FAQ . . . p3

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DNA extracted from

rice plants in High

School Labs - see page

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(Photo by Claire Hebbard,

Gramene)

International Barley Sequencing Consortium (IBSC) (http://barleygenome.org/) members:

Australian Centre for Plant Functional Genomics (ACPFG), AUS; USDA-Agri-

cultural Research Service (USDA-ARS) at Iowa State University, USA; Leibniz

Institute of Plant Genetics and Crop Plant Research (IPK), DEU; National

Institute of Agrobiological Sciences (NIAS), JPN; Okayama University (OU),

JPN; Scottish Crop Research Institute (SCRI), GBR; MTT Agrifood Research

(MTT) & University of Helsinki (UH), FIN

A New Era for Barley Genetics . . . p1

High School Outreach . . . p 2

Opportunities . . .p 3

Recommended Reading . . . p4

Figure 3. Barley chromosome 7H Illumina SNP graphical genotypes for a series of European barley lines clustered by their similarity at 7H telomeric markers, using the GVT Java applica-tion (http://germinate.org.uk/)

Figure 2. Single locus SNP genotypes from a set of barley lines visualized us-ing the Illumina Bead Studio software.

Recent developments in sequencing and genotyping technologies are changing the landscape of scientific opportu-nities for large genome cereal species such as wheat and barley. The existing sequence of rice, to-gether with the rapidly accumu-lating sequence information from the maize, sorghum and Brachy-podium genomes, are providing a valuable set of comparative cereal sequence and functional genomics resources that can be exploited in large genome species. Despite the inherent difficulties that come from work-ing with a large genome, barley (Hordeum vulgare), with with 5.3 billion letters of genetic code, has many advantages - an extensive collection of mutants (http://ace.untamo.net/) and a continuum of interfertile germplasm that spans the range from wild H. spontaneum (Figure1 ) material in the Fertile Crescent to landraces and advanced modern cultivated germplasm. It is also a simple diploid with 7 chromosome pairs, which are essentially equivalent to those in each of the 3 ge-nomes of hexaploid wheat.

One of the first major devel-

opments in barley genomics was the generation of a BAC library from the American cul-tivar, Morex. This was followed by the creation of significant EST sequence resource (cur-rently standing at >450,000; see http://harvest.ucr.edu) which led in turn to a series of sequence based genomics resourc-es, including the Barley1 Affymetrix GeneChip (one of the first major arrays for a crop plant [see http://www.plexdb.org/]) and a series of Barley TILLING populations (e.g.

http://germinate.scri.sari.ac.uk/barley/mutants/).

The International Barley Sequencing Consortium (IBSC) (http://barleygen-ome.org/), formed from a nucleus of leading barley

research groups, is now working to develop a physical map

based on BAC on High Infor-mation Content Fingerprint-ing and BAC end sequencing from a recently extended series of Morex BAC libraries.

A recent major advance in barley genetics has come from the development of a high

throughput SNP platform for barley based on the Illumina Golden Gate Assay (Proc Natl Acad Sci USA (Figure 2) 103:18656–18661). This high throughput SNP platform will provide barley research-ers around the world with a unique integrated mapping

and diversity analysis platform based on more than 3,000 gene sequence based markers and will lay the foundation for a series of major new projects such as the UK, SEERAD and BBSRC LINK funded, AGOUEB (http://www.agoueb.org) and the US, USDA

funded, Barley-CAP (http://www.barleyCAP.org) projects inte-grated through a common infor-matics infrastruc-ture (Figure 3 and http://germi-nate.org.uk/).

These de-velopments are bringing a new

dimension to barley breeding and genetics which will lay the foundation for our understand-ing of the barley genome and increase the value of barley as the temperate cereal crop of choice to exploit major scientific developments in “model” plants such as Arabidopsis and rice.

Article and images contribut-ed by Dr David Marshall, Genetics Programme, SCRI. Invergowrie, Dundee, DD6 5DA Scotland. David.Marshall@scri.ac.uk

GRAMENE NewsA New Era for Barley Genetics

Volume 2 Issue 3

May/June 2007

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Figure 1. A stand of wild barley (H. sponta-neum) in the foreground growing in a mixed sward of other wild barley and wheat species in a reserve in Northern Israel.

Check out these educational resources:WheatCap http://maswheat.ucdavis.edu/education/RiceCap http://www.ricecap.uark.edu/outreach.htmDolan DNA Learning Center http://www.dnalc.org/home.htmlAn exciting part of working at a University is to do out-

reach to local schools and to get kids excited about science. For the past 5 years the McCouch Rice Lab group from Cornell (http://ricelab.plbr.cornell.edu/) has worked with three upstate NY schools to bring equipment, re-sources and experi-enced researchers into the classroom to benefit their students taking the Living Environment course, usually students in 9th or 10th grade. Once again, early in May, Dr. Susan McCouch worked with students who participated in two laboratory exercises - DNA extraction and gel electrophoresis – that helped them to understand the biological concepts behind modern DNA testing procedures.

