Wenzl (Global Crop Diversity Trust, Bonn, Germany)

Diversity Seek (DivSeek): An international partnership to harness the genetic potential of crop diversity’

10:30 Coffee break Chair: Carl-Otto Ottosen

10:50 Rong Zhou (Aarhus University, Denmark) Screening for chilling tolerance in soya and broad bean

11:10 Ivan A. Paponov (Bioforsk, Norway)

Phenotyping of nitrogen use efficiency in plants: field vs. control conditions

11:30 Kenny Paul (Biological Research Center, HAS, Hungary)

Non-invasive plant phenotyping using photosynthetic tools to characterize ’biomass and grain yield’ under water stress in wheat

11:50 Dew Kumari Sharma (University of Copenhagen, Denmark)

Hunting QTLs to maintain photosynthetic efficiency under heat stress in bread wheat

12:10 Lunch Chair: Eva Rosenqvist

13:00 Guided tour through IPK Genebank 14:30 Christoph-Martin Geilfus (KU Leuven, Belgium)

Chloride-inducible transient apoplastic alkalinizations trigger stomata closure by controlling abscisic acid distribution: a pilot study linking proteome and phenome in salt stressed Vicia faba L.

14:50 Carl-Otto Ottosen (Aarhus University, Denmark) Screening for chilling tolerance in soya and broad bean

15:10 Jeremy Harbinson (Wageningen University, The Netherlands) Phenotyping and gene localisation of plant photosynthetic traits

15:30 Coffee break Chair: Ulrich Schurr

15:50 Dionysia A. Fasoula (Agricultural Research Institute, Cyprus)

On the appropriate conditions to perform single-plant root phenotyping concurrently with direct selection for efficient resource utilization: a field study with cowpea

16:10 Diego Rubiales (CSIC, Spain)

Screening for powdery mildew resistance in pea: complementation of field and growth chamber studies with histology, genomics and proteomics

16:30 Katja Witzel (Leibniz Institute of Vegetable and Ornamental Crops, Germany)

Profiling of plant secondary metabolites and identification of mQTL in an Eurasian Brassica rapa mapping population


XI

Wednesday, 24.6.2014 Session 3: From gene to phene: screening natural diversity

16:50 Ewaut Kissel (KU Leuven, Belgium) Unraveling early leaf stress response by -omics integration in Musa

17:10 Open discussion between scientists and industry about the outreach of the COST action

18:30 Closing remarks

Abstracts for oral presentations


Session 1 2

Session 1: Novel sensors and sensor integration: from low tech to high tech


Session 1 3

KEYNOTE LECTURE

Root Phenotyping: uncovering novel traits using tomographic tools

Malcolm Bennett

University of Nottingham, United Kingdom

Crop production has to double by 2050 to keep pace with global population growth. This target is even more challenging given the impact of climate change on water availability and the drive to make agriculture more sustainable. Root architecture traits are known to influence water and nutrient uptake efficiency. I will initially describe the Hounsfield CT Facility, a fully roboticised root-imaging platform, designed to screen for crops with improved root architecture-based water and nutrient foraging traits.

The vast majority of genes that regulate root traits such as angle, depth and density still remain to be identified in crops. I will describe how we are exploiting our knowledge of root regulatory genes in model plants to either manipulate crop root architecture using transgenic approaches or pinpoint closely related crop genes that control root traits using genome wide association studies with US collaborators.

Keywords

root architecture, root phenotyping, tomography


Session 1 4

Estimating the nutrient status of plants by hyperspectral imaging

Ralf C. Sammler, Benjamin D. Gruber, Nicolaus von Wirén


Knowing the nutrient status of a plant provides the key for understanding its growth. Such insight may enable growers to identify nutrient-efficient lines, counteract malnutrition, and improve yield. So far, this information requires high expenses, e.g. by wet-lab analysis. Hyperspectral imaging (HI) promises a deeper insight into a plant’s nutrient status. Our first aim is to establish HI as method to estimate a plant’s nutrient status. This includes the training of prediction models that interpret spectral changes over time or caused by fertilization. The final goal is to employ HI for phenotyping genotypes for root growth or nutrient efficiency. Two platforms were established for imaging barley leaves either in the field or the laboratory. First focus was on monitoring plant growth during senescence and triggering spectral changes by leaf fertilization. Second focus was on investigating the spectral response in leaves to roots striking nutrient bands in the subsoil. First prediction models were trained on plants grown either in a potting mix in the greenhouse or in the climate chamber in hydroponics under various nutrient supplies. Resulting prediction models showed fair to high accuracies for estimating the element concentrations of various nutrients. Furthermore, the spectral information allowed to identify age and part of a leaf and the nutrition treatment with fair to high accuracies. In general, hyperspectral imaging proved to be suitable for estimating the nutrient status of plant leaves. Tests on the applicability and accuracy of HI-based prediction models in the field are ongoing.

Keywords

Hyperspectral, Imaging, Spectral, Phenotyping, Field


Session 1 5

Elucidating the quantitative nature of virulence in an important wheat pathogen using high throughput automated image analysis

Ethan Stewart, Mark Lendenmann, Daniel Croll, Bruce McDonald

ETH Zurich, Switzerland

Zymoseptoria tritici (aka Mycosphaerella graminicola) causes Septoria tritici blotch, a damaging disease on wheat worldwide. Symptoms include chlorotic and necrotic lesions containing asexual fruiting bodies called pycnidia. The reduced photosynthetic capacity caused by leaf lesions can reduce yields by up to 40%. Despite its significance, little is known about virulence mechanisms in this pathogen.

A high throughput phenotyping method based on automated digital image analysis was developed to accurately measure the percentage of leaf area covered by lesions (PLACL) as well as the number, size and pigmentation of the pycnidia (Stewart & McDonald, 2014). This method allowed us to accurately quantify phenotypic differences in two different Z. tritici mapping populations. Measuring the density and size of pycnidia on a leaf gives a direct measure of the reproductive output of the pathogen that has not been feasible until now. Pycnidia size, density and pigmentation were found to be quantitative traits that showed a continuous distribution in both mapping populations.

Using the next generation sequencing technology RADseq, ~8500 informative SNP genetic markers were generated in each mapping population and were used in conjunction with the phenotype data to carry out a QTL mapping study. QTLs underlying all measured virulence traits were identified. In some cases, the same QTLs were associated with PLACL and pycnidia production, but in other cases they mapped as separate characters. Different QTLs were found between different mapping populations and different wheat cultivars. Based on the QTL mapping results, several candidate genes associated with virulence were identified.

Whilst the current study focused on the pathogen populations, it would be equally suited to screen plant populations with the goal of identifying disease resistance traits. The method is freely available and also has the potential to be adapted to other plant diseases.

References

Stewart, E.L. & McDonald, B.A. 2014. Measuring quantitative virulence in the wheat pathogen Zymoseptoria tritici using high-throughput automated image analysis. Phytopathology. 104(9):985-92.

Keywords

Image analysis, QTL mapping, plant pathology


Session 1 6

High-throughput phenotyping in vineyards

Reinhard Töpfer, Anna Kicherer, Katja Herzog

Julius Kühn-Institut, Germany

Grapevine Breeding is very time-consuming and labor-intensive. To increase breeding efficiency efficient genotyping methods were integrated into the breeding program within the last decade. This allows a significant improvement in the selection of new resistant breeding lines at early seedling stage. A bottleneck, however, is the very time-consuming and labor-intensive phenotyping. So far, phenotyping is mainly done mostly by visual estimations. With the recent development of sensor techniques, a new field of application emerged providing non-destructive measurements of plant characteristics. Simultaneous, reliable and objective measurements are possible by using different sensors and provide the basis of a quantitative and qualitative trait determination.

Within two interdisciplinary projects (CROP.SENSE.net, PHENOvines) funded by the Federal Ministry of Education and Research (BMBF) an phenotyping pipeline for high-throughput (HT) field phenotyping was assembled and tested in the vineyard. The method is based on two automated components. It uses GPS data for automatic navigation of a carrier vehicle with a multi-camera system for image acquisition in the vineyard. The subsequent analysis is also done automatically for individual traits.

The automated phenotyping pipeline consists of several components: (1) data collection, using an automatically GPS tracked vehicle with a camera system, (2) the data management established on an image database, (3) data analysis with various automatically running programs that have access to the database and (4) the application for genetic analysis or selection of breeding material. The high-throughput phenotyping pipeline was tested in the vineyard using 600 varieties, each represented by three plants (image data of 1800 vines) of the grapevine repository at Geilweilerhof to extract the characteristics of berry size and berry color. The data collection took about 8 hours, which subsequently was followed by the automatic image analysis. After establishing the phenotyping pipeline a future task is the development of further evaluation modules as well as the integration of additional sensors.

Keywords

Grapevine breeding, Phenotying pipeline, Field robot, Berry size


Session 1 7

Infra-red thermography as new tool for screening Fusarium wilt resistance in pea

Nicolas Rispail and Diego Rubiales

Institute for Sustainable Agriculture - CSIC, Spain

The recent development of image-based phenotyping such as the evaluation of surface temperature by infra-red imaging system is revolutionizing agriculture and plant science. Infra-red thermography is a non-contact, non-destructive and rapid technique which provides a temperature map of the targeted material or plant. Plant surface temperature is dependent on transpiration rate which is directly related with its physiological status. Thus it has been largely applied to monitor plant water status and to identify stressed plants. This approach was also successfully used to screen for drought or salinity tolerance. To determine whether infra-red thermography could also be useful for disease resistance breeding, we monitored surface leaf temperature of several pea accessions with contrasting response to Fusarium wilt, one of its major constraints. Inoculation with Fusarium oxysporum f. sp. pisi induced a significant temperature increase of at least 0.5 °C after 10 days in the susceptible pea accessions, while the temperature of resistant accessions remained at control level. The increase in leaf temperature at 10 days post-inoculation was positively correlated with the AUDPC calculated over a 30 days period. Thus, this approach allowed the early discrimination between resistant and susceptible accessions. As such, applying infra-red imaging system in breeding for Fusarium wilt resistance would contribute to considerably shorten the process of selection of novel resistant sources.

Keywords

Infra-red thermography, fusarium wilt, disease resistance, Pisum sativum


Session 1 8

Image denoising techniques for computational imaging in plant sciences

David ROUSSEAU, Etienne BELIN, François CHAPEAU-BLONDEAU

Université Lyon 1, France

Computational imaging refers to all imaging techniques where the acquired data are not ready for direct visualization but require some numerical preprocessing beforehand. In plant sciences these techniques are widely used with multispectral imaging systems when a small number of gray level images captured around selected spectral bands are further combined to produce vegetation indices [1]. These indices, among which normalized difference vegetation index, enhanced vegetation index, anthocyanin reflectance indices, carotenoids reflectance indices, photochemical reflectance index or quantum yield of photosynthesis…, are mainly computed with differences and ratios. Such vegetation indices are known to saturate in practice with pixels seemingly giving extreme values although none of the native acquired images are actually saturated. This is usually partially solved by resorting to costly high dynamics (in bits) imaging sensors which also increase (dramatically in the perspective of high-throughput phenotyping) the memory cost of data storage. However, even with very high sensor dynamics, the computed vegetation indices are known to still be noisy with saturating pixels (please take a look on the top right vegetation indice image on the website of this meeting http://meetings.ipk-gatersleben.de/COST_IPK_2015/index.php). Conventional methods for such noise removal are local adaptive or non adaptive median filters which reduce the effective spatial resolution in such applications of computational imaging for plant sciences.

In this communication, we propose to briefly explain the statistical origin of the saturation of vegetation indices commonly used in plant sciences, and review the main denoising techniques for such indices with special focus on recent techniques [2] which draw benefit from the multiscale properties of plants to remove noise with a very limited loss of spatial resolution by comparison to the conventional methods. This points to possible lines of collaborations between information science groups and plant imaging groups concerned with maximizing the value of quantitative information extracted from vegetation indices.

References:

[1] Fiorani, F., Rascher, U., Jahnke, S., & Schurr, U. (2012). “Imaging plants dynamics in heterogenic environments”. Current Opinion in Biotechnology, 23(2), 227-235.

[2] Rousseau, D., Chéné, Y., Belin, E., Semaan, G., Trigui, G., Boudehri, K., Chapeau-Blondeau, F. (2015). “Multiscale imaging of plants: current approaches and challenges”. Plant Methods, 11(1), 6.

Keywords: Vegetation indices, image denoising


Session 1 9

Micro-climate Monitoring for Crop Phenotyping

Mark Neal, Marie Neal

Aberystwyth University, United Kingdom

We have developed a low-cost wireless micro-climate sensor network for deployment in field environments that can collect high resolution climate data in order to assess the potential effects of micro-climate on crop performance. The sensors are currently configured to measure air temperature, humidity and light intensity/colour at three heights: 1 metre, 10cm (variable) and 30cm (variable) and soil temperature/humidity. This has potential for both assessment of the effects of micro-climate on growth in an in-field scenario, and assessment of growth-rate using the active light sensors. We are currently considering the possibilities that such a system could present when used to “clone” a field environment inside a controlled environment such as a greenhouse. By deploying identical sensors in both environments it should be possible to reproduce the outdoor growth environment to fine granularity in a greenhouse. This could be useful in scenarios such as when studying genetically modified crops or developing crops for difficult/remote environments. It also offers the possibility to realistically “replay” recorded growing seasons repeatedly during crop development trials. The cost of the sensor stations is currently around £200 each. The major cost would be in the environment control systems (such as HVAC) required to accurately control a greenhouse environment. Wind-speed and direction monitoring is feasible although currently rather more expensive and is a topic of on-going work.

Keywords

sensor, network, temperature, light, humidity


Session 1 10

Chlorophyll fluorescence – protocols for medium throughput phenotyping

Eva Rosenqvist

University of Copenhagen, Denmark

Non-invasive phenotyping for stress tolerance to various climate parameters often involve chlorophyll fluorescence (CF). Depending on the aim of the measurement CF can be measured in light to estimate the effective quantum yield at the given light level or after 20-30 minutes dark adaptation to estimate the maximum quantum efficiency of PSII. Combining dark-adapted measurements with measurements in light will enable a full quenching analysis where the energy balance between photochemical and non-photochemical processes of PSII can be calculated at different light levels.

CF in high-throughput phenotyping by fluorescence cameras will often only give a snapshot of photosynthesis. Monitoring-PAM (Moni-PAM) is a tool for medium-throughput phenotyping, where CF can be measured several leaves simultaneously. It can follow the development of stress in situ.

Even though CF is non-invasive the saturating pulses (SP) do affect photosynthesis. Too frequent SP’s will contribute to the formation of non-photochemical quenching, NPQ. Measuring protocols should be designed to avoid this. For full quenching analysis dark adapted values of the initial Fo and saturated maximum Fm are needed. This can be achieves by applying a saturating pulse during the night. The effect of the CF sampling frequency in medium-throughput measurements and examples of how several species respond to naturally fluctuating light and high temperature will be shown. Both the fluctuating nature of daylight and the sampling frequency have implications for how protocols for high-throughput phenotyping by CF.

Keywords

Chlorophyll fluorescence, stress detection


Session 1 11

A non-invasive method, using microstrip patch antennas, to measure the volumetric soil moisture content in the profile of a rhizobox.

Paulo Sergio de Paula Herrmann, Viktor Sydoruk, Siegfried Jahnke, Fabio Fiorani, Ulrich Schurr

Forschungszentrum Jülich, Germany

New tools or approaches are considered important to investigate and evaluate soil-water-plant interactions in the plant phenotyping investigations. A central parameter determining root system response to water availability is that water is usually not homogeneously distributed in the soil and the heterogeneity significantly increases when drought stress occurs. Thus the development of non-invasive instruments and sensors to measure soil moisture distribution would open up new approaches to investigate plant strategies to deal with low water content or, in particular, heterogeneities in water availability of soils during periods of drought cycles. The variation of water content profiles over time was monitored under laboratory conditions. Rhizoboxes are normally used to study root growth during plant development. The scattering parameters (S21 or S12 parameter) at transition of microwaves, close to 4,8GHz, is strongly depends on soil moisture, and were measured with two microstrip patch antennas on the both sides of a rhizobox. Additionally, we observed dependence on temperature, density of soil and its conductivity that should be taken into account in 2D monitoring of soil moisture distribution.

Calibration curves were obtained to four kinds of samples with different bulk densities (dens b), i.e., three of them are considered soil (Null Erde (dens b=0,28 g*cm-3), Dachstau den substrat Somi 513 (Kaktus soil (dens b=0,56 g*cm-3)) and dystrophic Red Latosol (Oxisol) (Cerrado – Brazil (dens b=1,19 g*cm-3)), and one is a porous media (PM) (Glass Beads (dens b=1,54 g*cm-3)).

The non-invasive microwave method, using microstrip patch antennas, is considered a system that could be applied as a sensing method to measure the water status in rhizoboxes.

Keywords

Sensor, microstrip, S-Parameter, soil moisture, rhizobox


Session 1 12

Field Phenotyping: Combining low-tech with high-tech paving the road to high throughput field phenotyping

Onno Muller, M.Pilar Cendrero Mateo, Hendrik Albrecht, Francisco Pinto, Anke Schickling, Roland Pieruschka, Ulrich Schurr, Uwe Rascher

Forscchungszentrum Juelich, Germany

Phenotyping in the field is an essential step in the phenotyping chain from well-defined and controlled conditions in the laboratory and greenhouse to the heterogeneous and fluctuating environment in the field. Field measurements represent a significant reference for the relevance of the laboratory and greenhouse approaches and an important source of information on potential mechanisms and constraints for plant performance to be tested at controlled conditions. Here we present a range of methods that are being deployed within the German Plant Phenotyping Network focusing on three main areas: photosynthesis, plant water water relations and canopy structure. Specialized field platforms for automated sensor positioning are established (a) to test innovative phenotyping technologies (b) to install semi-controlled field installation to support breeding approaches for future CO2 – concentrations (breed-FACE) and (c) to study the transfer of phenotypic properties from controlled environments to stands in the field. The methods used showed thus far that; sun induced fluorescence and light induced fluorescence transients techniques allow for remote estimating of photosynthesis at canopy and leaf to plant level respectively and active thermography estimates leaf water content and transpiration rates. These methods will be further tested and incorporated in (semi-) automated systems positioning sensors in the field introducing a promising portfolio to measure plant traits for field phenotyping and to enhance our understanding of relevant traits under natural conditions.

Keywords

Field positioning systems, Field Phenotyping, Chlorophyll fluorescence, Optical methods, hyperspectral


Session 1 13

Tuber growth analysis using x-ray computed tomography

Stefan Gerth, Norman Uhlmann

Fraunhofer IIS, Development Center X-Ray Technology EZRT, Germany

During the last years, x-ray computed tomography (CT) has been applied to study below ground growth of plant organs such as potato tubers (Ferreira et al., 2010). With x-ray CT the 3D volume information of objects can be reconstructed using x-ray projections of the object from different aspects.

