This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grantagreement No 727230 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contractnumber 17.00090. The information contained in this communication only reflects the author’s view. Neither the Research

Executive Agency nor SERI is responsible for any use that may be made of the information provided.

Workshop 3 Innovative breeding approaches

for organic agriculture24 November 2020Time: 11.10-12.10h

Edwin Nuijten - moderator

Persons involved

• Edwin Nuijten – moderator

• Matteo Petitti – chat box moderator

• Veronique Chable - reporter

• Speakers:

o Edith Lammerts van Bueren - Systems based breeding

o Pedro Mendes Moreira - Breeding for diversity

o Adrian Rodriguez Burruezo - Breeding networks

• 1 Provide inspiring guiding principles to breed for resilience and quality improvement in OA;

• 2 Develop/optimize breeding designs/ selection tools for more diverse and resilient cropping systems (annual/perennial crops/agroforestry);

• 3 Exploring the importance of the plant-plant and plant-microbiome interface with the holobiont as selection target;

• 4 Establish crop specific breeding and knowledgenetworks to close major breeding gaps.

Co

ncep

tsR

esearch

Practice

LIVESEED Work Package 3 on organic breeding4 objectives (4 tasks):

from trait to system-based strategies

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grantagreement No 727230 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contractnumber 17.00090. The information contained in this communication only reflects the author’s view. Neither the Research

Executive Agency nor SERI is responsible for any use that may be made of the information provided.

Systems based breeding concept

Edith Lammerts van Bueren

Wageningen University

The Netherlands

To provide inspiring guiding principles to breed for resilience and quality improvement in Organic Agriculture

Scientific article on the concept on systems-based breeding:

Lammerts van Bueren et al. Towards resilience throughsystems-based plant breeding. A review.

In: Agronomy for Sustainable Development (2018, Open Access)

Report on ‘Innovative organic breeding concepts: challenges and example (Sept 2020, LIVESEED)

Report on the workshop ‘Organic plant breeding in a systems‐based approach and integration of organic plant breeding in value chain partnerships’ (2019, LIVESEED)

Report on Solutions, obstacles and examples -workshop in Witzenhausen (2018, LIVESEED)

Roles and positioning of breeding and seed systems within their economic, scientific, institutional and cultural

environment (Fig. 3, Lammerts van Bueren et al. 2018)

Lammerts van Bueren et al. 2018. Towards resilience through systems-basedplant breeding. A review. Agronomy for Sustainable Development.

Systems-based breeding:six goals for ecological and social resilience

Example 1:Required change in attitude

Three key-elements:1. Corporate Social

Responsibility

2. Circular Economy & True Cost accounting

3. Fair & Green Policy

In 2017, in NL full commitment of all supermarkets achieved tosell only resistant cultivars for organic potato by 2020

Example 2:Required change in attitude

Three key-elements:1. Corporate Social

Responsibility

2. Circular Economy & True Cost accounting

3. Fair & Green Policy

(1) EU experiment (2014-2021) to allow heterogeneous materialto be described and marketed

Composite cross populations versus pure line varieties

(2) Allowing changes in official Variety testing protocols (VCU)(3) New Organic Regulation

Example 3:From attitude to action

Three key-elements form attitude to action:

1. Knowledge Development & Integration

2. Breeding strategies & Tools

3. EntrepreneurshipOrganic farmer breederFrank Morton Oregon-USA

10% turn over of Frank’s free varieties

Deliverable 3.10: Solutions, obstacles and examples mentioned at the workshop in Witzenhausen 2018

• Most-mentioned Obstacles: – law and regulations

– short term profit

– long term funding

• Most-mentioned Solutions

– collaboration in breeding,

– market reorganization

– knowledge sharing

• Together they describe a common idea for organisingbreeding in a different way, with more collaboration of the value chain

M3.5: Organic plant breeding in a systems‐based approach and integration of organic plant breeding in

value chain partnerships

• Main questions:– Why should different value chain actors support organic plant

breeding?

– The advantage of organic plant breeding for value chain (farmer, processors, traders)

– The advantage of organic plant breeding for consumers and society (local and global)

• Tailor-made approaches are needed

– Needs to include approaches for: knowledge exchange, communication, marketing, education, etc

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grantagreement No 727230 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contractnumber 17.00090. The information contained in this communication only reflects the author’s view. Neither the Research

Executive Agency nor SERI is responsible for any use that may be made of the information provided.

