Volume 2 Issue 3 GRAMENE News May/June 2007 A New Era for Barley Recent developments in opments in barley and diversity analysis platform sequencing and genotyping was the generation of a BAC based on more than 3,000 gene Gramene News technologies are changing the library from the American cul- sequence based markers and will landscape of scientific opportu- tivar, Morex. This was followed lay the foundation for a series FAQ . . . p3 nities for large genome cereal by the creation of significant of major new projects such as species such as wheat and barley. EST sequence resource (cur- the UK, SEERAD and BBSRC LINK Upcoming Outreach The existing sequence of rice, to- rently standing at >450,000; see funded, AGOUEB (http://www. . . . p3 gether with the rapidly accumu- http://harvest.ucr.edu) which led agoueb.org) and the US, USDA

lating sequence information from in turn to a series 5520-925 funded, Barley- 2.00

the maize, sorghum and Brachy- of sequence based 1.80 CAP (http://www. podium genomes, are providing genomics resourc- 1.60 barleyCAP.org) Community News 1.40 a valuable set of comparative es, including the 1.20 projects inte- R 1 A New Era for Barley rm cereal sequence and functional Barley1 Affymetrix o grated through a Genetics . . . p1 N0.80 genomics resources that can GeneChip (one 0.60 common infor- be exploited in large genome of the first major 0.40 matics infrastruc- High School Outreach 0.20

. . . p 2 species. Despite the inherent arrays for a crop 0 ture (Figure 3 34 0 62 difficulties that come from work- plant [see http:// -0.20 and http://germi- 0 0.20 0.40 0.60 0.80 1 Opportunities . . .p 3 ing with a large genome, barley www.plexdb. Norm Theta nate.org.uk/). Figure 2. Single locus SNP genotypes (Hordeum vulgare), with with 5.3 org/]) and a series These de- Recommended Reading from a set of barley lines visualized us- . . . p4 billion letters of genetic code, has of Barley TILLING ing the Illumina Bead Studio software. velopments are many advantages - an extensive populations (e.g. bringing a new collection http://germinate. dimension to barley breeding of mutants scri.sari.ac.uk/barley/ and genetics which will lay the (http://ace. mutants/). foundation for our understand- untamo. The International ing of the barley genome and net/) and a Barley Sequencing increase the value of barley as continuum Consortium (IBSC) the temperate cereal crop of of interfertile (http://barleygen- choice to exploit major scientific germplasm ome.org/), formed developments in “model” plants that spans from a nucleus of such as Arabidopsis and rice.