The geometry used within the project is the axial 3D-CT, where a conical x-ray beam projects the object onto a flat 2D image detector. The available detector size and the focal spot size of the x-ray tube used limits the maximum pot size to about 20 cm in diameter, with a spatial resolution of about 85 µm. Using axial 3D-CT, projections of the object are taken under different viewing angles, rotating the object perpendicular to the central x-ray beam. The reconstructed volume data set consists of volumetric elements, called voxels, containing grey levels which represent information about the x-ray attenuation characteristics depending on the mass attenuation coefficient and the density distribution of the material. The mass attenuation coefficient itself is dependent on the applied x-ray spectrum and the effective atomic number of the analyzed material. Therefore, a careful selection of exposure conditions is necessary to achieve sufficient data quality. This comprises x-ray parameters and filters as well as the condition of the soil. The calculation of tuber volumes of potted plants embedded in soil requires the segmentation from other materials in the x-ray CT volume data. To address the quality of the segmentation additional comparison measurements between Magnetic Resonance Imaging (MRI) and CT were conducted (Metzner et. al, 2015) .

Adapting this technique for the visualization and analysis of growth processes of potato tubers in soil under controlled external stress conditions enables new phenotyping options. As an example the analysis for heat and drought stressed potato tubers is shown in this presentation. Time resolved measurements are conducted for four different treated batches starting directly after tuber initiation: a) Control Condition without any external stress, b) Drought stress c) Heat stress and d) Heat and drought stress combined. The stress was applied using two A1000-PG growth chambers from Conviron. It is possible to correlate the effect of the external stress to the volume and growth rate of the individual tuber itself.

Keywords

CT, tuber analysis, drought, heat, image segmentation


Session 1 14

Imaging belowground dynamics with MRI and PET

Ralf Metzner, Dagmar van Dusschoten and Siegfried Jahnke

Forschungszentrum Jülich GmbH, Germany

The development of a root system which is adequate for the respective growing conditions of a plant is critical for its survival and performance. In particular for so-called `root crops´ where the yield-relevant organ is developing belowground, the hidden half of the plant is of paramount importance for both yield and quality of the desired product at harvest. The opaque nature of soil generally prevents direct observation and, while a number of approaches for observing 2D root development such as rhizotrons have been applied successfully, roots naturally develop in interaction with the soil environment and form complex 3D structures for which 2D methods are not appropriate. Non-invasive monitoring the 3D structure and function of roots or other belowground (storage) organs may thus yield high potential for gaining new insights into development, regulation and stress responses of the particular plant structures. Magnetic resonance imaging (MRI) can be used for 3D visualization of root system architectures in soil and to quantify traits such as root length, total root mass or even internal structures of belowground storage organs. Positron emission tomography (PET) using short-lived radiotracer 11C provides additional imaging of photoassimilate partitioning and tracer flow characteristics can be extracted with model-based analysis tools. We will present applications of these techniques for visualization and quantification of root system architecture, anatomy and photoassimilate allocation.

Keywords

Root imaging, RSA, Belowground phenotyping, MRI, PET


Session 1 15

LeasyScan – a novel semi-field platform to phenotype traits controlling plant water budget

Vincent Vadez, Jana Kholová, Grégoire Hummel, Uladzimir Zhokhavets, SK Gupta, C Tom Hash

PHENOSPEX, Netherlands, The

We describe the concept and realisation of a high-throughput phenotyping platform (LeasyScan) combined with lysimetric capacity, to assess canopy traits affecting water use. The platform is based on a novel 3D scanning technique to capture canopy development, a scanner-to-plant concept to increase throughput (2500 plants/h), and analytical scales to combine gravimetric transpiration measurements. We present how the technology functions, how data are visualised via a web-based interface, and how data extraction and analysis is interfaced through ‘R’ libraries. Close agreement between scanned and observed leaf area data of individual plants in different crops was found (R2 between 0.86 and 0.94). Similar agreement was found when comparing scanned and observed area of plants cultivated at densities reflecting the field conditions. Example of the monitoring, the plant transpiration by the analytical scales is presented. Moreover we present some on-going applications of the platform to target key phenotypes: (i) the comparison of the leaf area development pattern of fine mapping recombinants of pearl millet; (ii) the leaf area development pattern of pearl millet breeding material targeted to different agro-ecological zones; (iii) the assessment of the transpiration response to high VPD in sorghum and pearl millet.

Keywords

high-throughput phenotyping, drought, vapour pressure deficit, lysimetric platform, gravimetric transpiration, 3D laser scanner


Session 1 16

Reproducibility of phenotyping platforms

Rick van de Zedde, Eric Boer

Wageningen UR, Netherlands, The

Phenotyping offers the horticultural sector a powerful tool for optimising plant performance and productivity. For effective use phenotyping platforms need to be fast, accurate and objective. Several phenotyping systems are already intensively being used world-wide and one of the objectives within the EPPN project (WP4 - Good Phenotyping Practice) is to test the reproducibility of these existing phenotyping platforms from partners within the EPPN-project. So, how comparable are the results of the different phenotyping platforms as a same set of plants is measured by every platform. Measuring the reproducibility is done with a set of fake plants, on all available phenotyping platforms. Of course differences are found between the resulting measurements of the phenotyping platforms. The interesting challenge is to explain and explore the differences in outcome. After the determination of the cause of the differences, guidelines to improve the results can be made. For example, how many recordings at which viewing angles per plant should be taken to have reliable results?

Keywords

computer vision phenotyping imaging reproducibility


Session 1 17

The Light Induced Fluorescence Transient (LIFT) method for active leaf fluorescence measurements from field to lab.

Beat Keller, Onno Muller, MaPi Cendrero-Mateo, Shizue Matsubara, Imre Vass, Uwe Rascher, Roland Pieruschka


Phenotyping at plant level is restricted by the sessile nature of plants which is surmounted by non-invasive remote sensors and dedicated positioning systems. One of the key traits of plant performance is photosynthesis and a number of different methods have been developed to quantify that process. For remote measurements of leaf photosynthesis the co-occurring fluorescence signal, when light is absorbed by the chlorophyll in the leaf, has been shown to be a useful parameter to quantify photosynthetic performance. In the LIFT method the fluorescence signal is quantified by manipulating the photosystems by applying a large number of very short light pulses and thereafter increasing the pulse intervals. From the resulting fluorescence transient a range of photosynthesis related parameters are obtained, from quantum yield of photosystem II to kinetics of the electron transport chain. After extensive testing of the first prototype of the LIFT in our group a new generation LIFT was developed that is suitable to mount on multiple positioning systems. In this presentation we will show the new LIFT and first results dedicated to the interpretation of the fluorescence signal in chloroplast thylakoids exposed to different electron transport inhibitors as well as a study to monitor diurnal changes of photosynthetic efficiency of maize leaves using an automated positioning system. These results indicate the potential of the new LIFT for phenotyping of different photosynthetic performance at plant level.

Keywords

LIFT, photosynthetic efficiency, quantum yield


Session 1 18

EMPHASIS - European Multi-environment Plant pHenotyping And Simulation InfraStructure

Ulrich Schurr, Francois Tardieu


The EMPHASIS proposal aim to establish a European Infrastructure within the ESFRI framework, based on national phenotyping infrastructure (Belgium, France, Germany and UK). The partnership will be extended in the future.

EMPHASIS will develop and provide access to infrastructures addressing multi-scale phenotyping for analysing genotype performance under diverse environmental conditions and quantify the diversity of traits contributing to performance in diverse environmental scenario (i.e. plant architecture, major physiological functions and output, yield components and quality).

EMPHASIS will address the technological and organizational limits. EMPHASIS will

• develop an integrated pan-European network of instrumented phenotyping platforms using current and future agro-climatic scenarios.

• link data acquisition to a European-level data management system and to state-of-the art crop models to simulate plants and crops in current and future climates.

• develop, evaluate and disseminate novel technologies, thereby providing new opportunities for research involved in phenotyping and precision agriculture

• make these infrastructures and concepts accessible to European plant science community in academia and industry

EMPHASIS infrastructures will include

• platforms in (semi-)controlled conditions for high resolution and throughput phenotyping

• Intensive field experimental sites

• a coordinated network of field experiments with phenotyping infrastructure

• Modelling platforms for testing existing or virtual combinations of alleles

Keywords

plant phenotyping, Europe, infrastructure


Session 1 19

Plant Phenomics at IPK: multi-sensor setups for a comprehensive and integrated analysis of plant phenotypes

Astrid Junker, Henning Tschiersch, Thomas Altmann


Plant phenomics allows for screening of large plant populations for favorable traits such as higher yield or biomass accumulation, plant resistance to biotic and abiotic stresses as well as plant nutrient use efficiency. Currently, the IPK runs three plant phenotyping facilities for high-throughput imaging of whole plants of small size (such as Arabidopsis thaliana), medium size (such as Hordeum vulgare) and large size (such as Zea mays, Junker et al. FIPS 2015). In each of these phenotyping systems plants are captured in near-infrared (NIR) and visible spectra (for RGB and fluorescence imaging) from top and side views. The Image analysis pipeline (IAP, Klukas et al. Plant Phys 2014) automatically extracts plant architectural traits (plant height and width, projected leaf area, estimated volume), physiological traits (color-related, autofluorescence, moisture content-related parameters. The existing high throughput plant phenotyping facilities are currently extended for the analysis functional chlorophyll fluorescence using pulsed amplitude-modulated chlorophyll fluorescence imaging systems and for the acquisition of 3D height profiles of plants and plant stands.

The presentation will give an overview about the different sensors used for plant phenotyping, will show exemplary applications for different plant species thereby outlining the capabilities of the phenotyping facilities for different biological questions and the importance of the integrated analysis of multi-sensor image data.

Keywords

high throughput, phenomics, sensor integration


Session 2 20

Session 2: Phenotyping the metabolome


Session 2 21

KEYNOTE LECTURE

Investigating plant performance using metabolic phenotyping

Yves Gibon

INRA, France

Carbon central metabolism, which encompasses the ‘ancient’ metabolic pathways such as glycolysis and tricarboxylic acid cycle, is at the crossroad between quality and biomass production. It supplies energy and building blocks for growth and is responsible for the accumulation of sugars and organic acids, which are major determinants of the quality of many crops, especially fruits and vegetables. By exploiting robust biochemical principles and microplate robotics, we have developed a series of assays targeting enzyme activities and metabolites of this network. They enable precise analyses of very large numbers of samples at fair costs, and in a wide range of species or tissues. Combined to metabolomics, we use them to phenotype crops grown under various conditions, to search for biomarkers. We also use them to develop, parameterise and validate mechanistic models of metabolism. The platform is involved in a number of collaborations dealing with very diverse organs and species. A consequence is the accumulation of a large and unique dataset, which already provides the possibility to perform data-mining.

Keywords

Metabolism, phenotyping, systems biology


Session 2 22

Kinematic analysis of cell division in maize leaves: a basis for sampling for "omics" to gain an integrated understanding of the growth response to drought

Gerrit T.S. Beemster, Viktoriya Avramova, Hamada Abd Elgawad, Yves Guisez, Han Asard

University of Antwerp, Belgium

The cellular level processes cell division and cell expansion form a crucial level linking regulatory processes at the molecular level to whole plant growth rates and organ size and shape. With the rapid progress in molecular profiling, quantification of cellular activities becomes increasingly important to determine sampling strategies that are most informative to understand the molecular basis for organ and plant level phenotypes. Inversely, to understand phenotypes caused by genetic or environmental perturbations it is crucial to know how the cell division and expansion parameters are affected spatially and temporally. Kinematic analyses provide a powerful and rigorous mathematical framework to quantify cell division and cell expansion rates. Monocotyledonous leaves have a persistent spatial gradient, with an intercalary meristem where division takes place, an expansion zone, and a mature part of the leaf. We use kinematic analyses to investigate the effect of mild and severe drought in the leaves of contrasting Zea mays lines. We then sample equivalent developmental stages (proliferating, expanding and mature cells) despite their location being affected by the stress and perform transcriptome (NGS), proteome, metabolome (hormones and antioxidant metabolites) and even enzyme activity measurements. Moreover, the velocity profiles obtained from kinematics can be used to calculate local rates of deposition (i.e. import + local production - export - local degradation). This way we generate a comprehensive insight into the growth response to drought in tolerant and sensitive lines.

Keywords

maize, drought, kinematics, transcriptome, proteome, metabolome, enzyme activity


Session 2 23

Metabolic Signalling in Temperature and Light Acclimation of Arabidopsis

Giles N Johnson, Beth C. Dyson and Matthew Miller

University of Manchester, United Kingdom

Improving the tolerance of crop species to abiotic stress is a key priority for researchers world wide and is made urgent by the increasing frequency of extreme weather events being seen. We have been examining the responses of plants to fluctuations in environmental conditions, in particular focusing on the responses of Arabidopsis to light and temperature. We have identified mutants that are deficient in their ability to acclimate photosynthetic capacity to either increases in light or decreases in temperature and have found that these mutations affect metabolic processes downstream of primary photosynthetic reactions. We are exploring the impact of these mutations on acclimation responses using targeted and non-targeted metabolomics and label-free proteomic approaches.

Keywords

photosynthesis, acclimation, abiotic stress


Session 2 24

Discriminating between good quality and bad quality cork by means of polyphenol profiling

Adelaide Machado, Olfa Zarrouk, Cecilia Brunetti, Sébastien Planchon, Antonella Gori, Massimiliano Tattini, Cândido Pinto Ricardo, Jenny Renaut, Rita Teresa Teixeira, Carla Pinheiro

ITQB, Portugal

Cork is a highly valuable non-wood forest product, and plays an important role in the Portuguese economy. Not all trees produce cork of good quality (GQC), and cork industry is faced with growing amounts of bad-quality cork (BQC). This poses serious concerns for orchard management, as only cork of good quality (GQC) is valuable for stoppers production. Cork quality was closely related with phenolic profile as revealed by a multivariate analysis showing that more than 75% of variation is explained along the 1st axis. In contrast, transcriptome profile was unable to discriminate GQC from BGQ, as only 5% of the variation is explained and along the 2nd axis (Teixeira et al 2014). The protein profile exhibited an intermediate discrimination power, as it can explain 39% of the variation along the 1st plus the 2nd axes of a multivariate analysis. Our work suggests that cork quality, though largely controlled at genomic level, could be linked to some specific responses adopted by plants and likely due to post-transcriptional variations. In particular, individual trees exposed to the same environmental conditions, may produce different amounts of polyphenols which may constitute an excellent marker for the cork quality.

Teixeira et al 2014 Journal of Experimental Botany 65, 4887-4905. doi10.1093/jxb/eru252

Keywords

Quercus suber, proteome, transcriptome


Session 2 25

Meta(l)bolomics: metabolomics analysis of iron (Fe) deficiency responses in soybean

Marta M. Lima, Carla Santos, Mariana Roriz, Michael A. Grusak, Ana M. Gil, Marta W. Vasconcelos

Universidade católica Portuguesa, Portugal

Iron (Fe) is a metal in the first transition series, and it is the fourth most common element on the Earth’s crust. Despite its high abundance, Fe is very often unavailable for plant uptake. A better understanding of Fe deficiency responses at the metabolome level can help designing strategies to ameliorate Fe deficiency problems. Here we hypothesized that the antioxidant system and the porphyrin biosynthesis pathway, which are involved in plant defense and in the biosynthesis of chlorophyll and heme, are involved in the Fe deficiency responses. Liquid 1H nuclear magnetic resonance (NMR) and high resolution magic angle spinning (HRMAS) NMR spectroscopy were used to conduct metabolomics analysis of Fe-sufficient and Fe-deficient soybean leaves showing increasing severity of Fe deficiency symptoms. Detailed analysis confirmed that amongst the main metabolic impacts of Fe deficiency these included: 1) enhanced tricarboxylic acid cycle activity; 2) enhanced amino acid accumulation and 3) enhanced activation of oxidative stress protection mechanisms. To further confirm the role of the antioxidant system and the porphyrin biosynthesis pathway in the Fe deficiency response, photosynthetic pigments, Fe accumulation, root reductase activity, ALA and hemin (the oxidized version of heme) concentration and antioxidant enzymes activities were evaluated. The combined metabolomics and biochemical approaches showed that metabolites showing accumulation differences in Fe starved, but visually asymptomatic leaves, could serve as biomarkers for early detection of Fe-deficiency stress.

Keywords

Iron, chlorosis, NMR, metabolomics, Porphyrin biosynthesis


Session 2 26

Employment of kresoxim-methyl as a priming agent towards protection of Medicago truncatula plants grown under abiotic stress conditions

Panagiota Filippou, Chrystalla Antoniou, Toshihiro Obata, Katrien Van der Kellen, Vaggelis Harokopos, Loukas Kanetis, Vassilis Aidinis, Frank Van Breusegem, Alisdair R Fernie, Vasileios Fotopoulos

Cyprus University of Technology, Cyprus

Biotic and abiotic stresses, such as fungal infection and drought, cause major yield losses in modern agriculture. Kresoxim-methyl (KM) belongs to the strobilurins, one of the most important classes of agricultural fungicides displaying a direct effect on several plant physiological and developmental processes. However, the impact of KM treatment on salt and drought stress tolerance is unknown. In this study we demonstrate that KM pre-treatment of Medicago truncatula plants results in increased protection to drought and salt stress. Foliar application with KM prior to stress imposition resulted in improvement of physiological parameters compared with abiotic-stressed plants. This protective effect was further supported by increased proline biosynthesis, modified reactive oxygen and nitrogen species signaling and attenuation of cellular damage. In addition, comprehensive transcriptome analysis identified a number of transcripts that are differentially accumulating in drought and salinity-stressed plants (646 and 57, respectively) after KM pre-treatment compared with stressed plants. Metabolomic analysis suggests that the priming role of KM in drought- and to a lesser extent in salinity-stressed plants is attributed to the regulation of key metabolites (including sugars and amino acids) resulting in protection against abiotic stress factors. Focused analysis of metabolites and transcripts identified suppression of proteolysis as a key element of the compound’s protective modus operandi. Overall, the present study highlights the potential use of this commonly used fungicide as a novel priming agent against key abiotic stress conditions.

Keywords

abiotic stress, strobilurins, priming, drought, salinity


Session 2 27

A valuable “omics” platform for plant fingerprinting: the lipidome of marine macroalgae as a case study

Eliana Alves, Tania Melo, Pedro Domingues, Ricardo Calado, Maria H. Abreu, Maria Rosario Domingues

University of Aveiro, Portugal

The improvement in mass spectrometry and chromatography technologies with high sensitivity and capability of high throughput analysis has brought new insights on the role of lipids in plant biochemistry at molecular and cellular levels. Lipids are major components of plant membranes playing key roles in the regulation of metabolism. Besides their structural role, they are important signaling molecules.