Breeding for diversity

Pedro Mendes Moreira

Polytechnic of Coimbra, Portugal

• 1 Provide inspiring guiding principles to breed for resilience and quality improvement in OA;

• 2 Develop/optimize breeding designs/ selection tools for more diverse and resilient cropping systems (annual/perennial crops/agroforestry);

• 3 Exploring the importance of the plant-plant and plant-microbiome interface with the holobiont as selection target;

• 4 Establish crop specific breeding and knowledgenetworks to close major breeding gaps.

Co

ncep

tsR

esearch

Practice

LIVESEED Work Package 3 on organic breeding4 objectives (4 tasks):

from trait to system-based strategies

More diverse and resilient

cropping systems

Annual

AgroforestryPerennial

Plant-microbiome

Winter

Spring

BarleyN

S

7 Countries

Lv

D

Ch

Fr

Nl

Po

Pt

pea+s.wheat faba beans+ s.wheat, s.triticale, s.vetch

maizemaize+beans

cereals (oat and spring triticale) + grain legumes (yelow lupine and narrowleaf lupine)

s.wheat+lupine s.wheat

Winter wheat, CCP crosses

Blue and White lupin + different cereals →W. lupin + triticale

Pea + Barley (or triticale)

Winter pea in winter triticale

T3.2.1 Optimised annual crop mixtures, with a focus on cereals (Leader: AREI)

Annual

Trials structure

OrganicConventional

Lattice design

Low input

RCBD

Years4

Years1

15Locations

1

Cro

p p

hen

olo

gy

and

mo

rph

olo

gy

Pro

du

ctio

n/

eco

no

mic

yiel

d

Interactions with the agroecoystem

Product quality for which foodsystem

Traits/ breeding methods

• Phenology e.g. growth cyclelength, flowering time

• Morphology e.g. height, growthhabit

• Establishment/Cover• Health (disease response)• Weed competitiveness• Abiotic stress responses• Nutrient use efficiency• Microbiome

• Yield per surface unit/ Yield losses (…)

• Kernel / straw• Protein content• Stability• Wide/specific

adaptation• Processing• Protein Quality• Nutritional / Organoleptic• Taste / Cultural values• (Other Intangible)

Systems-based Frame of Analysis

Practical guidelines for breeding for more diversity: A new toolbox

• statistical methods for:

– Variety mixtures

– Crop mixtures

– Populations

ANOVA and multiple tests, descriptive analise, Coefficient of variation

Ranking (genotypes in pure and mixed stand)

Regression

LER

Correlation, Mixing efect, MARS, CART, RF, DiversityIndexSpearman rank

Nearest NeighbourNei indexesBoxplotsPCA

Example 1:The statistical tools that we have

Forst, E., Enjalbert, J., Allard, V., Ambroise, C., Krissaane, I., Mary-Huard, T., ... & Goldringer, I. (2019). A generalized statisticalframework to assess mixing ability from incomplete mixing designs using binary or higher order variety mixtures and application to wheat. Field Crops Research, 242, 107571.

van Frank, G., Goldringer, I., Rivière, P., & David, O. (2019). Influence of experimental design on decentralized, on-farm evaluation of populations: A simulation study. Euphytica, 215(7), 126.

Meeting 18 September

Meeting 10 November

Meeting 8 December

Meeting 21 January

Example 2:A statistical tool for selection

Leitão, S. T., Ferreira, E., Bicho, M., Alves, M. L., Pintado, D., Santos,

D., ... & Vaz Patto, M. C. (2019). Maize Open-Pollinated PopulationsPhysiological Improvement: Validating Tools for Drought Response

Participatory Selection. Sustainability, 11(21), 6081.

The ABC of phenotypic recurrent selection

Two parental control mass

selection:

in the field

before pollen shedding

before harvesting

at the storing facilities Hight

Ear insertion

Husks

Leaf angle

ABC – Phenotipic Recurrent Selection (Massal)

Before harvesting (one week before)

Two parental control mass selection:

Before pollen sheddingmale flowers-detasseling to undesirable plants, weakest,

disease and pest susceptible

In t

he

fiel

dUse 2 bags

A

B

Yield – Look at the ear!

Ear size

More than one (prolific)

2nd

4th

a

b

Health – Look to leaves, stalk and …kick!