the range leading barley

from wild H. Figure 1. A stand of wild barley (H. sponta- research groups, neum) in the foreground growing in a mixed spontaneum sward of other wild barley and wheat species is now working (Figure1 ) in a reserve in Northern Israel. to develop a material in physical map the Fertile Crescent to landraces based on BAC on High Infor- and advanced modern cultivated mation Content Fingerprint- DNA extracted from germplasm. It is also a simple ing and BAC end sequencing rice plants in High diploid with 7 chromosome pairs, from a recently extended School Labs - see page which are essentially equivalent series of Morex BAC libraries. 2. to those in each of the 3 ge- A recent major advance Figure 3. Barley chromosome 7H Illumina SNP graphical genotypes for a series of European (Photo by Claire Hebbard, nomes of hexaploid wheat. in barley genetics has come barley lines clustered by their similarity at 7H Gramene) One of the first major devel- from the development of a high telomeric markers, using the GVT Java applica- throughput SNP platform for tion (http://germinate.org.uk/) International Barley Sequencing Consortium (IBSC) (http://barleygenome. barley based on the Illumina org/) members: Golden Gate Assay (Proc Australian Centre for Plant Functional Genomics (ACPFG), AUS; USDA-Agri- Natl Acad Sci USA (Figure 2) Article and images contribut- cultural Research Service (USDA-ARS) at Iowa State University, USA; Leibniz 103:18656–18661). This high ed by Dr David Marshall, Genetics Institute of and Crop Plant Research (IPK), DEU; National throughput SNP platform Programme, SCRI. Invergowrie, Institute of Agrobiological Sciences (NIAS), JPN; Okayama University (OU), will provide barley research- Dundee, DD6 5DA Scotland. JPN; Scottish Crop Research Institute (SCRI), GBR; MTT Agrifood Research ers around the world with a [email protected] unique integrated mapping (MTT) & University of Helsinki (UH), FIN Check out these educational resources: High School Outreach WheatCap http://maswheat.ucdavis.edu/education/ RiceCap http://www.ricecap.uark.edu/outreach.htm Encouraging the next generation Dolan DNA Learning Center http://www.dnalc.org/home.html An exciting part of working at a University is to do out- reach to local schools and to get kids excited about science. crops, all with larger genomes than rice. Teachers commented For the past 5 years about feedback from the students on the the McCouch Rice presentation. “They are always amazed Lab group from by her (McCouch’s) presentation, because Cornell (http:// they have not previously been forced to ricelab.plbr.cornell. see food and water as a privilege.” edu/) has worked The students learned about techniques with three upstate that molecular biologists and geneticists NY schools to bring use in their labs everyday to try to solve equipment, re- some of the problems that the world is sources and experi- facing. This challenge was accepted Susan McCouch teaching rice genomics to high school students. enced researchers by grinning students, who froze and into the classroom to benefit their students taking the Living crushed plant leaves in liquid nitrogen and used finely cali- Environment course, usually students in 9th or 10th grade. Once brated pipettes to measure DNA into the agarose gel plates. again, early in May, Dr. Susan McCouch worked with students Their interest was obvious as they asked questions about how who participated in two laboratory exercises - DNA extraction genomics and biotechnology affect them. A student from one and gel electrophoresis – that helped them to understand the school stated, “That was cool, everything we did in lab I saw on biological concepts behind modern DNA testing procedures. CSI (a television drama) last week.” A ninth grader said “I’m go- The teachers participate because students get the oppor- ing to go home and tell my father about this, and he isn’t going tunity to do college level activities while gaining insight into to believe it!” Some students also had the option to grow a rice future roles that science plays in the world. Traditionally the plant and to view a rice flower under a microscope. concepts of genomic DNA are taught to high school students in One of the senior teachers said that guest presenters are abstract form – through discussion and reading. “This lab allows important in order to keep the students’ interest. His comment, the students to apply it in real life, to understand the process, “There are so many job opportunities in science . . . When you and to work with tools that are otherwise unavailable to them,“ tell kids about them they don’t ‘get it’, but when they see it they one teacher reported. “It also allows them to interact with pro- get excited,” proved true as many students remarked that grind- fessionals in the field - to ask them about their experiences and ing rice leaves and using pipettes was fun, and they were inter- get answers to questions they have about working in a lab.” ested in doing further laboratory work. Another teacher had his McCouch captivated students as she set the background for students participate in the event because “This class puts it all the lab work. She told of how rice and rice genomics together – taking are crucial to addressing the challenges facing the the different con- world today. Although agricultural grain production cepts and units has more than tripled since 1945, the world popula- that we teach tion growth has outgrown grain production. And and putting them many of the world’s poorest people consume the into one lab.” less nutritional white rice because it uses less fuel for McCouch and cooking and has better storage characteristics in hot her laboratory moist climates. With over 250,000 germplasm acces- staff - includ- sions of rice available to researchers, the genomic ing graduate diversity from these varieties can be used to breed students - plan rice cultivars adaptable to a wide range of environ- A student pipettes DNA into an agarose gel as Prof. McCouch, Mr Knight (principal) and Mrs Krichbaum-Stenger (teacher) observe. on continuing ments and with better nutritional quality and higher to offer this lab yield production. For example, in Africa flooded rice fields would experience to the local schools, and are looking forward to new harbor diseases such as malaria – which is the number -one students and new experiences next year. killer of children under the age of five, so current work is on de- veloping better varieties for the production needs of Africa. Im- Share your lab experiences here. Send them to provements in rice can also direct improvements in other cereal the GrameneNews editor at [email protected] Upcoming Outreach: Gramene FAQ Gramene will be at these upcoming meetings. Contact Gramene through the “Feedback” link at the top of any page to ask ques- You may attend these workshops and post- tions. Here are some recent questions that have been answered. ers to learn about Gramene or get answers to questions. See the Calendar below for dates and locations.. 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 • Molecular Techniques in Plant Breeding pathway are down regulated . Please explain this contradiction. - lecture • ASPB - Dem- A: When there are multiple genes involved in a single step, the soft- onstration ware makes a decision whether to display a pathway as being up or with TAIR and down regulated based upon a weighted average of all the known SGN data. Any choice made will be misleading in some set of circumstanc- • RCN PO/TO es. As Omics viewer chooses the color based on the value that has the Workshop- greatest deviation from zero, the discrepancy in your results can be participant explained by the fact that the seven-fold upregulation of one of the • Environmen- genes overwhelms the four-fold downregulation of the other three tal ontology Poster and grain display at K-12 genes. workshop- par- Ag Fair, Poplar Ridge, NY ticipant • AOS Workshop at FAO - participant Q: I’m trying to find a whitepaper that was referenced in the 2006 highlights of the • Crop Sciences - Posters NPGI, http://www.nsf.gov/bio/pubs/reports/npgi2006/highlights.htm, regarding bioinformatics. Community Calendar 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. 2007 org/sitemap.html May 31- June 3. 9th Annual Plant Sciences Institute Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories. Q. How do I get the full set of rice genome annotations - for Ames, Iowa, USA. the entire genome? The BioMart interface seems to limit me June 10-11. RCN3 Plant and Trait Ontology Workshop, CSHL to doing a single chromosome at a time. Woodbury Campus, NY June 20-21. Joint Western Wheat Workers - Regional Extension A. If you do not enable the chromosome filter, then you Meeting. Washington State University. should be able to download all genes. June 29-July 19. Molecular Techniques in Plant Breeding. CSHL. July 7-11. ASPB Chicago, Illinois, USA. Opportunities July 21-25. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference Here are opportunities for researchers and students. Please on Computational Biology (ECCB). Vienna, Austria. check with each organization to confirm due dates. (Due Aug. 13-17. Computational Systems Bioinformatics, UC San dates are in mm/dd/yy format). Diego. • 2nd International Biocurator’s Meeting, Abstract Aug. 20-21. 2007 Rice Breeding Course: Laying the Foundation 7/1/07. http://tesuque.stanford.edu/biocurator.org/ for the Second Green Revolution. Philippines Mtg2007/index.html Aug. 29-31. Environmental ontology workshop. Oxford, England • 4th International Rice Blast Conference Abstract sub- Sept 21-22. Eighth Agricultural Ontology Service (AOS) Work- mission deadline 7/31/07. http://www.4thirbc.org/ shop on “7 years of AOS: Achievements and Next Steps”, Rome, • 5th ISRFG abstract for oral and poster presentation. Italy. The deadline 8/15/07 http://www.isrfg2007.com/ Oct. 9-14. 4th International Rice Blast Conference, Vaya Huatian • IJPG call for papers for Bioinformatics Tools for Plant International Hotel, Changsha, Hunan, China Genomics Due: 9/1/07 Oct. 15-17. 5th International Symposium for Rice Functional • RTWG Meeting Title-Summary due: 11/1/07, Ab- Genomics, Tsukuba, Japan stracts due: 12/1/07 Nov 4-8. Crop Sciences International Meeting (ASA-CSSA-SSSA), • Monocots IV. Abstracts for oral contributions and New Orleans, LA, USA posters due 5/31/08. 2008 Suggest a Gramene workshop topic or venue to January 12-16. PAG-XVI. San Diego, CA, USA Gramene through [email protected] Feb 18-21. RTWG Meeting, San Diego, CA, USA 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, A GENOMIC RESOURCE FOR CEREALS interpretation of biochemical pathways, gene and QTL localization and BLAST Ontologies descriptions of phenotypic characters and mutations. Genome Browser Pathways email [email protected] CMap Literature Genetic Diversity Proteins For updates on releases and other information, join Genes & Alleles Markers Gramene’s mailing list or view the mailing list archive. Maps and CMap GrameneMart www.gramene.org/mailarch/ QTL www.gramene.org