The teachers participate because students get the oppor-tunity to do college level activities while gaining insight into future roles that science plays in the world. Traditionally the concepts of genomic DNA are taught to high school students in abstract form – through discussion and reading. “This lab allows the students to apply it in real life, to understand the process, and to work with tools that are otherwise unavailable to them,“ one teacher reported. “It also allows them to interact with pro-fessionals in the field - to ask them about their experiences and get answers to questions they have about working in a lab.”

McCouch captivated students as she set the background for the lab work. She told of how rice and rice genomics are crucial to addressing the challenges facing the world today. Although agricultural grain production has more than tripled since 1945, the world popula-tion growth has outgrown grain production. And many of the world’s poorest people consume the less nutritional white rice because it uses less fuel for cooking and has better storage characteristics in hot moist climates. With over 250,000 germplasm acces-sions of rice available to researchers, the genomic diversity from these varieties can be used to breed rice cultivars adaptable to a wide range of environ-ments and with better nutritional quality and higher yield production. For example, in Africa flooded rice fields would harbor diseases such as malaria – which is the number -one killer of children under the age of five, so current work is on de-veloping better varieties for the production needs of Africa. Im-provements in rice can also direct improvements in other cereal

crops, all with larger genomes than rice. Teachers commented about feedback from the students on the presentation. “They are always amazed by her (McCouch’s) presentation, because they have not previously been forced to see food and water as a privilege.”

The students learned about techniques that molecular biologists and geneticists use in their labs everyday to try to solve some of the problems that the world is

facing. This challenge was accepted by grinning students, who froze and

crushed plant leaves in liquid nitrogen and used finely cali-brated pipettes to measure DNA into the agarose gel plates. Their interest was obvious as they asked questions about how genomics and biotechnology affect them. A student from one school stated, “That was cool, everything we did in lab I saw on CSI (a television drama) last week.” A ninth grader said “I’m go-ing to go home and tell my father about this, and he isn’t going to believe it!” Some students also had the option to grow a rice plant and to view a rice flower under a microscope.

One of the senior teachers said that guest presenters are important in order to keep the students’ interest. His comment, “There are so many job opportunities in science . . . When you tell kids about them they don’t ‘get it’, but when they see it they get excited,” proved true as many students remarked that grind-ing rice leaves and using pipettes was fun, and they were inter-ested in doing further laboratory work. Another teacher had his students participate in the event because “This class puts it all

together – taking the different con-cepts and units that we teach and putting them into one lab.”

McCouch and her laboratory staff - includ-ing graduate students - plan on continuing to offer this lab

experience to the local schools, and are looking forward to new students and new experiences next year.

High School OutreachEncouraging the next generation

A student pipettes DNA into an agarose gel as Prof. McCouch, Mr Knight (principal) and Mrs Krichbaum-Stenger (teacher) observe.

Share your lab experiences here. Send them to the GrameneNews editor at cer17@cornell.edu

Susan McCouch teaching rice genomics to high school students.

2007May 31- June 3. 9th Annual Plant Sciences Institute Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories. Ames, Iowa, USA.June 10-11. RCN3 Plant and Trait Ontology Workshop, CSHL Woodbury Campus, NY June 20-21. Joint Western Wheat Workers - Regional Extension Meeting. Washington State University.June 29-July 19. Molecular Techniques in Plant Breeding. CSHL.July 7-11. ASPB Chicago, Illinois, USA. July 21-25. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB). Vienna, Austria. Aug. 13-17. Computational Systems Bioinformatics, UC San Diego. Aug. 20-21. 2007 Rice Breeding Course: Laying the Foundation for the Second Green Revolution. PhilippinesAug. 29-31. Environmental ontology workshop. Oxford, EnglandSept 21-22. Eighth Agricultural Ontology Service (AOS) Work-shop on “7 years of AOS: Achievements and Next Steps”, Rome, Italy.Oct. 9-14. 4th International Rice Blast Conference, Vaya Huatian International Hotel, Changsha, Hunan, ChinaOct. 15-17. 5th International Symposium for Rice Functional Genomics, Tsukuba, JapanNov 4-8. Crop Sciences International Meeting (ASA-CSSA-SSSA), New Orleans, LA, USA

2008January 12-16. PAG-XVI. San Diego, CA, USA Feb 18-21. RTWG Meeting, San Diego, CA, USA

Community Calendar

Opportunities

Gramene will be at these upcoming meetings. You may attend these workshops and post-ers to learn about Gramene or get answers to questions. See the Calendar below for dates and locations..

• Molecular Techniques in Plant Breeding - lecture• ASPB - Dem-onstration with TAIR and SGN• RCN PO/TO Workshop- participant• Environmen-tal ontology workshop- par-ticipant• AOS Workshop at FAO - participant • Crop Sciences - Posters

Upcoming Outreach: Gramene FAQ

Here are opportunities for researchers and students. Please check with each organization to confirm due dates. (Due dates are in mm/dd/yy format).• 2nd International Biocurator’s Meeting, Abstract 7/1/07. http://tesuque.stanford.edu/biocurator.org/Mtg2007/index.html• 4th International Rice Blast Conference Abstract sub-mission deadline 7/31/07. http://www.4thirbc.org/• 5th ISRFG abstract for oral and poster presentation. The deadline 8/15/07 http://www.isrfg2007.com/• IJPG call for papers for Bioinformatics Tools for Plant Genomics Due: 9/1/07 • RTWG Meeting Title-Summary due: 11/1/07, Ab-stracts due: 12/1/07• Monocots IV. Abstracts for oral contributions and posters due 5/31/08.