3rd

Diseases (fungi)

Pests (insects)

Roots

a

c

b

Arquitecture – Look to the plant

Normal

ProlificPic the upper ear of

the selected plants

1st Length

Row number

Heath (look at cob basis)

Determined versus indetermined

At store – look at the ear!

Eliminate top and bottom of the ear

Hight

Ear insertion

Husks

Leaf angle

ABC – Phenotipic Recurrent Selection (Massal)

Before harvesting (one week before)

Two parental control mass selection:

Before pollen sheddingmale flowers-detasseling to undesirable plants, weakest,

disease and pest susceptible

In t

he

fiel

dUse 2 bags

A

B

Yield – Look at the ear!

Ear size

More than one (prolific)

2nd

4th

a

b

Health – Look to leaves, stalk and …kick!

3rd

Diseases (fungi)

Pests (insects)

Roots

a

c

b

Arquitecture – Look to the plant

Normal

ProlificPic the upper ear of

the selected plants

1st Length

Row number

Heath (look at cob basis)

Determined versus indetermined

At store – look at the ear!

Eliminate top and bottom of the ear

Silas Pêgo

Photo by Felipe HanowerTable by André Pereira

Vagem 2020

1510 309 5815 334 8489 335 3363 360 4888 361 8254 3861048

0 387 8014 412 3300 413 3642 438 4489 439

5373 310 7664 333 8065 336 2579 359 8491 362 3746 385 4655 388 3984 411 1785 414 2995 437 3228 440

3567 311 7253 332 10467 337 6136 358 6443 363 6619 384 8808 389 9688 410 5702 415 3799 436 6476 441

9721 312 6843 331 10081 338 5919 357 6335 364 8202 383 7268 390 3876 409 6037 416 7105 435 6625 442

4354 313 6800 330 7946 339 6597 356 7945 365 7217 382 6931 391 5781 408 4534 417 6935 434 5856 443

5437 314 5531 329 7285 340 5527 355 10444 366 7476 381 8204 3921030

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4691 315 5938 328 8134 341 3696 354 6429 367 5793 380 5460 393 5947 406 9156 419 7406 432 7561 445 5554 458

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6791 320 7804 323 7330 346 5603 349 4536 372 6146 375 6979 398 4222 401 5153 424 3421 427 6343 450 4783 453

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Disease

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♀ ♂Flow ering

Moist.

Traits used for

population

characterization

• Deliver and registration

• Paredes cooperative (Farmersassociation)

Maize Ears

• Registration

• Number attributed to each earEar deliver

• Ear and reception number• Data registration and photos, taking 4 ears

for moisture and conservation in BPGV

• Ear Value Formula

• EV= (0.6 KW + 0.2 L + 0.15 R + 0.05 KN)/4

• Other data available only at the end of the competition

• Breeder information

NUMI, Pt (earsevaluation)

Best Ear of Sousa Valley

Kernel type

-flint

-dent

Colour

- White

- Yellow

Best Ear of Sousa Valley

Mendes-Moreira, P. M., et al. (2014). Is ear value an effective indicatorfor maize yield evaluation?. Field Crops Research, 161, 75-86.

Ear Value

Ear Value Adjusted

Mendes-Moreira, P. M., Mendes-Moreira, J., Fernandes, A., Andrade, E., Hallauer, A.

R., Pêgo, S. E., & Patto, M. V. (2014). Is ear value an effective indicator for maizeyield evaluation?. Field Crops Research, 161, 75-86.

Random Forest 2nd runRandom Forest 2nd run

Agroforestry System since 1999- maize co-breeding

Microbiome analysesObjectives:

• Polytechnic de Coimbra did establish and analyze the differences between the rhizosphere microbiota of two maize populations in three different production systems.

•

32

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grantagreement No 727230 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contractnumber 17.00090. The information contained in this communication only reflects the author’s view. Neither the Research

Executive Agency nor SERI is responsible for any use that may be made of the information provided.

Breeding networks in PPB to close major breeding gaps: Tomato

Adrian Rodriguez Burruezo

Universitat Politècnica València (UPV)

Spain

• 1 Provide inspiring guiding principles to breed for resilience and quality improvement in OA;

• 2 Develop/optimize breeding designs/ selection tools for more diverse and resilient cropping systems (annual/perennial crops/agroforestry);

• 3 Exploring the importance of the plant-plant and plant-microbiome interface with the holobiont as selection target;

• 4 Establish crop specific breeding and knowledgenetworks to close major breeding gaps.