The research in plant lipidomics is still in its infancy, being mainly focused on Arabidopsis and on some algae species. Algae are very attractive in many levels. They are natural fertilizers used in agriculture and thickeners and stabilizers in the food industry. In Western countries, they have been has envisaged as important “functional food” as used for direct consumption. Besides, seaweeds produce a number of metabolites with biological activity, assuming great relevance in the pharmaceutical and biomedical fields. As such, the bioprospecting of these organisms has significantly increased in the last decades.

Our research on the lipid fingerprint of the red macroalga Chondrus crispus, using a liquid chromatography coupled to mass spectrometry technique, has revealed 8 polar lipid classes including glycolipids, glycosphingolipids bearing ceramide backbones, inositolphosphoceramides, glycerophospholipids, and betaine lipids. A total of 233 molecular species have been identified as well as their fatty acyl composition, showing the promising value of the lipidomics platform.

Keywords

lipidomics, mass spectrometry, seaweed, polar lipids, fatty acids


Session 2 28

Phenotyping translates the gobbledygook of the speaking plant: the story of the sucrose feedback in nutrient sensing and the role of trehalase in transpiration efficiency

Michal Janiak, Ewaut Kissel, Ricky Van Pelt, Christoph-Martin Geilfus, Patrick Van Dijck, Sebastien Carpentier

KU Leuven, Belgium

Sugar pathways are essential for plant metabolism. They play multiple roles in reaction to a changing environment. One of them – the trehalose pathway – has been shown to play a role in nutrient sensing and stress signalling. The last enzyme of this pathway - trehalase - has been proven to be highly abundant in guard cells. Modifications of its abundance causes changes in response to abscisic acid and hence in stomatal closure. Our phenotypical studies in banana, bean and different mutants of Arabidopsis thaliana have enabled us to bring forward a new hypothesis: trehalase plays a role in the feedback of sucrose as a closing signal for stomata in response to a saturated photosynthesis. The advantage of this feedback mechanism might be that when photosynthesis is so efficient and saturated, stomates can close leading to a higher transpiration efficiency. To characterize the phenotype we measured: the online water loss, the dynamic leaf surface temperature, and the stomatal conductance in several banana genotypes with a differing transpiration efficiency. Based on the phenotyping results we have determined the time points for the cellular phenotyping via proteomics. The exact role of trehalase and related proteins are being evaluated via mass spectrometry and western blotting and the role of this feedback phenomenon in transpiration efficiency is being determined

Keywords

arabidopsis, sugar pathway, trehalase, photosynthesis, banana


Session 2 29

The comparison of phytohormone functions in salt and phosphate deficiency stress responses

Sylva Prerostova, Petre Dobrev, Alena Gaudinova, Vojtech Knirsch, Radomira Vankova

Institute of Experimental Botany AS CR, Czech Republic

Phytohormones play an important role in the regulation of plant growth and development as well as in the interactions with the environment. Hormonal responses of Arabidopsis thaliana have been compared during salt stress (NaCl in a range 2 – 150 mM, for 1 week) and phosphate deficiency [7-day phosphate (P) starvation after 3 weeks of full nutrition (100 µM)]. The impact of stress was evaluated by membrane stability index and by expression of stress-induced genes. Severe stress was sensed by Arabidopsis above 75 mM NaCl (in hydroponics). During this stress, Arabidopsis gradually faded and died. Strong stress led to reduction of active cytokinins (mostly trans-zeatin), while levels of the low active cis-zeatin rose sharply. Indole-3-acetic acid content decreased in especially heavily stressed roots, simultaneously with root growth suppression. High salt concentrations caused the rise of ABA predominantly in shoots. P deficiency resulted in the decrease of active cytokinins in shoots. Mild elevation in roots was at the expense of cis-zeatin and its riboside. P deficiency decreased auxin levels in shoots, mild positive effect was found in roots. Lack of P had negative effect on abscisic acid content in apices. P deficiency resulted in elevation of salicylic acid in roots. Physiological consequences of the hormonal changes as well as cross-talk among plant hormones will be discussed.

Acknowledgement: This work was supported by MEYS CR grant no. LD14120.

Keywords

salinity; phosphate deficiency; phytohormones; cytokinin; abscisic acid


Session 2 30

Impact of plant nutrition towards enhance drought tolerance – a different perspective

David Lyon, Cristiana Staudinger, Ma-Ageles Casillejo, Vlora Mehmeti and Stefanie Wienkoop

University of Vienna, Austria

Environmental stress is reducing crop production. Thus, significant efforts are being made on genetic and molecular level to improve stress tolerance. In general, the major focus lies in the identification of biomarker that allow for genetic engineering and smart breeding. However, so far little success has been achieved in QTL mapping and genome-wide association studies. This might be due to missing markers for selection but also in missing comprehension of the complex metabolic mechanisms involved in stress acclimation and recovery. In addition to the investigation of stress induced markers, it seems important to identify metabolic properties of the unstressed plant that are crucial for molecular stress elasticity. Consequently, this elasticity might also be regulated through plant nutrition and/or plant-microbe interactions.

In the particular case of legumes, the effect of differential optimal nitrogen nutrition and root nodule symbiosis on drought stress and rehydration responses was investigated using Medicago truncatula. A nutritional induced priming effect on the molecular level of unstressed plants was observed. Furthermore, molecular systems biology approaches unravelled a nutrition dependent delay in drought-induced leaf senescence. A protein turnover analysis was utilized for the first time revealing novel insights into the molecular elasticity, required for the recovery of drought stressed plants.

A strategy to improved drought tolerance of crops will be discussed.

Keywords

drought stress, legumes, metabolite and protein turnover, nutritional priming


Session 2 31

Plant lipidomics based on HILIC-MS to valorisation of autochthonous halophyte plants

Elisabete Maciel, Bruna Marques, Ricardo Calado, Ana Lillebø and Rosário Domingues

University of Aveiro, Portugal

Plant lipidomics is a newly emerging omics platform aiming to cover the most diverse topics related to lipid identification, quantification and metabolism adaptation to external conditions. Plants with their wide range of lipids provide specific lipid signatures for specific environment or seasonal conditions.

Halophytes are salt tolerant plants rich in lipids. These plants have great potential for different biotechnological applications, namely for phytoremediation of organic rich effluents and as food for human consumption. However, the lack of information on its lipidome is currently a gap in knowledge that impairs researchers to unravel the true biotechnological potential of these remarkable plants. To overcome this drawback we used a lipidomic approach based on hydrophilic interaction chromatography coupled to mass spectrometry to characterize the lipidome of halophytes (Halimione portulacoides). Results allowed to identify the lipidome signature picture in phospholipids, glycolipids, galactolipids and sulfolipids molecular species. Higher content of ω-3 fatty acids were found in these species, further confirmed by GC-MS. This presentation will highlight the advantage of lipidomic platform in the bioprospecting of bioactive phytochemical and the valorization of autochthonous pantheism, such as halophytes as an added value crop driving new applications on the fields of healthy and functional food products, nutraceuticals and source of multiple bioactive compounds.

Keywords

Lipidomics, Halophytes, Mass Spectrometry, HILIC, Bioactive compounds


Session 2 32

The role of phenolic compounds, salicylic acid and PR-proteins in the Coffea arabica-Hemileia vastatrix interactions

Leonor Guerra-Guimarães, Rita Tenente, Marta Sá, Sofia Leitão, Carla Pinheiro, Inês Chaves, Sebastien Planchon, Danielle R. Barros, Jenny Renaut, João P. Ferreira, Vagner T. Queiroz, Luis Vilas Boas, Maria Helena Almeida, Maria Rosário Bronze, Cândido P.

Instituto de Investigação Cientifica Tropical, Portugal

Coffee leaf rust, due to the biotrophic fungus Hemileia vastatrix (Hv), is the most widespread and devastating disease of Coffea arabica. The hypersensitive reaction (HR) was induced by Hv in incompatible (resistant; R) and compatible (susceptible; S) interactions, from 24hai onwards. However, in the R samples, this response was observed in a higher percentage of infection sites and was associated with the early accumulation of salicylic acid (SA) and phenolic compounds. Furthermore, in the R samples, the increase in phenylalanine ammonia lyase (PAL) activity at 24hai was detected supporting the involvement of the referred compounds in the HR. SA is an important signaling compound that can be involved in the regulation of PR proteins during the resistance response. The proteomic analysis of coffee leaf proteins in response to Hv infection did reveal increased levels of PR proteins (e.g. chitinases, osmotins) in both infected tissues, but more markedly in the R samples. Other proteins that were also shown to increase during the R reaction were, peroxidases, superoxide dismutase, reticulin oxidase and germin-like proteins (oxalate oxidase-like), which can have a role in the oxidative cross-linking between phenolic compounds and the plant cell wall polysaccharides at the infection sites. Deposition of chorogenic acids and lignin has also been associated with coffee resistance to Hv. The crosslinks enhance the protection of the cell wall to digestion by microbial degrading enzymes and, thus, lead to the overall resistance to fungi. The proteomic studies support the activation of various metabolic pathways that seem relevant for the resistance response of coffee to Hv.

Keywords

Coffee Leaf Rust, Cytology, 2-DE, MALDI-TOF/TOF-MS, HPLC/ESI-MS/MS


Session 2 33

Early detection of drought stress in young sugar beet plants (Beta vulgaris L.) by metabolite analysis and thermography

Monika Wimmer, Rita Krechel, Anne-Katrin Mahlein, Ulrike Steiner, Erich-Christian Oerke, Heiner Goldbach

University of Bonn, Germany

The early and non-destructive detection of drought stress is important for the selection of drought tolerant sugar beet cultivars. In the present work, destructive analysis of growth and cell morphology, water status, osmotic adjustment and membrane damage were combined with non-destructive determination of leaf temperature using infrared thermography (IRT) in 6 week old sugar beets subjected to a progressive drought stress and subsequent re-watering. Four distinct stress levels were identified; an increase in leaf temperature, suggesting reduced transpiration, was the primary stress-induced event (level I), followed by a metabolic adjustment (level II). Membrane destabilization and cellular damage was characterized by significant metabolic changes (level III), ultimately leading to senescence and cell death (level IV). During re-watering, young sugar beets rapidly re-established water balance, but membrane damage and partial stomatal closure persisted, representing long lasting stress effects. This study indicates that IRT is especially suitable for the detection of initial drought stress, before metabolic changes are detectable, and represents a highly useful screening tool for the early selection of drought tolerant genotypes in high-throughput phenotyping studies.

Keywords

drought stress, infrared thermography, non-invasive detection, re-watering


Session 2 34

Plant phenotyping for analysis of genetic variation and heterosis of growth and metabolism

Thomas Altmann


Heterosis, the enhanced performance and resilience of hybrids over their inbred parents is exploited in hybrid breeding to achieve high crop yields and yield stability. This phenomenon is studied in Arabidopsis and maize through integration of genotyping, transcript and metabolite profiling, and automated phenotpying using dedicated platforms. The Arabidopsis C24 x Col-0 accession cross exhibiting strong biomass-heterosis has been analysed for gene expression and metabolite composition. 10 and 232 heterotic QTL for biomass and metabolites, respectively, were detected using 429 recombinant inbred lines, 140 introgression lines, and test crosses thereof. A prominent heterotic QTL region of 14 genes was investigated using mutants and transgenic plants. Complex correlation analyses revealed a close link between plant biomass and a specific metabolic composition with predictive power for biomass heterosis. To explore its potential for hybrid crop breeding, diverse maize inbred panels and corresponding hybrids are phenotyped for biomass accumulation and growth rates, genotyped (50k SNPs, aCGH, and targeted re-sequencing), and subjected to metabolite and transcript profiling. In 285 diverse Dent lines prediction accuracies of 0.72 to 0.81 or 0.60 to 0.80 for SNPs and metabolites, respectively, were achieved for combining abilities of several biomass-related traits. This is extended to a Dent / Flint factorial cross using optimized controlled cultivation conditions. Furthermore, 264 Dent lines were characterized for biomass accumulation, water consumption, and thus, for water use efficiency. Using 50k SNP information, QTL of these traits and of the growth dynamics are identified.

Keywords

heterosis, prediction, QTL, Arabidopsis, maize


Session 3 35

Session 3: From gene to phene: screening natural diversity


Session 3 36

KEYNOTE LECTURE

Trait discovery and trait mapping in ex situ collections: challenges and opportunities

Andreas Graner

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany

To date some 7 million seeds representing the genetic resources of all major crop plants are stored in Ex-situ genebanks world-wide. Until recently, the vast majority of these resources have been left untouched. Recent progress in several areas has opened up new avenues to valorize Plant Genetic Resources (PGR) for research and breeding.

Substantial advances regarding the analysis of plant genomes have resulted in the development of vast numbers of genetic markers and DNA-sequence resources. These now allow for the systematic characterization of PGR at the genome level.

As to phenotypic analysis, genebank curators characterize individual accessions during the multiplication process for a series of basic characters and traits. Large data sets are available comprising many decades of observations and await further analysis.

For most quantitative traits, per se performance is an improper predictor for the presence of useful alleles in a genetic resource. To assess the agronomic potential of PGR novel approaches are needed to harness major adaptive traits (e.g. flowering time, plant height), such as the use of test cross designs between genetic resources and selected elite lines.

Finally, the deployment of automated, non-invasive imaging technologies blazes the trail for trait discovery, trait mapping as well as gene identification.

In the years to come, the orchestrated application of genotyping and phenotyping technologies along with the development of bioinfomatics tools for analysis, data storage and query will help leveraging the intrinsic potential of PGR to uncover the molecular mechanisms of trait expression and to adapt crop plant to future needs.

Keywords

Plant Genetic Resources, PGR, agronomic traits, genotyping, phenotyping


Session 3 37

KEYNOTE LECTURE

Diversity Seek (DivSeek): An international partnership to harness the genetic potential of crop diversity

Peter Wenzl, Ruth Bastow, Daniele Manzella, Wayne Powell, Susan McCouch

Global Crop Diversity Trust, Germany

More than 1,700 genebanks globally conserve approximately seven million accessions of crop species and their wild relatives. In addition, farmers conserve and adapt germplasm to social, economic and ecological conditions across diverse farming systems. The genetic diversity encapsulated in all these materials underpins and drives crop improvement. Yet efforts to identify and mobilize beneficial genetic variation into breeding programs have been limited, compared to the size of this global resource. Game-changing ‘omics’ and ‘big data’ platforms now enable a more effective and broad-based approach to harnessing crop diversity. The recently launched Diversity Seek initiative (DivSeek; http://www.divseek.org) aims to capture this opportunity to accelerate the development of climate-ready, high-yielding and nutritious varieties for a growing global population. DivSeek provides a platform to generate synergies and add value to like-minded, but otherwise autonomous efforts by germplasm holders, breeders, geneticists, and database and computational experts to make crop diversity more readily accessible and usable. It is a community-driven initiative based on voluntary membership, which focuses on common challenges encountered by individual projects. Priority areas of work will include (i) the establishment of a ‘cross-crop meeting platform’ to share experiences and rapidly spread innovative research approaches and technology platforms, (ii) the development and advocacy of common data standards and interoperable data sets/repositories, (iii) a broadly accepted framework for ‘rights management’ that helps individual projects comply with data-sharing principles, and (iv) capacity-building efforts in these areas. We welcome colleagues and organizations interested in mining crop diversity for food security to join the growing group of the 60-some institutions that have come together to establish DivSeek.

Keywords

crop diversity, genetic resources, genebanks, characterisation, evaluation


Session 3 38

Screening and validation of tomato genotypes under heat stress using Fv/Fm and heat-responsive miRNAs by high-throughput sequencing

Rong Zhou, Katrine H. Kjær, Eva Rosenqvist, Carl-Otto Ottosen and Zhen Wu

Nanjing Agricultural University, China, People's Republic of

Our aim was to screen tomatoes under heat stress for differences in the maximum quantum efficiency of photosystem II (Fv/Fm), uncover the physiological traits for heat tolerance and identify heat-responsive miRNAs by high-throughput sequencing (HTS). Totally 67 tomato genotypes were ranked by Fv/Fm in three-step heat stress. Two genotypes with higher Fv/Fm (heat-tolerant group) and two genotypes with lower Fv/Fm (heat-sensitive group) were selected. Physiological responses of the four genotypes under heat stress were validated. The heat-responsive miRNAs in heat-tolerant tomato were identified by HTS. The results showed that the heat-tolerant group maintained higher leaf pigment contents and higher total phenolic content than the heat-sensitive group under heat stress. The heat-tolerant group maintained unaltered stomata, pore area and net photosynthesis rate, but increased stomatal conductance under heat stress compared with the control. Chloroplasts in the heat-tolerant group maintained normal shape, whereas the chloroplasts in the heat-sensitive group became swollen with decomposed starch grain after heat stress. There were 82 up-regulated and 66 down-regulated miRNAs under heat stress as compared to control identified in the selected heat-tolerant tomato. The physiological and miRNAs responses to heat stress play critical roles in heat-tolerant tomatoes.

Keywords

tomato, heat stress, Fv/Fm, miRNAs, high-throughput sequencing


Session 3 39

Phenotyping of nitrogen use efficiency in plants: field vs. control conditions

Ivan A. Paponov, Christof Engels

Bioforsk, Norway

High prices for nitrogen (N) fertilizers and the need to reduce N losses are the main reasons motivating the breeding of new crop varieties with high N use efficiency (NUE). Yield potential under sub-optimal levels of N is defined by the efficiency of N acquisition from the soil and utilization of acquired N. Variability in soil and weather conditions and complex cross-talk between N acquisition and utilization in the field affect crop responses and complicate the interpretation of results. Sub-optimal N conditions also stimulate competition between individual plants in a population, leading to population segregation into groups with different adaptation strategies to available N resources. The result of this segregation is low inheritance of physiological and agronomic traits and difficulties in identifying QTL and genes responsible for plant resistance to stress conditions. We suggest overcoming these difficulties with the following scheme for phenotyping NUE plants. First, start with a field experiment to identify the main yield component responsible for yield reduction under sub-optimal conditions. Analysis of individual plants in a population gives more information about the real reason for yield reduction than does the average value over many plants and helps to identify different strategies in plant adaptation. Second, it is important to estimate the dosage response to the main growth-limiting factor (N in a sub-optimal N condition). Third, simulation of plant growth and yield under different conditions should be done by modelling that considers the dose response of plants to the main limiting factor and includes the competition between individual plants in order to predict the response of the whole population to sub-optimal N.