2005 Grain 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 800,000 700,000 calories for the world’s poorest people, many of who consume 340-930 grams 600,000 500,000 per day (.75-2 pounds per day) (FAOSTAT, 11 May 2007, http://faostat.fao.org/). 1,000 400,000 Production tonnes Consumption Global calorie consumption per capita 300,000 200,000 Maize 74.72 100,000 0 Rice, paddy 121.87 Maize Rice Wheat Wheat 192.64

New Integrated Genome Browser for Plants - http://www.bioviz.org/plant_igb/ Recommended Reading Gramene Staff

Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. , PI (2007) McCouch, S.M.; Sweeney, M; Li, J.; Jiang, H.; Thomson, M.; Septiningsih, E.; Edwards, J.; Monca- Susan McCouch, Co-PI da, P.; Xiao, J.; Garris, A.; Tai, T.; Martinez, C.; Tohme, J.; Sugiono, M.; McClung, A.; Yuan, L.P.; and Ahn, Doreen Ware, Co-PI S. Euphytica, 154:3, pp 317-339. Pankaj Jaiswal, Co-PI, Curator Ed Buckler, Co-PI The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare). (2007) Faure, S., Higgins, J., Chengzhi Liang, Coordinator Turner, A., Laurie, D. A. Genetics. 2007; 176:599-609. Junjian Ni, Curator Immanuel Yap, Curator Rapid Determination of Rice Cultivar Responses to the Sheath Blight Pathogen Rhizoctonia solani Anu Pujar, Curator Using a Micro-Chamber Screening Method. (2007) Jia, Y.; Correa-Victoria, F.; McClung, A.; Zhu, L.; Liu, Isaak Yosief Tecle, Curator G.; Wamishe, Y.; Xie, J.; . Marchetti, M. A; Pinson,S. R. M. ; Rutger, J. N.; and Correll, J. C. Plant Disease, Dean Ravenscroft, Curator 91:485-489. Chih-Wei Tung, Curator Ken Youens-Clark, Developer MaizeGDB’s new data types, resources and activities. (2007) Lawrence, CJ, Schaeffer, ML, Seigfried, Shulamit Avraham, Developer TE, Campbell, DA, and Harper, LC. Nucleic Acids Research 35:D895-900. Liya Ren, Developer William Spooner, Developer An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 2007. Nobuta K, Venu RC, Lu C, Payan Canaran, Developer Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ,Wang GL, Meyers BC. Apr;25(4):473-7. Sharon Wei, Developer Epub 2007 Mar 11. Terry Casstevens, Developer Jim Thomason, Developer The Universal Protein Resource (UniProt) The UniProt Consortium. 2007. Nucleic Acids Research, Vol. Claire Hebbard, Outreach 35, Database issue D193–D197. doi:10.1093/nar/gkl929 To submit items for this newsletter, contact the editor Permission is given for eductional reproduction of articles and photos with use of proper credits. at: [email protected]