Co

ncep

tsR

esearch

Practice

LIVESEED Workpackage 3 on breeding4 objectives (4 tasks):

from trait to system based strategies

CONVENTIONAL APPROACH:➢ Scientists/Breeders➢ Farmers to evaluate pre-commercial varieties (e.g. F1s)

SOME CONSEQUENCES: • Breeding process mostly depending on scientist and

breeders• Very specific conditions (mainly company´s facilities) in

breeding process• Very limited feedback from other socioeconomic

agents in the agri-food chain during breeding process• Socioeconomic agents do not feel involved

Why building networks in PB?

BENEFITS FROM PARTICIPATORY PB:

• In a rational fashion, a range of socioeconomic agents may contribute with their opinion in the breeding process.

• Increasing the opportunities to success

• Solve local breeding aims, when working with small-medium-scale farmers

• Each socioeconomic agent becomes a “little breeder”… Feel involved in the process… Strenghtens the links from seed to fork

Why building networks in PB?

SOCIOECONOMIC AGENTS:

Why building networks in PB?

• Provide alternatives to small farmers, diversifying varietal availability

• Recovery of✓OP landraces, ecotypes, heirlooms✓Heterogeneous populations (CCPs, DPs)

i) adaptation to organic farming, ii) higher plasticity and iii) high added value (sust. farming, “taste-of-the-past”, nutritional value)

• Solve local breeding aims (and others at higher scale)

• Strengthen local links from farmers to consumers. Citizens aware of their role in organic production and conservation of local agrobiodiversity

• Larger gene pool mitigates genetic erosion

PPB opportunities in organic farming

Encompassing 5 different crops (and peculiarities):

LIVESEED Task 3.4

White lupin

Tomato

Winter wheat

Apple

Brassica

• The most important fruit vegetable in Europe, high added value. Spain and Italy main EU organic producers

• BUT… low organic seed availability and most varieties are modern F1's from gene pool bred for high input farming

• THUS, NEED OF: i) high-quality cultivars (flavor and taste), ii) specifically adapted to organic farming and iii) support small initiatives aimed to preserve and use tomato diversity

• Partners from both countries: RSR (ITA) and UPV (SPAIN),in collaboration with other associations, encompassing experiences with different approaches and agents

LIVESEED: Support networks for organic participatory breeding in tomato

• Assessing adaptation of Tomato Evolutionary Population: CCP “Cuore di bue” from to different environments and organic farming management

• 5 different agroclimatic conditions

• Yearly particip. evaluations, with farmers: i) 400 pl./location + controls (local & modern varieties)

• Two approaches: a) seeds from best plants for next generation, b) natural selection

• Field evaluations: yield, growth & management, incidence pests and diseases, farmers´preference, etc.

Experience 1CCPs “Cuore di bue” in Italy

• 250 varieties evaluated 2018-2020 under organic farming in different conditions: Mediterranean (Val) and Southwest (Cadiz)

• On-farm participatory evaluations: farmers, breeders, technicians, nurseries. Yield, vigor, earliness, incidence of pathogens, farmer´s preferences, ….

• Additional LAB analyses of sugars, acids, phenolics, volatiles

• Each year (after on-farm selection): open days, diffusion events with consumers and retailers in local markets and fairs, on-farm facilities, taste panels to include consumers´ opinion

Experience 2 Heirlooms and landraces in Spain

• PPB highly necessary (and fruitful) in tomato

• Efficient breeding of local populations/varieties adapted to organic farming. “To shape” the variety from several approaches, preserving remarkable intra-varietal genetic diversity

• Very attractive for consumers (strongly involved)

• One of the most expensive in costs. Farmers in-kind contribution. But also thank economic support, particularly in large trials.

• Very important: strongly committed agents

LESSONS LEARNED

Your involvement

Follow our activities on

Liveseed

@LIVESEEDeu

www.liveseed.eu

Participate in:

• Surveys

• Interviews

• Workshops

• Events

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grantagreement No 727230 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contractnumber 17.00090. The information contained in this communication only reflects the author’s view. Neither the ResearchExecutive Agency nor SERI is responsible for any use that may be made of the information provided.