Keywords

nitrogen use efficiency, field, control conditions, nitrogen


Session 3 40

Non-invasive plant phenotyping using photosynthetic tools to characterise ’biomass and grain yield’ under water stress in wheat

Kenny Paul1, János Pauk2, Zsuzsanna Deák1, László Sass1 and Imre Vass1

Biological Research Center, HAS, Hungary, Hungary

Plant phenotyping in combination with non-invasive photosynthetic tools have great potential in making reliable trait predictions acting from biochemical to the morphological level. Here we studied the effect of drought on biomass accumulation and grain yield in sensitive and tolerant wheat cultivars. During initial 2-3 weeks period of drought stress, the sensitive Cappelle Desprez variety exhibits an early ground cover and growth habit which help to maintain higher photosynthetic electron transport and enhanced cyclic electron flow. Higher CO2 uptake rate in flag leaves of the drought stressed Plainsman cv. during grain filling period correlates well with its higher grain yield and prolonged transpiration rate through spikes. Interestingly, we observed higher biomass production, but lower grain yield stability in the sensitive cultivar, as compared to the resistant Plainsman cv. Higher biomass production in the sensitive variety was correlated with enhanced water use efficiency (WUE). The increase in drought factor (DFI) and performance (PI) indices calculated from the induction of variable chlorophyll fluorescence also showed correlation with higher biomass during the biomass accumulation period. However, during the grain filling period, the DFI and PI parameters were higher in drought tolerant cultivar and showed correlation with grain yield stability. Our results suggest that under drought stress, secondary trait associated mechanisms like delayed senescence, lower transpiration rate together with higher photosynthetic efficiency are correlated with increased biomass, but lower grain yield stability in the drought sensitive wheat cultivar in contrast to decreased biomass and higher grain yield stability in the drought tolerant variety.

Keywords

Biomass, Grainyield, Drought phenotyping, Triticum aestivum, Cyclic electron flow, OJIP, Gas exchange measurements


Session 3 41

Hunting QTLs to maintain photosynthetic efficiency under heat stress in bread wheat

Dew Kumari Sharma, Eva Rosenqvist, Carl-Otto Ottosen, and Sven Bode Andersen

University of Copenhagen, Denmark

The future climate is predicted to be more variable with higher frequency of heat waves and dry spells. Wheat (Triticum aestivum L.), a major cereal crop worldwide is a heat sensitive crop especially at the reproductive phase.

In the present study, a combined approach of physiological phenotyping based on chlorophyll fluorescence parameter, Fv/Fm, that measures the maximum quantum efficiency of photosystem II (a heat stress sensitive process in the light reaction of photosynthesis) and its quantitative genetics was used to dissect the complex nature of heat tolerance into photosynthesis related traits with a top-to-bottom (forward) approach.

The naturally existing variation amongst 1274 wheat cultivars of diverse origin were phenotyped repeatedly at increasing severity of heat stress, to be able to select cultivars that are extreme for Fv/Fm in the first step. Subsequently, evaluation of selected cultivars under moderate heat stress condition mimicking natural heat waves revealed that the cultivars selected for high Fv/Fm better tolerated the heat stress as compared to the low Fv/Fm cultivars by maintaining higher overall photosynthesis and dry matter accumulation.

As a result, three heat tolerant cultivars (origin: Pakistan & Afghanistan) and a common heat sensitive cultivar (origin: Germany) were used to generate three bi-parental mapping populations (F2) segregating for Fv/Fm in order to hunt for quantitative trait loci (QTL) associated with the underlying physiological differences. A total of 140 F2 plants in each population were phentoyped under heat stress by Fv/Fm and genotyped by around 5000 polymorphic single nucleotide polymorphism (SNP) markers (DArTseq, Australia) for linkage analysis and QTL mapping. Three QTLs, one each in three populations were identified. Each QTL explains about 12-16% of the phenotypic variation for Fv/Fm and the heat tolerant parents donated the positive allele.

Further, recombinant inbred lines (RILs) were derived from the three bi-parental F2 populations and have been evaluated under outdoor summer conditions in Denmark to study possible pleiotropic effects of these identified QTLs. The results obtained so far will be summarized and discussed.

Keywords

Heat stress, wheat, phenotyping, chlorophyll fluorescence, QTL


Session 3 42

Chloride-inducible transient apoplastic alkalinizations trigger stomata closure by controlling abscisic acid distribution: a pilot study linking proteome and phenome in salt stressed Vicia faba L.

Christoph-Martin Geilfus, Axel Mithöfer, Jutta Ludwig-Müller, Karl-Hermann Mühling, Sebastien Carpentier

KU Leuven, Belgium

Salt stress causes the apoplast transiently to alkalize, an event that is presumed to contribute to the ability of plants to adapt to saline conditions. However, the initiation of coordinated processes downstream of the alkalinization is unknown. We hypothesize that salinity-induced pH dynamics are a key feature modulating the compartmental distribution of ABA and, as a consequence thereof, affect stomata aperture. Apoplastic pH and stomata aperture dynamics in intact leaves of Vicia faba were phenotyped by microscopy-based ratio-imaging and porometer-based measurements of stomatal conductance. The ABA levels in the leaf apoplast and guard cells were investigated against pH dynamics by using GC-MS and LC-MS/MS. Our results demonstrate that an alkalizing factor that initiates the pH dynamics propagates from root to leaf in a way similar to xylem-distributed water. In leaves, it finally induces a systemic transient apoplastic alkalinization that causes the apoplastic ABA level to increase, followed by an elevation of ABA in the endogenous guard cells. We conclude that the transient alkalinization, which is a remote effect of chloride stress, modulates the compartmental distribution of ABA between the leaf apoplast and the guard cells and, by these means, is instrumental in inducing stomata closure during the beginning of salinity. To evaluate the downstream effects of pH change, a proteomics study was performed on the important dynamic time points dictated by the phenotyping.

Keywords: Salinity, Apoplastic pH, Stomata, Abscisic Acid, Vicia faba L, Ratio Imaging


Session 3 43

Screening for chilling tolerance in soya and broad bean

Carl-Otto Ottosen, Rong Zhou and Benita Hyldgaard

Aarhus University, Denmark

Many important annual crops cultivated in temperate climates have been introduced from the tropics, but might develop chilling injury at temperatures below about 12°C that result in impaired plant growth. For crops sown in early spring the risk of encountering chilling temperatures is high. The interaction of chilling temperatures and light might cause more serious injuries than chilling alone. At chilling temperatures photoinhibition can occur at light intensities below that of full sunlight. However, prolonged exposure to light and low chilling temperatures can be debilitating and associated with severe and irreversible photoinhibition followed by photooxidative destruction.

Soya and broad bean are potential new protein crops for the northern European farmers. While broad bean has traditionally been grown in smaller volume soya bean have hardly been grown in Northern Europe, but is in high demand for animal feed so introduction of suitable genotypes might be a way to substitute the export of soya protein.

Screening for stress responses often involves growing germplasm lines in contrasting conditions. A solution is to use controlled-environment screening, where the response may be evaluated uniformly and rapidly. The system needs to be based on simple selection criteria and provide rapid and accurate screening of large numbers of lines, is non-destructive, reproducible and ideally related to field performance.

The purpose of the current experiment was to pinpoint differences in responses to either chilling stress and/or interaction of light intensity by using chlorophyll fluorescence as a phenotyping tool aiming to clarify genetic differences in responses to both chilling and light.

Keywords

chlorophyll fluorescence, stress, protein crops


Session 3 44

Phenotyping and gene localisation of plant photosynthetic traits.

Jeremy Harbinson, Padraic Flood, Aina Prinzenberg, Roxanne van Rooijen, Mark Aarts

Wageningen University, Netherlands, The

In order to be able to phenotypic plant photosynthetic properties at the leaf level, we have built a high throughput system based on chlorophyll fluorescence and other imaging technologies. This system can measure the light-use efficiency for photosystem II electron transport of 1440 small plants (Arabidopsis or very young crop plants or similar) per hour. We have used this system to phenotype various populations of Arabidopsis (the HapMap, the Swedish reg map, RILs), Brassica RILs, and less well defined populations of Lycopersicum under various conditions (normal growth conditions and various stresses). The phenotyping data has so far largely been used to localise those genetic factors that give rise to the phenotypic variation we identify. In the case of Arabidopsis, it has been possible to quickly produce reasonable sized lists of candidate genes using GWAS approaches, while for the crop plants the procedure is more laborious owing the more limited genetic resources available to us. Nonetheless, we believe that localisation of genes for photosynthetic traits, and in the longer term the identification of the actual causal genes, is possible. This offers the possibility to effectively breed for improved photosynthesis and should also accelerate our understanding of the control photosynthetic variation in plants in terms of physiology, population genetics, environmental physiology and evolution.

Keywords

photosynthesis, natural variation


Session 3 45

On the appropriate conditions to perform single-plant root phenotyping concurrently with direct selection for efficient resource utilization: a field study with cowpea

Dionysia A. Fasoula, Michalis Omirou, Ioannis M. Ioannides

Agricultural Research Institute, Cyprus

The starting material for experimentation was a local cowpea landrace with prostrate habit, greatly preferred for fresh pod consumption, produced and harvested at approximately weekly intervals for a period of 2.5 months. The initial trials studied the within-landrace variation from multiple seed sources and performed single-plant field phenotyping for superior yielding performance. This phase demonstrated the existence of cryptic, non-useful variation, manifested in traits like sensitivity to photoperiod, bareness etc. Plants with the above traits consume substantial resources without pod production, but remain undetected due to the conventionally used dense planting conditions and the negative correlation between yielding and competitive ability. At the end of this 4- year phenotyping and selection phase, a number of family lines were identified, outyielding the initial controls in productivity. Then, a new single-plant phenotyping cycle was initiated, comparing the root, shoot and pod biomass of these elite selections under three different watering and fertilization regimes. Rhizobia counts were also performed on each plant under all regimes. The wide distances excluding interplant competition employed in the trials, enable root excavation and phenotyping at the single plant level, while minimizing the CV of single plant traits. Intriguingly, the results show that the input distribution in the initial control material favour bigger shoot and root development, but not pod formation, while the opposite is the case in the elite materials. In addition, the elite material showed improved homeostasis by a factor of 2.5, validating the goal of plant breeding to create materials with optimal utilization of growth resources.

Keywords

interplant competition, prognostic breeding


Session 3 46

Screening for powdery mildew resistance in pea: complementation of field and growth chamber studies with histology, genomics and proteomics

Diego Rubiales, Sara Fondevilla

CSIC, Spain

Pea powdery mildew, caused by the obligate biotrophic fungus Erysiphe pisi is an air-borne disease with a worldwide distribution, being particularly important in climates with warm dry days and cool nights. Only two resistance genes, named er1 and er2 were available so far. In order to extend the availability of sources of resistance, a germplasm collection has been screened resulting in the identification of quantitative and qualitative resistance to E. pisi. In P. fulvum we have identified a new gene for resistance to E. pisi that we called Er3. This resistance gene has been successfully used in pea breeding, resulting in the release of a resistant pea cultivar (“Eritreo”) containing this gene. We have identified SCAR markers linked to this gene that will facilitate the early selection of individuals carrying the gene in breeding programs. The mode of action at the cellular level of the three resistance genes has been characterized at the macroscopic and cellular level, and genes and proteins involved in the resistance have been identified.

A major concern in durability of available resistance is not only their stability against new races of E. pisi that might evolve but more worrying, their stability against Erysiphe species different from E. pisi, that might overcome these genes, as we recently found that E. trifolii was able to overcome er1 and Er3 genes. At present we are approaching deeper the study of the molecular and biochemical mechanisms of response to E. pisi in pea and looking also for resistance to E. trifolii, and developing the tools and knowledge needed for the introgression of the resistance into pea cultivars

Keywords

powdery midew, resistance, pea


Session 3 47

Profiling of plant secondary metabolites and identification of mQTL in an Eurasian Brassica rapa mapping population

Rebecca Klopsch, Katja Witzel, Anna M. Artemyeva, Nataliya V. Kocherina, Melanie Wiesner, Silke Ruppel, Monika Schreiner, Franziska S. Hanschen

Leibniz Institute of Vegetable and Ornamental Crops, Germany

Subspecies of B. rapa are wildly cultivated and contain root and leaf vegetables, such as pak choi, Chinese cabbage and turnip. The VIR harbors one of the largest collections of Brassicas, including a core collection of B. rapa, representing a wide variation in morpho- and metabolite-types of different geographical origins consisting of 92 accessions. A characteristic feature of brassicaceous plants is the presence of glucosinolates (GLS), a group of sulphur-containing secondary metabolites which contribute to the plant’s defence against a range of biotic and abiotic stresses. In order to explore the natural genetic diversity with respect to GLS profile and the composition of GLS breakdown products in leaves, we profiled those metabolites in targeted analyses and revealed a great range in qualitative and quantitative differences among the accessions. Hierarchical clustering and principle component analysis identified accession groups of similar and distinct metabolite patterns. Profiles of GLS and GLS breakdown products were then evaluated for an association mapping based on an established linkage map. Markers were identified that correlated with the abundance of aromatic, indole and aliphatic GLS. Those markers can now be used to breed for B. rapa cultivars with a tailored GLS composition.

Keywords

Brassica, glucosinolate, association mapping


Session 3 48

Unraveling early leaf stress response by -omics integration in Musa

Ewaut Kissel, Yassmine Zorrilla-Fontanesi, Nicolas Roux, Rony Swennen, Sebastien Carpentier

KU Leuven, Belgium

Water deficit is one of world’s major constraints in agriculture and will aggravate in the future. An important crop that needs vast amounts of water for optimal production is banana (Musa spp.). Millions of people depend on it as a staple food, while it is mostly grown in rain fed systems and hence very prone to fluctuating water availability. In-depth knowledge on this matter is therefore of utmost importance. However, not much is known about the genes involved in early stress response in banana and their link to long term stress response. In the light of crop improvement, we intend to fill this gap.

Two genetically diverse cultivars, “Cachaco” (ABB) and “Grande Naine” (AAA), were subjected to an osmotic stress treatment (5% PEG8000) in vitro. The leaf transcriptome (37,582 genes, using RNA-Seq) was assessed after three days of stress, while the phenome (67 phenotypic variables) was assessed after 3 and 21 days. Using the phenome at day 21, we discerned 9 long term phenotypic stress responses present in both cultivars. Subsequently, the phenome was used to disentangle the highly multidimensional transcriptome data. More specifically, we uncovered the early stress genes that were most related to one of the envisioned 9 core long-term processes at the third day after stress induction. This gene set is therefore most likely involved in the early development of some of the core osmotic stress responses at the phenome level in Musa.

Keywords

omics, drought, musa, abiotic stress, RNA-Seq


49

Poster Abstracts


Session 1 50

Session 1: Novel sensors and sensor integration: from low tech to high tech


Session 1 51

POSTER 1

DPPN PATHO: Phenotyping plant responses to infection by non-invasive confocal imaging and online mass spectrometry

Bishu Niederbacher, Finni Häußler, Stephan Dräxl, J. Barbro Winkler, A. Corina Vlot, Jörg-Peter Schnitzler

Helmholtz Zentrum München, Germany

Plant phenotyping, the assessment of complex plant traits such as growth, development, tolerance, resistance, etc., has become a major bottleneck and quantitative information on genotype-environment relations is the key to address major future challenges. Development of novel technologies, including high-throughput and automated approaches, within the German Plant Phenotyping Network (DPPN) addresses this specific question. DPPN PATHO focusses on phenotyping plant-microbe interactions and here, we introduce two non-invasive platforms.

VOCs Platform: Plants emit a great variety of volatile organic compounds (VOCs) that play an important role in atmospheric chemistry and actively participate in plant growth and protection against biotic and abiotic stresses. We will focus on the importance of VOCs as possible markers for plant phenotyping. The emissions will be captured in an array of air-sampling cuvettes and the analysis of the entire plants’ gas exchange (VOCs, NO, CO2 and H2O) will be achieved by parallel analysis of air samples with the respective gas analyzers. The coupling of proton transfer reaction time of flight mass spectrometry (PTR-ToF-MS) with fast GC analysis enables time-resolved measurement of VOC emissions and the identification of molecular structures with the same molecular weight, e.g. monoterpenes and sesquiterpenes.

Confocal imaging platform: plant resistance against different pathogens is crucial to the reliable production of food, feed, etc. via crop plants. Therefore, the investigation of plant diseases and defense markers in larger collections is of major importance. An automated high-throughput and non-invasive confocal imaging platform is being developed to address this point. This novel tool will allow gaining knowledge about the effectiveness of resistance mechanisms and pathogen spread in different plants. Large populations of model and crop plants will be analyzed for disease resistance and stress tolerance in order to be put forward as candidates for field application. GFP-marked pathogens for model and crop plants were developed to monitor disease progression. In addition, transgenic plants expressing fluorescent disease resistance markers and defense-associated metabolites will give further insight into plant resistance establishment.

Keywords

Phenotyping, Pathology, Emissions, Microscopy


Session 1 52

POSTER 2

Synergistic effects of salt and drought stress on the growth and photosynthetic parameters of wheat

Imre Vass, Kenny Paul, János Pauk, Ankica Kondic-Spika, Heinrich Grausgruber, Tofig Allahverdiyev, Zsuzsanna Deák, László Sass

Biological Research Center, Hungary

Combined effects of water limitation and high salinity was studied in 14 wheat (Triticum aestivum L.) cultivars, from Serbia (5), Austria (4) and Azerbaijan (5) by a semi-automatic plant phenotyping system, which provided information on plant height, and total green biomass. Photosynthetic parameters were also followed by gas exchange and variable Chl fluorescence measurements, and grain production parameters were determined. Salt stress (0.2 NaCl/kg soil) induced retardation of water uptake, especially at 20% field capacity. Green biomass was not significantly affected by salt stress under well watered conditions (60% field capacity). However, when salt was applied at 20% field capacity the green biomass decreased to ca. 30 % of the well watered no salt control. Total grain yield responded also to a small extent to salt stress under well watered conditions, but decreased to 10-25% of its control value when salt stress was combined with limited water availability. Interestingly the ratio of the grain yield and dry biomass remained practically constant even under the combined effect of salt stress and water limitation, showing that carbon partitioning to grains is not affected specifically by the salt + water stress. Net photosynthesis rate and accumulation of the osmoprotectant proline decreased also most significantly by the combination of salt stress and water limitation. These data indicate that the effect of salt stress is synergistically enhanced by water limitation.

Keywords

Salt stress, drought stress, wheat, photosynthesis, grain yield


Session 1 53

POSTER 3

Phenotyping Portuguese common bean germplasm for drought tolerance

Susana Trindade Leitão, Catarina Bicho, Susana Sousa Araújo, Maria Carlota Vaz Patto

Instituto de Tecnologia Quimica e Biologica Antonio Xavier, Portugal

Common bean (Phaseolus vulgaris L.) is a valuable source of proteins, vitamins and minerals, and the worldwide most important grain legume for human consumption. Like other legumes, it is also able to establish endosymbiotic associations with rhizobia leading to nitrogen fixation and enrichment of soil fertility, with benefits in cropping systems. However, common bean production is underused in Europe due to yield instability caused by, among other factors, abiotic stresses, namely water deficit. A deeper understanding of these stresses and their effects on plants is of vital importance to develop effective strategies to counter them.