Contact Gramene through the “Feedback” link at the top of any page to ask ques-tions. Here are some recent questions that have been answered.

Q: Using my data in the pathways module, a certain pathways are painted in red (upregulated). Further, the details analysis revealed that some of the genes of the pathway are down regulated . Please explain this contradiction.

A: When there are multiple genes involved in a single step, the soft-ware makes a decision whether to display a pathway as being up or down regulated based upon a weighted average of all the known data. Any choice made will be misleading in some set of circumstanc-es. As Omics viewer chooses the color based on the value that has the greatest deviation from zero, the discrepancy in your results can be explained by the fact that the seven-fold upregulation of one of the genes overwhelms the four-fold downregulation of the other three

genes.

Q: I’m trying to find a whitepaper that was referenced in the 2006 highlights of the NPGI, http://www.nsf.gov/bio/pubs/reports/npgi2006/highlights.htm, regarding bioinformatics. A: The paper can be found at http://www.gramene.org/resources/plant_databases.pdf It is linked from our site map at http://www.gramene.

org/sitemap.html

Q. How do I get the full set of rice genome annotations - for the entire genome? The BioMart interface seems to limit me to doing a single chromosome at a time.

A. If you do not enable the chromosome filter, then you should be able to download all genes.

Poster and grain display at K-12 Ag Fair, Poplar Ridge, NY

Suggest a Gramene workshop topic or venue to Gramene through cer17@cornell.edu

To submit items for this newsletter, contact the editor

at: cer17@cornell.edu

Gramene Staff

Lincoln Stein, PI Susan McCouch, Co-PI

Doreen Ware, Co-PI Pankaj Jaiswal, Co-PI, Curator

Ed Buckler, Co-PI Chengzhi Liang, Coordinator

Junjian Ni, Curator Immanuel Yap, Curator

Anu Pujar, Curator Isaak Yosief Tecle, Curator Dean Ravenscroft, Curator

Chih-Wei Tung, Curator Ken Youens-Clark, Developer Shulamit Avraham, Developer

Liya Ren, Developer William Spooner, Developer Payan Canaran, Developer

Sharon Wei, Developer Terry Casstevens, Developer Jim Thomason, DeveloperClaire Hebbard, Outreach

Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. (2007) McCouch, S.M.; Sweeney, M; Li, J.; Jiang, H.; Thomson, M.; Septiningsih, E.; Edwards, J.; Monca-da, P.; Xiao, J.; Garris, A.; Tai, T.; Martinez, C.; Tohme, J.; Sugiono, M.; McClung, A.; Yuan, L.P.; and Ahn, S. Euphytica, 154:3, pp 317-339.

The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare). (2007) Faure, S., Higgins, J., Turner, A., Laurie, D. A. Genetics. 2007; 176:599-609.

Rapid Determination of Rice Cultivar Responses to the Sheath Blight Pathogen Rhizoctonia solani Using a Micro-Chamber Screening Method. (2007) Jia, Y.; Correa-Victoria, F.; McClung, A.; Zhu, L.; Liu, G.; Wamishe, Y.; Xie, J.; . Marchetti, M. A; Pinson,S. R. M. ; Rutger, J. N.; and Correll, J. C. Plant Disease, 91:485-489.

MaizeGDB’s new data types, resources and activities. (2007) Lawrence, CJ, Schaeffer, ML, Seigfried, TE, Campbell, DA, and Harper, LC. Nucleic Acids Research 35:D895-900.

An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 2007. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ,Wang GL, Meyers BC. Apr;25(4):473-7. Epub 2007 Mar 11.

The Universal Protein Resource (UniProt) The UniProt Consortium. 2007. Nucleic Acids Research, Vol. 35, Database issue D193–D197. doi:10.1093/nar/gkl929

Recommended Reading

Gramene is a curated, open-source, web-accessible free data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

www.gramene.org

A GENOMIC RESOURCE FOR CEREALS

BLAST Genome Browser

CMap Genetic Diversity

Genes & Alleles Maps and CMap

QTL

Ontologies Pathways Literature Proteins Markers

GrameneMart

email gramene@gramene.org

New Integrated Genome Browser for Plants - http://www.bioviz.org/plant_igb/

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Permission is given for eductional reproduction of articles and photos with use of proper credits.

Unlike other cereals that are used for animal feed, the majority of rice is used for human consumption (83% of the 628,198,180 tonnes produced in 2005), for an average of 122 grams (4.3 ounces) per capita per day. Rice is the staple source of calories for the world’s poorest people, many of who consume 340-930 grams per day (.75-2 pounds per day) (FAOSTAT, 11 May 2007, http://faostat.fao.org/).

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Global calorie consumption per capitaMaize 74.72Rice, paddy 121.87Wheat 192.64