Portugal holds a unique collection of common bean landraces not yet explored for breeding. To evaluate their drought tolerance, 77 common bean landraces were screened under well-watered and water-deficit stress conditions. Water deficit was induced by withholding water until soil water content fell to 40% of field capacity. Net photosynthetic rate, transpiration, stomatal conductance and water-use efficiency were assessed using an infrared gas exchange system coupled to plant and soil water status. The impact of water deficit was also evaluated by pigment (chlorophylls and carotenoids) quantification in leaves. The variability of drought responses found anticipates great potential of the national germplasm for the discovery of new sources of drought resistance and landrace improvement in future breeding programs.

Keywords

Common bean, Phaseolus vulgaris, drought tolerance, infrared gas exchange, leaf pigments


Session 1 54

POSTER 4

The application of multiplex fluorimetric sensor for the analysis of flavonoids content in the medicinal herbs family Asteraceae, Lamiaceae, Rosaceae

Oksana Sytar, Klaudia Bruckova, Elena Hunkova, Marek Zivcak, Marian Brestic

Slovak agricultural university in Nitra, Slovak Republic

Background

The aim of this work was to determine the content of total flavonoids in the leaves 13 plant species family Asteraceae, 8 representatives of family Lamiaceae and 9 plant species belonging to family Rosaceae, using the multiplex fluorimetric sensor for analysis flavonoid content. Fluorescence measurements were realized with optical fluorescence apparatus Multiplex®-3 (Force-A, France) for non-destructive flavonoids estimation. The content of total flavonoids was estimated by FLAV index (expressed in relative units), that is deduced from flavonoids UV absorbing properties.

Results

Among observed plant species the highest amount of total flavonoids has been found in leaves of Helianthus multiflorus (1.65 RU) and Echinops ritro (1.27 RU), Rudbeckia fulgida (1.13 RU) belonging to the family Asteraceae. Lowest flavonoid content has been observed in the leaves of marigold (Calendula officinalis) (0.14 RU) also belonging to family Asteraceae. The highest content of flavonoids among experimental plants of family Rosaceae has been estimated in the leaves of Rosa canina (1.18 RU) and among plant species of family Lamiaceae in the leaves of Coleus blumei (0.90 RU).

Conclusions

This research work was done as pre-screening of flavonoids content in the leaves of plant species belonging to family Asteraceae, Lamiaceae and Rosaceae. Results indicated that statistically significant differences (P>0.05) in flavonoids content were observed not only between families, but also among individual plant species within one family.

Acknowledgments

This work was supported by the European Community under the project no. 26220220180: “Construction of the “AgroBioTech” Research Centre”.

Keywords

multiplex flourimetric sensor, flavonoids, medicinal herbs, leaf


Session 1 55

POSTER 5

Monitoring canopy temperature patterns in two grapevine varieties under deficit irrigation: a tool to compare varieties and to optimize water use?

J. Miguel COSTA, Ivan GARCIA-TEJERO, Ricardo EGIPTO, Magdalena TOMÀS, Margarida VAZ, Carlos M. LOPES, Manuela CHAVES

ITQB -Univ. Nova de Lisboa, Portugal

Modern Mediterranean viticulture must have into account the increasing concern of consumers, wholesalers, and politicians on the environmental impact of grape and wine production. This applies to the use of irrigation water in the vineyard, in particular in dry areas such as the Mediterranean. A better understanding of grapevine physiological responses to drought and heat stress can help to optimize crop and soil management and improve water use efficiency, yield and berry quality. Canopy temperature (Tc) is commonly used to monitor water stress in plants/crops and to characterize stomatal physiology in species such as grapevine. Thermography permits the remote determination of leaf/canopy temperature in the field and also to assess the range and spatial distribution of temperature from different zones of the canopy. Our hypothesis is that grapevine genotypes may show different diurnal Tc patterns due to different stomatal behaviour and heat dissipation strategies. We have monitored the diurnal and seasonal course of Tc in two V. vinifera genotypes, Aragonez (syn. Tempranillo) and Touriga Nacional subjected to deficit irrigation under typical Mediterranean climate conditions. Assessment of diurnal course of Tc was complemented by determination of leaf water potential (ψleaf), leaf stomatal conductance to water vapour (gs) and net photosynthesis (An). Measurements were done in two consecutive years (2013 and 2014) and at different phenological stages: i) mid-June (green berry stage), ii) mid-July (veraison), iii) early August (early ripening) and iv) before harvest (late ripening). Correlations between Tc and minimal gs will be presented for the two genotypes. Results are discussed over the use of thermal imaging to derive information on genotype physiology in response to changing environmental conditions and to mild water stress induced by deficit irrigation. Strategies to optimize the use of thermography in field conditions are suggested.

Keywords

thermography, genotypes, diurnal and seasonal water stress, phenotyping, water


Session 1 56

POSTER 6

High throughput plant phenotyping at the Vienna Biocenter: Plant Sciences Facility (CSF GmbH)

Jakub Jez, Anneliese Auer, Jolanta Ambroz-Kumorowski

Campus Science Support Facilities GmbH, Austria

The Campus Science Support Facilities GmbH (CSF) is a public funded non-profit research institute, situated at the Vienna Biocenter Campus (VBC). We offer access to state of the art research infrastructure and scientific services. CSF is organized in ten scientific core facilities equipped with cutting edge instruments and highly skilled technical and scientific personnel.

The CSF Plant Sciences Facility (PlantS) operates 22 high quality, highly specialized and state-of-the-art plant growth chambers and provides professional support to the outstanding “green research” at the VBC. Several chambers are capable of providing exceptional environmental conditions i.e. low temperature (frost), high temperature, different light intensities, different light spectra (LED: UV375, blue405, blue450, white and red660,730) and different gas conditions (e.g. CO2) allowing precise environmental simulation across different climate zones and the simulation of various environmental stress conditions.

For the objective, reproducible and high-throughput assessment of plant phenotypic traits we operate an automated, chamber-integrated (sensor-to-plant) screening system linked to LemnaTec image analysis software. The system is designed for the screening of Arabidopsis. Pots and agar plates can be processed. Implementation of further sensors and increase of the phenotyping capacity by novel custom-made solutions are planed for the near future.

Furthermore, in close collaboration with the CSF pcIMAG Facility we are currently developing plant root phenotyping methods based on a state-of-the-art 15.2 tesla MRI.

Keywords

chamber-itegrated high-throughput phenotyping, sensor-to-plant, environmental simulation, LED


Session 1 57

POSTER 7

Medicinal and aromatic plants in the field collections

Laima Šveistytė

Plant Gene Bank, Coordination Centre of Medicinal and Aromatic Plants, Lithuania

There are more than 460 species which are used in modern and traditional medicine in Lithuania. The majority of medicinal and aromatic plants are still collected from the wild.

In nowadays 3 institutions (Botanical Institute, Kaunas Botanical Garden of Vytautas Magnus University, Lithuanian University of Agriculture) are involved in the activity of collection, investigation and conservation of medicinal and aromatic plants genetic resources. Preliminary assessment of genetic diversity has been carried out according to the morphometric variation of phenotype in wild populations. On the second stage the evaluation and selection of accessions has been made according to their morphological characters and chemical composition as well susceptibility to diseases.

The collection of the Institute of Botany includes over 140 species of medicinal and aromatic, crop wild relatives and berry plants, about 90 % of the accessions are plants of wild origin native to Lithuania. In Kaunas Botanical Garden the plants are classified by the pharmacognostic principle in respect the biologically active compounds, the indigenous species comprise one fifth of the collection. The field collection of caraway, which vary in time of flowering, color of inflorescence and amount of essential oil are stored in Lithuanian Agricultural University.

Keywords

medicinal plants, aromatic plants, genetic resources, collection, conservation


Session 1 58

POSTER 8

Relative efficiency of biparental mating in black gram (Vigna mungo (l.) Hepper)

Poorand Chand

SVP University of Agriculture & Technology, Meerut (UP), India, India

The present study was conducted to study the effects of biparental mating and pedigree methods on mean performance, genetic variability, transgressive segregants and shifts in correlation coefficients. The analysis of mean squares due to males, females, and interactions (male x female) were significant for almost all the characters. This implied that sufficient genetic variability existed in the parents and F1's also, indicating that parents were genetically divergent to create highly variables in F2 populations and thus giving ample scope for selection. The mean values of biparental progenies were higher than the pedigree progenies for all the characters. However, it was lower for days to flowering and maturity, indicating the possibility of getting early segregants. The superior mean and wider ranges of variation in biparental progenies may be due to releasing of hidden genetic variability. A positive significant association was observed between seeds per pod and 100-seed weight, and seeds per pod and pod length in the progenies of Chikkuduminumu X L-400, which could have otherwise been negative due to limited source and sink relationship, indicate the breakage of undesirable linkages between these traits. It can be inferred from the study that biparental mating in early generation followed by selection would not only effectively accumulated the favorable genes but also maintain variability for selection to be more effective in blackgram.

Keywords

Biparental mating, genetic variability, correlation coefficient, transgressive segregants, pedigree method, male, female, blackgarm


Session 1 59

POSTER 9

Plant phenotyping with non-invasive sensors – what are the scientific benefits?

Marcus Jansen

LemnaTec GmbH, Germany

Plant science has always had the need for measuring and describing phenotypes as tool for characterising plants, their responses to the environment, and their genetic and metabolic functionality. In the recent two decades, the intense use of sensors and an increasing level of automation brought phenotyping from laborious manual work to high-throughput measurements. Beyond developing and improving methods and technology, many scientist used the phenotyping toolbox for generating scientific results. Multiple fields of basic and applied research profit from phenotyping, which is proven by a broad range of scientific publications. Examples from recent literature prove that plant pathology, ecotoxicology, plant breeding, basic and applied plant science, as well as climate change research benefit from using phenotyping technology. The survey proves that the recent technological developments largely improved research and opens perspectives for future developments in plant phenotyping at multiple levels.

Keywords

sensors, automation, science, publication


Session 1 60

POSTER 10

Towards interoperability of phenotypic data sets

Hanna Ćwiek, Wojciech Frohmberg, Paweł Krajewski, Cyril Pommier, Daniel Arend, Astrid Junker, Matthias Lange, Aalt-Jan van Dijk, Jan Peter Nap, Jan van Oeveren, Paul Kersey, Fabio Fiorani, Roland Pieruschka, Cezary Mazurek

Institute of Plant Genetics, Polish Academy of Science, Poland

Plant phenotyping is performed through application of diverse protocols which aim at the objective observation of a multitude of different traits. The collection of phenotypic data is currently not sufficiently governed by standards that would enable interoperability and convenient linking of phenotypes to corresponding molecular data and genotype information. The influence of environmental conditions on the phenotype is a feature that further complicates direct data integration. We propose a coordinated approach to phenotypic data standardisation based on recommendations concerning metadata content, data annotation and data formatting. We formulate a checklist of attributes that comprise a minimum metadata set. We discuss the availability of ontologies that can be used for efficient annotation of the metadata. We describe the mapping of this list to the hierarchical investigation-study-assay structure and to the ISA-TAB file format. We discuss the practical application of our recommendations in various experimental situations. All this is followed by the description of how our recommendations have been implemented to date in data management systems and tools designed to store or process phenotypic data.

Keywords

phenotypic data, standardization, ISA-TAB format, metadata description


Session 1 61

POSTER 11

Watershed and supervised classification based fully automated method for separate leaf segmentation

Danijela Vukadinovic, Gerrit Polder

Wageningen UR, Netherlands, The

In this paper we present a method for fully automated plant leaf segmentation for top view images of rosette plants of the following species: Arabidopsis thaliana and tobacco. The images are imaged in different light conditions, different stages of development, various presence of moss in the soil and with highly overlapping leaves.

The method consists of two steps: plant segmentation and separate leaves segmentation. Plants segmentation against the background, was done using supervised pixel based neural network classifier. For each pixel 6 features are used: R, G, B and excessive Green (2G-R-B), the pixel values of the variance filtered green channel, and the pixel values of the gradient magnitude filtered green channel. Propagation and blobs removal were done on the classification result images.

The second step, separate leaves segmentation, was achieved using a watershed method utilized on the Euclidean distance map of the resulting plant mask image of the first step of the method. Initially, the watershed transformation is computed without applying the threshold between the basins. In the second step, the basins are successively merged if they are separated by a watershed that is smaller than a given threshold. The threshold value was tuned in order to produce the best result.

The method was tested on the highly challenging data set provided by the Leaf Segmentation Challenge 2014 (http://www.plant-phenotyping.org/CVPPP2014-challenge). The Dice index for the foreground vs background segmentation of the complete plant was 0.96, 0.95 and 0.96 for the datasets A1-A3 respectively. The separate leaves segmentation Dice index was 0.74, 0.72 and 0.70 for the datasets A1-A3 respectively. This result is the same as the challenge winner result for A1 and significantly better for A3.

Keywords

Automated Leaf Segmentation, Distance Map, Supervised Classification, Watershed


Session 2 62

Session 2: Phenotyping the metabolome


Session 2 63

POSTER 12

Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds

Sylwia Swigonska, Stanislaw Weidner

University of Warmia and Mazury in Olsztyn, Poland

In the present study, a proteomic approach was employed to analyze influence of cold and osmotic stress on roots of germinating soybean (Glycine max, L.) seeds. Seeds were germinating under continuous conditions of cold stress (+10°C/ H2O), osmotic stress (+25°C/-0,2MPa) as well as cold and osmotic stress combined (+10°C/-0,2MPa). Proteome maps established for control samples and stress-treated samples displayed 1272 CBB-stained spots. A total of 59 proteins, present in both control and stress-treated samples and showing significant differences in volume, were identified with LC/nanoESI-MS. Identified proteins divided into functional categories revealed 9 proteins involved in plant defence, 8 proteins responsible for plant destination and storage and 10 proteins involved in various tracks of carbohydrate metabolism. Furthermore, a number of proteins were assigned to electron transport, range of metabolic pathways, secondary metabolism, protein synthesis, embryogenesis and development, signal transduction, cellular transport, translocation and storage. By analyzing differences in expression patterns, it was possible to trace the soybean response to long-term abiotic stress as well as to distinguish similarities and differences between response to cold and osmotic stress.

Keywords

cold stress, germination, osmotic stress, proteomics, soybean


Session 2 64

POSTER 13

Mapping of quantitative trait loci determining antioxidant activity in triticale (× Triticosecale Wittm.) anthers associated with androgenesis initiation

Iwona Żur, Ewa Dubas, Monika Krzewska, Franciszek Janowiak

The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Poland

A mapping population comprising 70 DH lines of triticale was selected for biochemical phenotyping to establish the role of antioxidant activity in androgenesis initiation. Total water-soluble antioxidant activity was determined by DPPH method in triticale anthers isolated from freshly cut and low temperature treated (3 weeks at 4°C) tillers. These data were then used to identify quantitative trait loci (QTL) responsible for controlling antioxidant capacity under both stress and non-stress conditions. QTL mapping was carried out by single marker analysis (SMA) and composite interval mapping (CIM) method using Windows QTL Cartographer version 2.5.

Although low temperature treatment distinctly enhanced antioxidative activity, no significant association between this trait and androgenesis efficiency was detected. CIM analysis localized three QTLs in anthers collected from control plants growing in stress-free conditions and five QTLs associated with antioxidative activity under low temperature stress. QTLs controlling antioxidative activity in control plants were localized on chromosome 3A and 4A. Each of them explained about 20% of phenotypic variation. Another QTL was detected on chromosome 7R and was characterized by slightly lower R2 (16%). Chromosomal regions controlling the response to low temperature stress were detected on 3A, 5R and 7R chromosomes with R2 in 12.1-21.5% range. The results of SMA confirmed the significance (p<0.01) of all QTLs detected with the use of CIM method.

Keywords

androgenesis, anther culture, antioxidant activity, QTLs, triticale


Session 2 65

POSTER 14

Pisum sativum´s cultivar specific taste for symbionts

Reinhard Turetschek, Stephan Holzbach, Tamara Epple, Stefan Sassmann, Getinet Desalegn, Hans-Peter Kaul, Stefanie Wienkoop

University of Vienna, Austria

Because of their nutritional value to man and life stock, legumes account for a big part of agricultural production. Their symbiotic interactions (Rhizobia & arbuscular mycorrhizal fungi - AMF) enhance nutritional what makes them substantial in sustainable agriculture. Each legume is capable of forming symbiosis with particular Rhizobia and commonly several species of AMF. The interaction with Rhizobia is to a great extent controlled by the plant and each species as well as cultivars show different nodule morphology. With regard to breeding strategies, agronomy is interested in the effect of below ground parts on above ground traits (e.g. biomass, pathogen resistance levels, and yield). We tested the effect of single and co-inoculation with Rhizobia and AMF on the plants´ morphology as well as the leaf proteome in two cultivars of P. sativum. The nodulation profile (weight and number of nodules) is remarkably distinct among cultivars and the proteome shows predominantly cultivar rather than symbiotic effects. However, we found that single Rhizobia inoculation shows the utmost effect on the proteome in a cultivar specific manner. The intensity of the host-symbiont interaction over a plants´ lifespan usually varies between cultivars. We found as well that fresh weight and number of nodules differ among the cultivars in a time dependent manner. We further aim to elucidate these time effects on the proteome as well as on the metabolome. These insights about cultivar specific symbiotic interaction provide knowledge for advanced sustainable breeding strategies.

Keywords

Pisum, Rhizobia, Mycorrhiza, biotic stress


Session 2 66

POSTER 15

Plant phenotyping in the risk assessment of emergent water contaminants in agriculture

Alexandre Campos, Joana Machado; Marisa Freitas; Remedios Guzmán-Guillén; Daniel Gutiérrez-Praena and Vitor Vasconcelos

CIIMAR, Portugal

The rapid changes in the climate are introducing novel challenges in the agriculture sector. In this context concerns are also centered in the use of water resources contaminated with harmful algal blooms (HABs) since the toxins produced by HABs may represent a potential stress factor to plants.

In this regard our group has been working with the aim of understanding the toxicity of these compounds and their impact in the agricultural / horticultural production systems. For this purpose a conjunct of experiments was performed, at the laboratory scale, and with different vegetable crops. The plant phenotype was investigated under variable toxin exposure scenarios. Our results reveal a number of changes in the phenotype of plants induced by toxin exposure which agree with a toxic or stress response. Stress effects are particularly evident in exposure scenarios with high toxin concentrations. We point out the effects produced in the proteome, photosynthetic capacity of plants and plant biomass. We also highlight the changes observed, for example, in the content of micro and macro elements in root vegetables. Despite the evidences reported we are aware that the real impact of HAB toxins is not fully understood, since a clear relationship of cause and effect (e.g. inhibition of plant development and yield) was not yet established in several relevant agricultural scenarios. In this way we consider that sensitive phenotyping strategies will be of critical importance to evaluate in particular the subtle effects in plants associated to the exposure to low, environmentally realistic, concentrations of HAB toxins.

Keywords

Horticultural crops, environmental contaminants, chemical stress, proteomics


Session 2 67

POSTER 16

Cross-talk between spermine homeostasis and reactive oxygen/nitrogen species increases tolerance to nitro-oxidative stress in Arabidopsis thaliana via modifications in root system architecture and RFO-related metabolites

Miren Sequera-Mutiozabal, Stefanie Schmidt, Joachim Kopka, Chrystalla Antoniou, Ruben Alcazar, Antonio Fernandez-Tiburcio and Vasileios Fotopoulos

Cyprus University of Technology, Cyprus

Polyamines (PAs) are molecules with diverse physiological roles on plant life cycle. These amine compounds are important components of signaling phenomena under challenging environments, leading to tolerance. However, their metabolic or signaling targets are not characterized. One of the essential elements regarding PA homeostasis is AtPAO4, a major polyamine oxidase isoform in Arabidopsis roots, which has been shown to be actively involved in spermine (Spm) content regulation in roots and leaves of plants. T-DNA insertional mutants of AtPAO4 accumulate 10-fold more Spm and present increased root length and lateral root density compared with wild-type (WT) plants under normal growth conditions, suggesting a role for this enzyme and/or Spm on root architecture. An established cross-talk exists between PAs and reactive oxygen/nitrogen species (RONS) under abiotic stress conditions, therefore exogenous addition of H2O2 or NO donor SNP generates changes on pao4 root architecture by increasing the number of lateral roots and last lateral root site of insertion, both important elements to increase root surface of absorption, indicating this as a possible mechanism to enhance tolerance to hostile environments. 15 day-old Arabidopsis seedlings demonstrated increased tolerance to nitro-oxidative stress. After both stresses, pao4 mutants showed increase in Spm content suggesting a link between its accumulation and the plant’s overall tolerance capacity. In order to identify down-stream signaling targets, metabolomic profiling by GC-TOF-MS after H2O2 and SNP treatment revealed that PA signaling pathway under nitro-oxidative stress conditions is related to glutamate-5-oxoproline regulation which influences glutathione homeostasis, as well as to galactinol-myo-inositol which is a key metabolite on Raffinose Family Oligosaccharides (RFO) biosynthesis pathway. RFOs are currently emerging as powerful antioxidant molecules in addition to their role as carbon re-allocation molecules in abiotic stress response. Our results indicate that PA down-stream signaling following nitro-oxidative stress imposition relies on antioxidant capacity regulation, establishing a novel connection between PAs and RFO homeostasis.

Keywords

polyamines, abiotic stress, reactive oxygen/nitrogen species, RFO metabolites


Session 2 68

POSTER 17

Metabolic profiling in wheat

Zsófia Juhász, Ákos Boldizsár, Tibor Nagy, Gábor Kocsy, Ferenc Marincs, Gábor Galiba, Zsófia Bánfalvi

NARIC Agricultural Biotechnology Institute, Hungary

Wheat was characterised at the metabolite level during cold acclimation and transition from the vegetative to the generative phase. The relationship between these changes and chromosome 5A (chr5A) and the maintained vegetative phase (mvp) mutation was also investigated. Five wheat lines were analysed: T. monococcum (Tm) and its mvp mutant in which the mutation encompasses the VERNALISATION (VRN1) gene and the moderately freezing-sensitive spring wheat T. aestivum cv. Chinese Spring (CS) and its two chromosome substitution derivatives, CS(Ch5A) with increased freezing tolerance and CS(Tsp5A) with increased freezing sensitivity. Samples were taken from the shoots and crowns during four developmental stages: plants grown at 20/17°C, after cold treatment but still during the vegetative phase, at the double ridge and during spikelet formation. The levels of 47 compounds were identified by GC-MS. The cold treatment, in general, increased the concentrations of osmolites. The accumulation of proline was not associated with the vernalisation process or with frost tolerance. In contrast, the pool size of galactinol and sucrose after cold treatment correlated with the freezing tolerance of T. aestivum genotypes. The mvp mutation and chr5A substitutions altered the amounts of several metabolites compared to those of the Tm and CS, respectively. The Ch5A substitution resulted in more substantial changes at the metabolite level than did the Tsp5A substitution. While Ch5A mainly influenced the sugar concentrations, Tsp5A altered the level of TCA cycle intermediates during the vegetative/generative transition. These results suggest that different genetic regulation of metabolism exists in different wheat species and cultivars.

Keywords

GC-MS, metabolite profiling, Triticum aestivum, Triticum monococcum, vernalisation


Session 2 69

POSTER 18

Androgenesis-specific protein expression pattern in winter triticale (× Triticosecale Wittm.).

Monika Krzewska, Gabriela Gołębiowska-Pikania, Ewa Dubas, Iwona Żur

The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Poland

Double haploid (DH) populations have proved to be advantageous in the studies of plant biodiversity on different levels. One of the methods for DHs production is androgenesis, the process of microspores reprogramming in in vitro cultured anthers. To gain a better understanding of the mechanisms controlling triticale (× Triticosecale Wittm.) androgenesis, qualitative changes in anther proteome profiles associated with androgenesis-inducing stress treatment were analysed.

The population comprised of 90 DH lines was phenotyped for androgenesis effectiveness in anther cultures. High level of variation in respect of androgenesis induction and plant regeneration was detected. Four significantly segregating DH lines were chosen for proteomic analysis. Protein profiles were made on isolated anthers. After spikes cold pre-treatment (2-3 weeks at 4°C), which seemed to be the most efficient method for androgenesis induction, the identification of proteins involved in the process was conducted. Proteins were isolated according to the phenol-based procedure (Hajduch et al. 2005). Protein expression patterns were examined using 2-D electrophoresis. Chosen proteins were identified by MALDI TOF/TOF MS/MS analysis.

The identified proteins were mainly associated with metabolism, stress response or cell energy management. To the best of our knowledge, this is the first report concerning androgenesis-specific protein expression patterns in triticale.

ACKNOWLEDGEMENT: The research was supported by National Project 2011/01/N/NZ9/02541

Keywords

androgenesis, double haploid, proteins, triticale


Session 2 70

POSTER 19

Unraveling seed development mechanism in Phaseolus vulgaris L.: a proteomic approach

José Ricardo Parreira, Jamila Bouraada, Susana Silvestre, Anabela Bernardes da Silva, Jorge Marques da Silva, Pedro Fevereiro, André Martinho Almeida, Maarten Altelaar, Susana de Sousa Araújo

Instituto de Tecnologia Química e Biológica, Portugal

Common bean (Phaseolus vulgaris L.) is the most consumed grain legume in developing countries in Latin America and Sub-Saharan Africa. Seed quality traits depend on accumulation of various storage molecules during the seed development (SD) process and influenced by the genotype and adaptive changes to environment. Concerning common bean, the lack of a deeper molecular characterization of SD is hampering the development of new biotech approaches for seed trait modulation and timely address challenges of agriculture or industry.

Our present work aims to unravel the molecular mechanisms underlying SD using a proteomic approach. To achieve this goal, we characterized SD in terms biomass, seed length and weight in the genotype SER16, one of the most promissory germplasm releases of the CIAT-CGIAR. Seed samples were collected at the 4 main SD stages: late-Embryogenesis (10 days after anthesis), early (20 d.a.a.) and late Maturation (30 d.a.a.) and Desiccation (40 d.a.a.).

The analysis of bean proteome was conducted using a gel-free proteomic analysis (LC-MS/MS) under the scope of EU-FP7-PRIME-XS project. We identified 523 proteins, with a total of 387 increased and 268 decreased differential accumulation among the major developmental phases. This study will contribute to reveal key metabolic pathways and mechanisms with major role in common bean seed development and yield.

Keywords

Seed, Phaseolus, Proteomics, Development


Session 3 71

Session 3: From gene to phene: screening natural diversity


Session 3 72

POSTER 20

Testing of experimental environments: a case study with photoperiodic plants

Ivan Tarakanov

Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Russian Federation

The design of experimental environments is of crucial importance both for the screening of genotypes within populations and norm of reaction studies. The local assortment of hereditary plant material is often represented by heterogenous populations consisting of many forms that differ one from another both physiologically and morphologically. It is important to recognize both genetic variation in performance and the environmental constraints within which this variation is expressed. The highest variation of physiological characteristics and morphological traits could be observed in the marginal conditions (analyzing environments). To measure environmental sensitivities of genotypes and to see how much of the interaction variance is ascribable to differences in sensitivity, different genotypes are grown in a range of specific environments. By the mean performance of all genotypes the specific environment can be quantified as more or less favorable for the expression of the character under investigation. In a phytotron case study, the sets of Indian mustard self-pollinated tester lines were used for the testing of environment capability to segregate experimental populations according to the variation between biotypes in critical day-length, length of juvenile phase, and sensitivity to civil twilight (environmental value estimation). Using analyzing environments as elements of high throughput techniques would facilitate various breeding programs. On the contrary, stabilizing environments should be provided for the successful seed production due to the synchronization of flowering, e.g., during germ plasm conservation ex situ.

Keywords

populations screening, analyzing environment, photoperiodic response


Session 3 73

POSTER 21

Combination of proteomic and metabolomic approaches in drought stress research

Gagan Paudel, Andrej Frolov, Tatiana Bilova, Robert Berger, Elena Tarakhovskaya, Claudia Birkemeyer, Ludger Wessjohann

Universität Leipzig, Germany

Drought is the main environmental factor limiting the productivity of crop plants. The accumulation of drought-related sugar osmolytes in parallel to developing oxidative stress might enhance protein glycation, i.e. interaction of carbonyl compounds (reducing sugars and α-dicarbonyls) with lysyl and arginyl side-chains yielding early and advanced glycation end-products (AGEs), respectively. Unfortunately, the possibility of AGE accumulation during the life time of the crop plants was not studied in details so far. In this context, the patterns of AGEs in crop plants and effect of environmental stress on their dynamics are to be characterized. For this, however, adequate drought stress models are required. The polyethylene glycol-based agar infusion model of drought stress was established with 6-week old Arabidopsis thaliana and Nicotiana tabacum plants. Our analytical strategy relied on the combination of LC-based bottom-up proteomics (LC x LC-ESI-Orbitrap-LIT-MS/MS) with metabolomics (GC-EI-Q-MS). The analysis revealed essential metabolome alterations accompanied with changes in protein patterns: up to 87 unique proteins were annotated in drought, 28 molecules demonstrated statistically significant abundance changes. In-depth proteomic analysis revealed 784 A. thaliana AGE-modified proteins (mostly represented with the enzymes of protein metabolism). A three-day drought treatment revealed 44 unique stress-specifically modified proteins representing 59 AGE sites, mostly originating from glyoxal. Moreover, label-free quantification revealed 29 proteins demonstrating significant alterations (p ≤ 0.05) in the abundance of AGE modifications in specific sites.

Keywords

AGEs, drought stress, glycation, metabolomics, proteomics, tandem mass spectrometry


Session 3 74

POSTER 22

Protein glycation as the marker of ageing in plants

Tatiana Bilova, Dominic Brauch, Elena Tarakhovskaya, Claudia Birkemeyer, Ludger Wessjohann, Andrej Frolov

Universität Leipzig, Germany

Plant ageing is associated with accumulation of carbohydrates and reactive oxygen species (ROS). It results in enhancement of α-dicarbonyl formation and advanced glycation. Resulting advanced glycation end products (AGEs) are the well-known markers of ageing in mammals. In contrast, no information about age-related changes of AGE patterns in plants is available. Here we provide this information and characterize possible mechanisms of time-dependent AGE formation in A. thaliana. Our analytical strategy relied on the combination of bottom-up proteomics (LCxLC-ESI-Orbitrap-LIT-MS/MS) and untargeted metabolomics (GC-EI-Q-MS). The analysis revealed 524 AGE-containing peptides representing 700 modified sites and slow increase of sugar tissue contents. The number of the AGE-residues decreased in the order: Nɛ-carboxymethyllysine > Nω-carboxymethylarginine > methylglyoxal-derived hydroimidazolone >glyoxal-derived hydroimidazolone > Nω-carboxymethylarginine > argpyrimidine >pyrraline > dihydroargpyrimidine. Though only few new modification sites appeared, essential age-related quantitative changes in the glycation profiles were observed. Thus, the abundance of 98 and 21 advanced glycation sites (mostly in the polypeptides related to signaling and protein metabolism) was increased and decreased, respectively. Early glycation patterns were less abundant and included arginine-derived Amadori/Heyns products. It was proved by MS/MS, to the best of our knowledge, for the first time. As only minimal overlap between early and advanced glycated sites was observed, we propose monosaccharide autoxidation and interaction of α-dicarbonyls with proteins to be the main AGE formation pathway.

Keywords

tandem mass spectrometry, glycation, AGEs, Amadori products, carbonyls, plant ageing


Session 3 75

POSTER 23

Use of manually operated chlorophyll fluorescence-based methods to assess the status of the photosynthetic apparatus in cereal crops

Marek Živčák, Marián Brestič, Katarína Olšovská, Oksana Sytar

Slovak University of Agriculture, Slovak Republic

The chlorophyll fluorescence methods are widely used in crop science with high possible applications for investigating changes of genotype x environment interactions. In phenomic research, the main attention is focused on fluorescence imaging and remote sensing. However, there is still space for the use of manually operated fluorescence-based methods, which can provide additional important information. The most widespread method in plant science is the pulse-amplitude modulated (PAM) technique, which can, however, provide useful information only when the prolonged measuring protocols are used, which precludes this method from being used routinely for screening and phenotyping. On the other hand, the analysis of the polyphasic fluorescence rise belongs to the most rapid; with over one hundred of records per hour, the method produces sufficient amounts of the data, especially in field applications. Our results document usefulness of the method in screening for abiotic stress tolerance and monitoring of spatial-temporal changes of plant photochemical apparatus. In addition to direct observations in situ, the method can be used also for assessment of the effects of different treatments in detached leaf samples, such as tests of photosynthetic heat resistance. Our results also suggest that applications of other chlorophyll fluorescence-based techniques, such as multispectrally-induced chlorophyll fluorescence records can be also very useful in phenotyping of genetic resources.

The work was supported by the European Community under the Project No. 26220220180: “Construction of the “AgroBioTech” Research Centre”.

Keywords

chlorophyll fluorescence, wheat, genotypes, fast fluorescence kinetics, screening


Session 3 76

POSTER 24

Tolerance of Soybean Cultivars to Different Types of (Metal) Stresses Reveal Specific Patterns

Peter Socha, Patrik Mészáros, Terézia Gálusová, Ľubomír Rybanský, Nadine Spieß, Jana Libantová, Jana Moravčíková, Ildikó Matušíková

Institute of Plant Genetics and Biotechnology SAS, Slovak Republic

Plants have potential to uptake, distribute and accumulate of essential and non-essential trace elements among species and within species. The ability to handle metals, however, depends on not only plant species but also dose and type of metal. The detailed mechanism operated for the metal tolerance and accumulation are still entirely unknown. In this work we examined a set of soybean cultivars for tolerance to different stressors such as Al as a representative of light metal, the metalloid As, and Cd as a typical phytotoxic heavy metal. We studied the tolerance/sensitivity of 22 soybean cultivars to these stressors, while NaCl was applied as a reference (non-metal) stressor. We screened the impact of these stressors on root growth of individual soybean cultivars to reveal if there are any general patterns of effects caused by the individual stressors. Our data enabled to identify cultivars with generally high- as well as low tolerance to all of tested metals. Salt as a stress factor did not exert a differentiating effect indicating to defense mechanisms similar (at least partially) to those involved during metal exposure. At the same time, the applied stressors yielded a distinguishable pattern of root responses indicating that such screens could be a good tool to identify similarly or differently acting agents. For cadmium stress the accumulation potential was determined using genetic markers and cultivars with potential health risk were identified.

Keywords

Aluminium, Arsenic, Cadmium, Glycine max, Tolerance


Session 3 77

POSTER 25

Genome-wide association study for root architectural traits in a diverse spring barley collection

Zhongtao Jia,Ying Liu, Benjamin D. Gruber, Kerstin Neumann, Nicolaus von Wirén

Lebniz-Institute of Plant Genetics and Crop Plant Research, Germany

Genome-wide association studies (GWAS) represent a powerful tool for detecting genetic factors controlling complex quantitative traits in crop plants. Root system architecture (RSA) is a complex trait and of profound impact on capturing water and nutrients from the soil and thus for plant performance and ultimate grain yield. Therefore, generating crop cultivars with superior root systems carries a great potential to enhance resource efficiency and plant adaptation to instable climates. In the present study, root traits of a widely used diverse spring barley association panel (Pasam et al. 2012) comprising of 224 genotyped accession lines were screened in rhizotrons in the greenhouse for different root traits and then subjected to GWAS to dissect the genetic architecture of root system architecture. A large phenotypic variation was observed for all traits within the population and across different subsets separated based on spike morphology and geographic origins. In addition, all traits analyzed showed repeatability of > 70%. Correlation analysis indicated that these traits might be genetically independent. Using 6336 SNPs markers originating from a 9K iSELECT chip, a genome-wide scan was performed with a mixed linear model including kinship to control false-positives and a total of 57 significant associations were detected at a significance threshold -log(P)>3. Future work will be focused on uncovering genetic loci and candidate genes behind these marker-trait associations and assessing the function of the most robust candidates shaping root architecture.

Keywords

Spring barley, GWAS, root architectural traits, MLM, Kinship


Session 3 78

POSTER 26

Phenotyping Phaseolus sp. Germplasm Collected From High Altitudes for Chilling Tolerance

Faik Kantar, Bilgehan Turan Certel, Akın Tepe, Volkan Gözen, Vahdettin Çiftçi, Hatice İkten, Cengiz Toker

Akdeniz University, Turkey

Cultivated beans (Phaseolus accutifolius A. Gray, P. coccineous L., P. lunatus L. and P. vulgaris L.) are one of the most important food legume species in the world and in Turkey. Chilling stress (temperatures below 10 oC) and frost damage (temperatures below 0 oC) at seedling stage in the spring and at generative stage in the autumn is primary stress factor limiting the growth and production of beans in Turkey. Utilisation of germplasm for the purpose of breeding to improve cold tolerant cultivars may lead to safer and extended production of beans in the growth season including early spring and late autumn. Furthermore, chilling tolerant cultivars have potential of reliable production for fresh pods in greenhouses in the winter. A project has been initiated to develop cold tolerant bean cultivars using a Phaseolus germplasm collection of 579 national accessions collected from high altitudes in all regions of Turkey in comparison with a collection of 17 cold tolerant common bean (Phaseolus vulgaris L. ) and runner bean (P. coccineus L.) accessions received from Department of Agriculture's (USDA's) Agricultural Research Service (ARS), The Gerrmplasm Resources Information Network (GRIN. Bean germplasm is currently phenotyped at plant and cellular level at seedling and flowering stage at 5 oC in controlled climatic conditions. Phenotyping is made on the bases of cell membrane leakage, Chlorophyll measurements, dry matter production and relative growth rate at seedling stage and additional tests of pollen viability and pollen germination at generative stage. Genotypes selected in controlled climatic conditions will be tested under cold conditions in early spring and late autumn in the field. Phenotyping will be made on the bases of cell membrane leakage, periodic measurements of plant leaf colour and leaf Chlorophyll contents, phenological and morphological plant growth characteristics as well as pod and seed yields.

Molecular characterisation will be carried out with SRAP (Sequence Related Amplified Polymorphism) on the Phaseolus bean core collection including 20 tolerant and sensitive genotypes. Expressing of COR (Cold Responsive Genes) genes and Cytochrome P450 gene in common and runner beans including other cold tolerant and sensitive accessions will be also tested with Real Time PCR.

Data from the first phase of tests show that considerable variation exists amongst bean accessions for chilling tolerance at early stages of plant growth supporting the hypothesis that accessions from higher altitudes will be more likely to include cold tolerant genotypes. This paper highlights data so far produced from the controlled climate growth chamber tests conducted.

Keywords: Phaseolus Germplasm, Phenotyping, Chilling Stress


Session 3 79

POSTER 27

Physiological studies on young poplar (Populus spp.) and willow (Salix spp.) saplings in pot experiment and field trials aimed at assessment of the biomass productivity potential

Ivaylo Tsvetkov, Nikolina Tzvetkova

Forest Research Institute, Bulgaria

Field trials and a pot experiment with some fast-growing woody species (Populus spp., Salix spp.) were established in 2013 with a goal for general assessment of their potential for biomass production and suitability for energy plantations. A field trial (cuttings, classic randomized block design) for studying the effect of 3 doses of waste water sludge generated by treatment plant (0.2, 0.4 and 0.6 t ha-1) on the early stage growth and development of two willow clones (S. alba L. and S. x rubra Huds.) was established on Vertisols. Two poplar clones (I-214 and I-45/51) were included in a pot experiment with waste water sludge treatments as well. Multifactorial experiment initiated by cuttings (Nelder wheel design) was established on Chernozems in order to test the effect of genotype, spacing (11 levels) and rotation (3 levels) on the early growth of five poplar clones (I-45/51, Agathe, BL, Panonia and NNDV). Net CO2 assimilation, transpiration and stomatal conductance of young leaves were measured during the period of active vegetation. The gas-exchange measurements were performed by portable infrared gas analyzer Li 6400. The photosynthetic measurements were performed between 10.00 and 13.00h, with only green and healthy leaves being selected for that purpose. The different poplar (pot trial) and willow clones (field trial) from the experiments with waste water sludge treatments showed contrast behavior in terms of the photosynthetic parameters measured. The photosynthetic activity of the clones included in the Nelder design is commented in connection with their productive potential.

Keywords

photosynthetic activity, clonal behaviour, biomass productivity


Session 3 80

POSTER 28

Screening diversity of natural hybrid Thymus × oglongifolius Opiz: from natural habitats to ex situ conservation

Kristina Loziene

Nature Research Centre, Lithuania

The many interspecific hybrids of natural origin were described in genus Thymus which is rich in essential oils bearing medicinal and aromatic species. One interspecific hybrid, namely Thymus × oblongifolius Opiz (T. pulegioides L. × T. serpyllum L.), grows wild in Lithuania. This hybrid stands an intermediate position compared with its parent species according to morphological features (Ložienė and Kamašina, 2006) and chemical composition of essential oils (Ložienė et al. 2002, Ložienė and Venskutonis, 2010; Ložienė et al. 2012): T. × oblongifolius is often high as parent species T. pulegioides and accumulates essential oils with wide diversity of chemical composition characteristic of both parent species. Therefore the wide spectrum of diversity of morphological and chemical features is favourable for screening of productive and chemically valuable individuals of this hybrid from natural habitats.

The individuals of T. × oblongifolius were screened from natural habitats according to the fragrance, the plant height or/and the plant size and moved into the field collection of medicinal and aromatic plants of the Nature Research Centre (Vilnius, Lithuania). There they were grew in field collection and analysed their qualitative and quantitative composition of essential oils. One selected valuable sample of T. × oblongifolius was registered in the central database of national genetic resources of the Republic of Lithuania; it is conserving ex situ by permanent field culture.

Keywords

medicinal plants, Thymus × oblongifolius Opiz, diversity, screening, ex situ conservation


Session 3 81

POSTER 29

Screening of a chickpea RIL population for biochemical and phenotypic traits under drought conditions

Hatice Şelale, Cantuğ Bar, Elvan Öztürk, Süleyman Öztürk, Asena Akköse, Şurhan Göl, Anne Frary, Sami Doğanlar

Izmir Institute of Technology, Turkey

Chickpea is a non-irrigated crop grown in arid and semi-arid regions and is an important source of protein and other nutrients in such regions.The major limiting factor for chickpea yield is drought conditions.Under drought conditions, physiological and biochemical changes occur in plants and are related both to the response and tolerance to drought. For example, elevated levels of the osmoprotectant proline and antioxidant enzymes are known to be related to drought tolerance. In addition, the amount of malondialdehyde (MDA), a measure of lipid peroxidation in cell membrane, is informative for understanding stress levels. Levels of photosynthetic pigments are also related to the efficiency of photosynthesis during drought. In this project, we screened a chickpea recombinant inbred line (RIL) population under drought conditions for determination of quantitative trait loci (QTLs) related to the physiological and biochemical responses to drought stress. The RIL population was developed by ICARDA (Syria) via intraspecific cross between kabuli chickpea cultivar ILC 558 which is drought tolerant and ILC 3279, a susceptible landrace. Biochemical (proline, MDA, photosynthetic pigment, total protein contents and guaiacol peroxidase, glutathione reductase, glutathione S-transferase antioxidant enzyme activities) and physiological (fresh and real weight, real and relative water contents) characters were screened both in shoot and root tissues of hydroponically grown plants under drought (6% PEG) and control conditions. QTLs will be determined for the above-mentioned traits using the genetic map developed for our RIL population.

Keywords

drought stress, chickpea, QTL


Session 3 82

POSTER 30

The cultivar-dependent attenuation of stomatal functioning at high relative air humidity is not due to the differential decrease of the transpiration stream

Habtamu Giday, Katrine H. Kjaer, Dimitrios Fanourakis, Carl-Otto Ottosen

Aarhus University, Denmark

High relative air humidity (RH ≥ 85%) during plant growth leads to the development of stomata that show attenuated response to closing cues such as water deprivation. Previous work revealed a large genetic variation, at which the above-mentioned effect appears. In this study, we analyzed the water relations of ten rose cultivars during growth at moderate (60%) or high (90%) RH. We hypothesize that tolerant cultivars to high RH transpire more at high growth RH as compared to the sensitive ones, and we expect that cultivar differences in plant transpiration could be monitored by measuring leaf temperature (Tleaf). Dehydration of detached leaves indicated a wide variation in the high RH-induced attenuation of stomatal functioning. Plants grown at high RH indeed transpired less (≈ 50%) than those grown at moderate RH, though no genetic variation was observed. Interestingly, growth RH-induced differences in the plant transpiration rate mainly lie in the light period, indicating that stomatal functioning is set during that time. Within cultivars, Tleaf was generally higher (1.5–3.7 °C) at high as compared to moderate RH. Cultivars with more responsive stomata transpired less during growth at moderate RH, whereas stomatal responsiveness was not related to plant water loss at high growth RH. Cultivar differences in plant transpiration rate both among and within growth RHs were also not detected by measuring Tleaf. It appears that the large genetic variation in stomatal functioning, following growth at high RH, does not originate from differential decrease of the transpiration stream during growth.

Keywords

genotypic variation, leaf temperature, selection criteria, stomatal functioning, plant transpiration


Session 3 83

POSTER 31

Hybridity and ploidy effects on photosynthesis and adaptation to varied irradiance in allotetraploid and its parents in Cucumis

Xiaqing Yu, Eva Rosenqvist, Carl-Otto Ottosen, Jinfeng Chen

Nanjing Agricultural university, China, People's Republic of

Cucumis ×hytivus J.F. Chen & J.H. Kirkbride is a newly synthesized allotetraploid between a wild germplasm, C. hystrix Chakr. and a cultivated cucumber (C. sativus L. cv. Beijingjietou), conferring possible heterosis and adaptive potential due to the hybridity and ploidy. Our aim is to characterize the photosynthesis of C. ×hytivus and investigate its photosynthetic response to varied light irradiance in relation to biomass, pigmentation, gas exchange and chlorophyll fluorescence, compared with it diploid parents. The results showed that C. hystrix had lower biomass contributed by lower photosynthetic capacity, lower light-saturated net photosynthesis rate (Pmax) and quantum efficiency of photosystem II (ΦPSII), and is shade-requiring with flexibility in acclimation to changes in light level, whereas C. sativus ‘BejingJietou’ had larger biomass with higher Pmax and ΦPSII that preferred higher light level and sensitive to changes of light irradiance. C. ×hytivus was observed with yellow green young leaves caused by chlorophyll deficiency, which was considered as a side-effect brought by the heterozygosity. C. ×hytivus exhibited intermediate in not only biomass and photosynthesis capacity, but also in adaptively response to varied light levels compared with it parents. The results demonstrate that C. ×hytivus has neither heterosis nor adaptive enhancement. Instead, it displays intermediate characteristics between it parents with no obvious dosage effect of ploidy.

Keywords

allotetraploid, Cucumis, adaptation, irradiance


Session 3 84

POSTER 32

Vigorous early growth of Spanish barley landraces cultivated in rhizotrons

Ridha Boudiar, Kerstin Nagel, Tania Gioia, Fabio Fiorani, Ana M Casas, M Pilar Gracia, Ernesto Igartua

CSIC, Spain

The objective of this study was to explore the early growth features of three promising barley landraces, compared to three modern cultivars.

Three lines derived from Spanish barley landraces, part of the Spanish Barley Core Collection, presented good agronomic features at field trials: SBCC042 and SBCC073 out-yielded 26 cultivars in field trials at low production sites across Spain, and SBCC146 had an outstanding early vigour. This study was proposed to find out whether early growth, particularly under drought, was related to this good agronomic performance. Three modern cultivars, Orria, Cierzo and Scarlett were used as checks.

The six genotypes were grown under two water treatments in rhizoboxes-rhizotrons (12 plants per genotype and treatment, in balanced incomplete blocks), for four weeks, at the GROWSCREEN-Rhizo phenotyping platform (Nagel et al. 2012), at the Forschungzentrum of Julich (FZJ-Jülich), Germany.

Growth of roots was monitored by automatic image analysis. Images were taken 2-3 times per week. At the termination of the experiment, the plants were extracted from the rhizoboxes, and shoot and root fresh and dry weights were determined

Landrace lines exhibited more vigorous growth than checks under no stress, although patterns differed, with enhanced root growth for SBCC073 and larger shoot growth for SBCC146. Two of these lines will be further explored as parents of BC populations.

Nagel KA et al. 2012. GROWSCREEN-Rhizo… Funct Plant Biol 39: 891–904

Keywords

barley, landraces, early growth, root/shoot ratio


Session 3 85

POSTER 33

Brassinosteroid signalling in barley: a genetic approach.

Claire Villette, Luc Didierjean, Hubert Schaller

CNRS, France

Semi-dwarf varieties of cereals have long been used in agriculture to increase yields by avoiding lodging. In fact, stem height is largely defined by the action of plant hormones including brassinosteroids (Vriet et al. 2012). This group of sterol-derived products act on cell elongation and therefore are essential for growth and fertility, according to molecular mechanisms quite well understood (Gruszka, 2013). In barley, a number of semi-dwarf varieties used in the fields are mutated on loci implicated in brassinosteroid biosynthesis or signalling. In order to further understand the complexity of brassinosteroid-mediated growth mechanisms, we currently examine the mutational spectrum obtained in a population derived from one of these mutated varieties and perform a targeted chemical profiling using UPLC-MS/MS methods.

Keywords

Semi-dwarf, brassinosteroids


Session 3 86

POSTER 34

Investigation of genotype x environment interactions for photosynthetic heat tolerance in wheat using fast chlorophyll fluorescence technique

Marián Brestič, Katarína Olšovska, Marek Živčák

Slovak University of Agriculture, Slovak Republic

The analysis of fast chlorophyll fluorescence kinetics represents useful and rapid tool for investigating changes of genotype x environment interactions for parameters related to status of photosynthetic apparatus in field or laboratory conditions. In addition to observations in situ, we applied also short heat treatment of field-grown leaf samples of thirty winter wheat (Triticum aestivum L.) genotypes to assess the level of photosynthetic heat resistance and the acclimation effects during the spring season. A gradual increase in temperature caused the appearance of K-bands at 300 μs on the chlorophyll fluorescence induction curve, indicating the impairment of the PSII donor side. An increase in basal fluorescence, commonly used as a criterion of PSII thermostability, was observed beyond a temperature threshold of 44 °C. Moreover, an acclimation shift (increase of critical temperature) observed for K-band appearance was significantly higher than those for a steep increase of basal fluorescence F0. The single temperature approach (40 °C) with regular weekly observations demonstrated that the acclimation effect was not gradual, but occurs immediately and it was associated with an increase of daily temperature maxima over 30 °C. In the non-treated plants the reduction of antenna size, increase of PSII connectivity and changes in the acceptor side occurred as a result of heat acclimation. The enhancement of PSII thermostability persisted over several weeks regardless of weather conditions. The genotype comparison identified three groups that differed either in initial PSII thermostability or in acclimation capacity; these groupings were clearly associated with the origin of the genotypes.

The work was supported by the European Community under the Project No. 26220220180: “Construction of the “AgroBioTech” Research Centre”.

Keywords

chlorophyll fluorescence, wheat, genotypes, heat resistance, genotype x environment interactions


Session 3 87

POSTER 35

A flax proteome atlas as a resource for analyses of cell wall

Estelle Goulas, Malika Chabi, Anne-Sophie Blervacq, Jean-Francois Hausman, Jenny Renaut, Simon Hawkins

UMR 8576 CNRS/Université Lille 1, France

Fiber quality is intimately related to cell architecture and cell wall composition. Improvement of flax fiber quality strongly relies on a better understanding of the molecular mechanisms controlling cell wall biosynthesis. Currently only limited proteomics data exist for different flax organs [1;2], and we therefore used various extraction protocols to obtain extracts enriched in i) soluble proteins (S), ii) cell wall proteins (C) and iii) membrane proteins (M) from four flax organs/tissues (leaves, roots, outer- and inner-stems). Trypsin-digested peptides were individually analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) using the sequenced flax genome as reference [3]. Altogether a total of 5711 proteins (2761 non-redundant) were identified: 66% in outer-stem tissues, 51.3 % in inner-stem tissues, 46.7 % in leaves and 42.2 % in roots. Some proteins were specific to one organ/tissue whereas others were common to 2, 3 or 4. The highest number of proteins was always recovered in the M fraction followed by the S and C fractions. Inclusion of previously published proteomics data on flax seeds allowed us to recover 934 additional proteins bringing the total of non-redundant proteins in the flax proteome atlas to 3695. The identified flax proteins were classified into distinct “Eukaryotic Orthologous Groups of proteins” (KOG) functional groups [4]. Four categories were particularly represented in all the organs: “O”: post translational modification, protein turnover and chaperones; “C”: energy production and conversion; “J”: translation, ribosomal structure and biogenesis; and “G”: carbohydrate transport and metabolism. A high number of proteins involved in hemicellulose metabolism were identified thereby contributing a major piece of the puzzle to our understanding about the role of these important polymers in structuring the 3D cell wall network in flax.

Keywords

flax, fiber quality, cell wall, proteomics, compartmentation


Session 3 88

POSTER 36

Overcoming the challenges to understand the totipotency: a case study on coffee embryogenic cell suspensions

Nádia Campos, Luciano Paiva, Bart Panis, Sebastien Carpentier

KU Leuven, Belgium

Somatic embryogenenis (SE) is a process where embryos are generated from somatic tissues and can be used in genetic engineering, improvement of plants, clonal propagation in the agricultural sector, somatic hybridization and also to conserve plants ecologically threatened. Protocols for SE in coffee and in many others species have been developed, but the molecular processes leading to these changes are still unknown. Therefore, the present proteomic study aims to investigate the molecular events taking place during early initiation of embryogenic calli, before to develop the phenotypic differences. One challenge in this study is the limited amount of the initial material, since sampling must take place before the differentiation of callus and, in this phase, the cells are not numerous and undifferentiated. We determined the minimal amount of cells and extracted proteins from 15, 20, 25 and 30 mg FW. More than 500 proteins were identified, whereof 9 directly correlated to somatic embryogenesis and 6 to stress response, what is important to induce embryogenesis. The identification was possible using 15 mg FW. This small amount proves the good precision of the method and was choosen as the minimal quantity to be used in further works. Complementary analysis will be performed on non-embryogenic and embryogenic calli to link multiple proteins to totipotency.

Keywords

Somatic embryogenesis; Proteomics; Totipotency, coffee


Session 3 89

POSTER 37

e!DAL: Infrastructure for a Culture of Data Publication

Daniel Arend, Jinbo Chen, Christian Colmsee, Uwe Scholz, Matthias Lange


The German Plant Phenotyping Project (DPPN) project focuses on new developments and technologies in the field of high-throughput plant phenotyping, with the IT infrastructure work packages from the TECHNO module addressing the planning, establishment and extension of hardware and software components for data management, analysis, exchange and publication.

The three participating institutions – IPK Gatersleben, Helmholtz Zentrum München and Forschungszentrum Jülich – have developed a shared concept for data representation and publication. Experimental metadata and references to raw and preprocessed measurement data are compiled into a defined file format using the international ISA-Tab standard (Sansone et al., 2012). To ensure long-term stable citability of datasets, digital object identifiers (DOIs) are registered together with the corresponding metadata at DataCite. The DataCite interface can be used to query and filter DPPN datasets. A user-friendly platform for file deposition and DOI registration, the e!DAL system (Arend et al., 2014), has been developed at IPK and is installed at the other nodes. Example datasets in ISA-TAB format are already accessible by DOIs.

Data storage, management and analysis are implemented internally at each node, to guarantee long-term availability by embedding the components into the infrastructure of the respective institute. Custom solutions have been advanced in three areas: (a) configuration of the hardware infrastructure, (b) database and information management systems and (c) data analysis and integration approaches. Established workflows and software will be exchanged and published as appropriate.

Sansone et al. (2012). Toward interoperable bioscience data. Nat. Genet. 44:121–126

Arend et al. (2014). e!DAL - a framework to store, share and publish research data. BMC Bioinformatics 15:214

Keywords

databases, bioinformtics infrastructure, data publication


Session 3 90

POSTER 38

Evaluation of faba bean germplasm for drought tolerance

Angel M Villegas-Fernández, Mahmoud H Soliman, Diego Rubiales

Spanish National Research Council, Spain

Drought is a recurrent challenge for agriculture around the world, compromising yields and even the survival of crops. Developing strategies to confront the lack of water is a key issue for modern agriculture, moreover in the context of a changing climate. Breeding plays a major role in this situation, with the introduction of varieties adapted to more dry ecosystems. The identification of genotypes showing tolerance to drought is, then, of great interest.

The aim of our work was the identification of genotypes of faba bean that might be employed in breeding for drought. We have tested the response to drought of genotypes previously selected for their performance under biotic stress, mainly diseases. A preliminary trial under controlled conditions permitted to define a visual scale for drought symptoms in faba bean, and to establish the experimental conditions for an optimal discrimination of responses. In a second experiment, a collection of 36 genotypes was assessed. Symptoms were scored for three weeks after the interruption of watering; relative water content of soil was also measured. Results have permitted the identification of a subset of genotypes presenting promising responses. The evaluation of physiological parameters as well as of enzymatic activities in the selected genotypes will be part of future work.

Keywords

Faba bean, breeding, drought, screening


Session 3 91

POSTER 39

Shoot growth pattern and degree of bud differentiation in apricot as the basis of fruiting potential modelling

Nikola Mićić, Gordana Đurić, Miljan Cvetković, Slobodan Stojnić

University of Banja Luka, Bosnia and Herzegovina

The degree of differentiation of apricot generative buds undergoing dormancy is quite varied and dependent on a number of factors, including climatic conditions, cultural practices, cultivar, etc. Differences in bud differentiation degree are particularly evident in different waves of long fruit-bearing shoot growth. The highest degree of bud differentiation is observed in the first growth wave, with the buds exhibiting higher resistance to low winter temperatures during physiological dormancy and ecological dormancy, as well as higher fruiting potential. However, in certain years, depending on climatic conditions at the beginning of the growing season and flowering, higher fruiting potential is realised from the generative buds in the second and third waves of growth. These buds have a lower degree of differentiation, and during their development at the beginning of the growing season they show delayed development, thus avoiding climate-related stress that adversely affects the buds in the first growth wave developing at an earlier stage. Histocytological analyses of the degree of differentiation of generative buds during the different waves of long shoot growth in two apricot cultivars under the environmental conditions of Banjaluka in 2011 and 2012 show variation in bud development dynamics depending on the wave of growth from which the buds arise. The degree of differentiation obtained had a very strong effect on fruit set and fruiting. Modelling agricultural and pomological practices for controlled induction of different growth waves for each cultivar under the specified environmental conditions requires setting limit values for the degree of differentiation of apricot generative buds during shoot growth waves to provide the basis for the control of fruiting under the defined agro environmental conditions.

Keywords

growth waves, generative buds, fruit set and fruiting


Session 3 92

POSTER 40

Production of virus-free citrus germplasm in Greece

E.M. Koutsioumari, T. Kapari-Isaia, A. Kyriakou, P.E. Kyriakopoulou,

T. Agorastou, G. Magripis, A.E. Voloudakis

Agricultural University of Athens, Greece

Citriculture is very important for Greece, but unfortunately is threatened by serious pests and diseases, as well as frost damage. Citrus tristeza virus (CTV) is the most serious viral disease that could be transmitted by aphids, as well as through grafting and was detected for the first time in Greece in 2000. Sour orange is the most well-adopted rootstock in greek citriculture, due to its tolerance to calcified soils and Phytophthora spp, but it is very susceptible to CTV. Poncirus trifoliata and its hybrids, proposed to be used as alternative to sour orange rootstocks due to their tolerance to CTV, are, however, susceptible to citrus viroids. A recent survey revealed that citrus mother trees in Greece were found infected by several graft-transmissible viruses and viroids. Consequently, the use of virus-free propagation material is crucial to sustain greek citriculture. In Agricultural University of Athens the production of healthy citrus propagation material is achieved by employing the “in vitro micrografting” technique, in which the apical meristem of infected trees of elite citrus cultivars are grafted in vitro on healthy rootstock seedlings under aseptic conditions. The new plantlets arising from meristem grafting are subjected to RT-PCR in order to confirm the absence of viroids. This process resulted in obtaining several elite greek cultivars -free of viroids- that could be used as pathogen-free mother material for the establishment of the primary citrus foundation blocks.

Keywords

citriculture, citrus, Greece, Citrus tristeza virus


Session 3 93

POSTER 41

Phenotyping genome dynamics at the cellular level: retrotransposon activity and response

Marko Jääskeläinen, Wei Chang, and Alan H. Schulman

University of Helsinki, Finland

Retrotransposons are ubiquitous and abundant in eukaryotic genomes. They are responsible for much of the variation in monoploid genome size and affect genes by both insertional mutagenesis and epigenetic mechanisms. Over 74% of the large (5.1 Gb) barley genome is comprised of long terminal repeat (LTR) retrotransposons. Retrotransposon copies may be passed to the next generation by one of two ways: replication of existing copies as part of the chromosome; synthesis and propagation of new copies by the combined activities of RNA polymerase II and reverse transcriptase in a “copy and paste” life cycle virtually identical to that of retroviruses, excepting infective movement from organism to organism. The retrotransposon life cycle within the cell involves both nuclear and cytoplasmic phases. Integrated copies are transcribed within the nucleus, but translation and virus-like particle assembly takes place in the cytoplasm. Following replication, the cytoplasmic, packaged cDNA copies need to be brought back into the nucleus for integration of new copies to occur. To shed light on the replication strategy of BARE in the plant, we are using immunolocalization and in situ hybridization to examine expression of the BARE on a tissue-specific level and transformation of marked BARE components to analyze intracellular trafficking. The goal is to develop an understanding of the mechanisms controlling the propagation of retrotransposons and consequences for the genome and plant.

Keywords

retrotransposon, barley, BARE, intracellular trafficking


Session 3 94

POSTER 42

Bridging landscape genomics and quantitative genetics for a regional adaptation of European grasslands to climate change

Anna M Roschanski, Evelin Willner, Klaus J Dehmer


Ongoing climate change is likely to cause damages in permanent grasslands during the next decades. Perennial ryegrass (Lolium perenne L.), one of the most important grassland species in Europe, is distributed across a broad environmental range from Mediterranean to sub-boreal and from oceanic to continental climate zones. The resulting ecotypic diversity provides the chance to recombine climate adapted and service traits to create improved grasslands able to cope with climate change.

The GrassLandScape project will combine Lemnatec high throughput as well as field phenotyping plus genotyping by sequencing of 550 populations with climate observation at regional scale in a landscape genomics approach. The neutral demographic and adaptive genetic structure of L. perenne will be assessed. Associations between loci, traits and environment will be mapped under current and future climate conditions to identify population harboring genetic resources relevant for maintaining European grasslands in the future.

Keywords

Lolium perenne, landscape genomics, climate change, adaptation


Session 3 95

POSTER 43

Combined phenotypic and transcriptomic approaches to evaluate drought-stress response in banana (Musa spp.), a non-model crop

Zorrilla-Fontanesi Y., Van Wesemael J., Kissel E., Mduma H., Uwimana B., Rouard M., Cenci A. , Roux N., Swennen R., Carpentier S.

KU Leuven, Belgium

With a production exceeding 122 million tons in 2012 (FAOstat), banana (Musa spp.) is a very important crop and a staple food for millions of people, especially in the least developed countries. Drought is the main abiotic constraint restricting banana production. To gain insight into the response of banana to water deficit, we created a lab model to simulate drought and performed an RNA-seq experiment on three different varieties. Using uni- and multivariate statistics, 78 genes were differentially expressed in the roots in all three genotypes, representing general drought-stress responsive genes. To confirm the mRNA-seq results, an independent experiment was set up with more biological replicates and the 20 most promising genes were selected for validation by qRT-PCR. 15 out of the 20 genes were confirmed to be significantly different under stress conditions. To validate our lab model and earlier phenotypic characterizations carried out in our greenhouse model, a field trial was set up at IITA-Arusha (with a long dry season of 5 months and a short dry season of 1.5 months). We characterized the level of tolerance/susceptibility in a Complete Randomized Block Design with 10 replicates per variety and 2 treatments (irrigated and not irrigated). Physiological and growth/yield-related parameters are being evaluated during 2 growth cycles together with the expression level of a subset of genes up-regulated under drought-induced conditions in the lab models. Simultaneously drought response is measured with Thermal Imaging.

Keywords

banana, Musa, drought, transcriptome, field phenotyping


96

Map of IPK


97

List of participants Participant name email Affiliation Alqudah, Ahmad [email protected] IPK Gatersleben, Germany Altmann, Thomas [email protected] IPK Gatersleben, Germany Alves, Eliana [email protected] University of Aveiro, Portugal Ampe, Eva [email protected] Limagrain, Netherlands, The Antoniou, Chrystalla [email protected] Cyprus University of Technology,

Cyprus

Araujo, Susana [email protected] Instituto de Tecnologia Quimica e Biologica da Universidade Nova de Lisboa (ITQB-UNL), Portugal

Arbona, Vicent [email protected] Universitat Jaume I, Spain Arend, Daniel [email protected] IPK Gatersleben, Germany

Bánfalvi, Zsófia [email protected] NARIC Agricultural Biotechnology Institute, Hungary

Beemster, Gerrit T.S. [email protected] University of Antwerp, Belgium

Bennett, Malcolm John [email protected] University of Nottingham, United

Kingdom Bertsch, Uwe [email protected] IPK Gatersleben, Germany Bienert, Gerd Patrick [email protected] IPK Gatersleben, Germany

Bilova, Tatiana [email protected] Universität Leipzig, Germany Campos, Alexandre Marnoto

[email protected] CIIMAR, Portugal

Campos, Nadia Alves [email protected] KU Leuven, Belgium

Carpentier, Sebastien [email protected] KU Leuven, Belgium

Costa, Joaquim Miguel [email protected] ITQB -Univ. Nova de Lisboa,

Portugal

Cwiek, Hanna [email protected] Institute of Plant Genetics, Polish Academy of Science, Poland

de P. Herrmann Jr, Paulo S. [email protected] Forschungszentrum Jülich,

Germany de Regt, Bas [email protected] Aris BV, Netherlands, The Dehmer, Klaus J [email protected] IPK Gatersleben, Germany

Djuric, Gordana [email protected] University of Banja Luka, Bosnia and Herzegovina

Dräxl, Stephan [email protected]

Helmholtz Zentrum München, Germany

Dubas, Ewa [email protected] The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Poland

Fahrentrapp, Johannes [email protected] Zurich University of Applied

Sciences, Switzerland Fasoula, Dionysia A [email protected] Agricultural Research Institute,

Cyprus

Feiner, Alexander [email protected] Simon H. Steiner, Hopfen, GmbH, Germany


98

Förster, Jutta [email protected] Saaten-Union Biotec GmbH, Germany

Frenzel, Juliane [email protected] KWS SAAT AG, Germany Friedel, Swetlana [email protected] BASF SE, Germany Gebraegziabher, Habtamu Giday [email protected] Aarhus University, Denmark

Geilfus, Christoph-Martin [email protected] KU Leuven, Belgium

Gerth, Stefan [email protected] Fraunhofer IIS, Development Center X-Ray Technology EZRT, Germany

Gibon, Yves [email protected] INRA, France

Goulas, Estelle [email protected] UMR 8576 CNRS/Université Lille 1, France

Graner, Andreas [email protected] IPK Gatersleben, Germany Guerra-Guimarães, Leonor

[email protected] Instituto de Investigação Cientifica Tropical, Portugal

Harbinson, Jeremy [email protected] Wageningen University,

Netherlands, The Hensel, Goetz [email protected] IPK Gatersleben, Germany Hummel, Grégoire [email protected] PHENOSPEX, The Netherlands

Hyldgaard, Benita [email protected] Aarhus University, Denmark

Igartua, Ernesto [email protected] CSIC, Spain

Janiak, Michal [email protected] KU Leuven, Belgium

Jansen, Marcus [email protected] LemnaTec GmbH, Germany

Jez, Jakub [email protected] Campus Science Support Facilities GmbH, Austria

Jia, Zhongtao [email protected] IPK Gatersleben, Germany Johnson, Giles Nicholas [email protected] University of Manchester, United

Kingdom Junker, Astrid [email protected] IPK Gatersleben, Germany KANTAR, Faik [email protected] Akdeniz University, Turkey

Kardam, Pooran Chand [email protected]

SVP University of Agriculture & Technology, Meerut (UP), India, India

Keller, Beat [email protected] Forschungszentrum Jülich, Germany

Kicherer, Anna [email protected] Julius Kühn-Institut, Germany Kissel, Ewaut [email protected] KU Leuven, Belgium

Koehl, Karin I [email protected] MPI of Molecular Plant Physiology, Germany

Kollist, Hannes [email protected] University of Tartu, Estonia Krechel, Rita [email protected] Bayer CropScience, Germany Lange, Matthias [email protected] IPK Gatersleben, Germany Loziene, Kristina [email protected] Nature Research Centre, Lithuania Ludmilla, Dahl [email protected] KWS SAAT AG, Germany


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Maciel, Elisabete [email protected] University of Aveiro, Portugal

Matušíková, Ildikó [email protected]

Institute of Plant Genetics and Biotechnology SAS, Slovak Republic

Metzner, Ralf [email protected] Forschungszentrum Jülich GmbH, Germany

Milkova, Elena [email protected] Sofia Invest, Bulgaria

Muller, Onno [email protected] Forschungszentrum Juelich, Germany

Neal, Marie [email protected] Aberystwyth University, United Kingdom

Olsovska, Katarina [email protected] Slovak University of Agriculture,

Slovak Republic Ottosen, Carl-Otto [email protected] Aarhus University, Denmark

Paponov, Ivan A. [email protected] Bioforsk, Norway Parreira Salvado, José Ricardo [email protected] Instituto de Tecnologia Química e

Biológica, Portugal Paudel, Gagan [email protected] Leipzig University, Germany

Paul, Kenny [email protected] Biological Research Center, HAS, Hungary, Hungary

Pinheiro, Carla [email protected] ITQB, Portugal Prudent, Marion [email protected] INRA, France

Rispail, Nicolas [email protected] Institute for Sustainable Agriculture - CSIC, Spain

Roschanski, Anna Maria [email protected] IPK Gatersleben, Germany

Rosenqvist, Eva [email protected] University of Copenhagen, Denmark

Rousseau, David [email protected] Université Lyon 1, France Rubiales, Diego [email protected] CSIC, Spain Sagervanshi, Amit [email protected] CAU Kiel., Germany

Sammler, Ralf Christian [email protected] IPK Gatersleben, Germany

Schaller, Hubert [email protected] CNRS-IBMP, France

Scholz, Uwe [email protected] IPK Gatersleben, Germany Schulman, Alan H. [email protected] University of Helsinki, Finland

Schurr, Ulrich [email protected] Forschungszentrum Jülich, Germany

Selale, Hatice [email protected] Izmir Institute of Technology, Turkey

Sharma, Dew Kumari [email protected] University of Copenhagen,

Denmark

Shi, Rongli [email protected] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany

Stewart, Ethan [email protected] ETH Zurich, Switzerland Stojnic, Slobodan [email protected] Genetic Resources Institute,

Bosnia and Herzegovina


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Šveistytė, Laima [email protected] Plant Gene Bank, Coordination Centre of Medicinal and Aromatic Plants, Lithuania

Sytar, Oksana [email protected] Slovak agricultural university in Nitra, Slovak Republic

Szabados, László [email protected] Biological Research Centre, Hungary

Tarakanov, Ivan [email protected] Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Russian Federation

Tene Tayo, Paul Martial [email protected] Biotechnology Center, University of

Yaounde I, Cameroon Töpfer, Reinhard [email protected] Julius Kühn-Institut, Germany Tschiersch, Henning [email protected] IPK Gatersleben, Germany

Tsvetkov, Ivaylo [email protected] Forest Research Institute, Bulgaria Turetschek, Reinhard [email protected] University of Vienna, Austria

van de Zedde, Rick [email protected] Wageningen UR, The Netherlands

Van Labeke, Marie-Christine [email protected] Ghent University, Belgium

Vankova, Radomira [email protected] Institute of Experimental Botany AS

CR, Czech Republic Vasconcelos, Marta Wilton [email protected] Universidade católica Portuguesa,

Portugal

Vass, Imre [email protected] Biological Research Center, Hungary

Vaz Patto, Maria Carlota [email protected] Instituto de Tecnologia Quimica e

Biologica Antonio Xavier, Portugal Vernoud, Vanessa [email protected] INRA, France

Villegas-Fernández, Ángel M

[email protected] Spanish National Research Council, Spain

Villette, Claire [email protected] CNRS, France Voloudakis, Andreas E. [email protected] Agricultural University of Athens,

Greece Vukadinovic, Danijela [email protected] Wageningen UR, Netherlands, The

Waßermann, Louise [email protected] Julius Kühn Institut, Germany

Weidner, Stanislaw [email protected] University of Warmia and Mazury in

Olsztyn, Poland Weigelt-Fischer, Kathleen [email protected] IPK Gatersleben, Germany

Wenzl, Peter [email protected] Global Crop Diversity Trust, Germany

Wienkoop, Stefanie [email protected] University of Vienna, Austria

Wiesner, Melanie [email protected] Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V., Germany

Wimmer, Monika [email protected] University of Bonn, Germany


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Witzel, Katja [email protected] Leibniz Institute of Vegetable and Ornamental Crops, Germany

Youssef, Helmy Mohamed [email protected] IPK Gatersleben, Germany

Yu, Xiaqing [email protected] Nanjing Agricultural university, China, People's Republic of

Zahn, Sarah [email protected] Martin-Luther-Universität Halle- Wittenberg, Germany

Zhou, Rong [email protected] Nanjing Agricultural University, China, People's Republic of

Zivcak, Marek [email protected] Slovak University of Agriculture, Slovak Republic

Zorrilla, Jassmine [email protected] KU Leuven, Belgium

Zur, Iwona [email protected] The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Poland

st general meeting june 22-24, 2015 ipk gatersleben,...

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