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GRAMENE News

Volume 2 Issue 3
May/June 2007

A New Era for Barley Genetics
High School Outreach: Encouraging the Next Generation
Upcoming Outreach
FAQ
Community Calendar
Opportunities
Recommended Reading

Do you have news to share?

The Gramene Newsletter is a community resource about cereals and cereal genomics. It is a forum for community members to share news and current events. Some ideas for contributions include:

Articles, news items, events, opportunities or inquiries should be submitted to the GrameneNews editor at cer17@cornell.edu. Gramene reserves the right to select contributions which meet the educational mission of the publication. Photos are also encouraged. Please provide print quality photos (300dpi) images, credit and caption information.


A New Era for Barley Genetics

Recent developments in sequencing and genotyping technologies are changing the landscape of scientific opportunities for large genome cereal species such as wheat and barley. The existing sequence of rice, together with the rapidly accumulating sequence information from the maize, sorghum and Brachypodium 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 working 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 genomes of hexaploid wheat.

One of the first major developments in barley genomics was the generation of a BAC library from the American cultivar, Morex. This was followed by the creation of significant EST sequence resource (currently standing at >450,000; see http://harvest.ucr.edu) which led in turn to a series of sequence based genomics resources, 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://barleygenome.org/), formed from a nucleus of leading barley research groups, is now working to develop a physical map based on BAC on High Information Content Fingerprinting 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 researchers 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, BarleyCAP (http://www.barleyCAP.org) projects integrated through a common informatics infrastructure (Figure 3 and http://germinate.org.uk/).

These developments are bringing a new dimension to barley breeding and genetics which will lay the foundation for our understanding 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.


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

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

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 application (http://germinate.org.uk/)

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




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

High School Outreach: Encouraging the Next Generation

An exciting part of working at a University is to do outreach 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, resources and experienced 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 opportunity 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 professionals 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 population 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 accessions of rice available to researchers, the genomic diversity from these varieties can be used to breed rice cultivars adaptable to a wide range of environments 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 developing better varieties for the production needs of Africa. Improvements 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 calibrated 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 going 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.


Susan McCouch teaching rice genomics to high school students.

A student pipettes DNA into an agarose gel as Prof. McCouch, Mr Knight (principal) and Mrs Krichbaum-Stenger (teacher) observe.
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 grinding rice leaves and using pipettes was fun, and they were interested in doing further laboratory work. Another teacher had his students participate in the event because "This class puts it all together - taking the different concepts and units that we teach and putting them into one lab."

McCouch and her laboratory staff - including 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.


Share your lab experiences here. Send them to the GrameneNews editor at cer17@cornell.edu
Check out these educational resources:

Upcoming Outreach

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

  • June - RCN PO/TO Workshop- participant
  • July - Molecular Techniques in Plant Breeding - lecture
  • July - ASPB - Demonstration with TAIR and SGN
  • Aug - Environmental ontology workshop- participant
  • Aug - AOS Workshop at FAO - participant
  • November -Crop Sciences - (Poster)

Community Calendar

2007

May 31- June 3. 9th Annual Plant Sciences Institute Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories. Ames, Iowa, USA.
June 10-11. RCN Plant and Trait Ontology Workshop, CSHL Woodbury Campus, NY
June 20-21. Joint Western Wheat Workers - Regional Extension Meeting. Washington State University.
June 27-29. Data Integration in the Life Sciences, Philadelphia, PA.
June 29-July 19. Molecular Techniques in Plant Breeding. CSHL.
July 7-11. ASPB Chicago, Illinois, USA.
July 21-25. ISCB: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB). Vienna, Austria.
August 13-17. Computational Systems Bioinformatics, UC San Diego.
Aug. 20-21. Rice Breeding Course: Laying the Foundation for the Second Green Revolution.
Aug. 29-31. Environmental ontology workshop. Oxford, England
Sept 21-22. Eighth Agricultural Ontology Service (AOS) Workshop 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, China
Oct. 15-17. 5th International Symposium for Rice Functional Genomics, Tsukuba, Japan
November 4-8 Crop Science, New Orleans, LA, USA.

2008

January 12-16, 2008. PAG-XVI. San Diego, CA, USA
Feb 18-21. RTWG Meeting, San Diego, CA, USA
August 11-15, 2008. 4th International Conference on The Comparative Biology of the Monocotyledons & 5th International Symposium on Grass Systematics and Evolution. Copenhagen, Denmark.

See also:

Gramene FAQ

Contact Gramene through the "Feedback" link at the top of any page to ask questions. 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 software 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 circumstances. 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.


Opportunities

Here are opportunities for researchers and students. Please check with each organization to confirm due dates, as they are prone to change. Due dates are in mm/dd/yy format.

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

Recommended Reading

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.; Moncada, 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. (2007). Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ,Wang GL, Meyers BC. Nat Biotechnol.Apr;25(4):473-7. Epub 2007 Mar 11.

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


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/).

Global calorie consumption per capita
Maize 74.72
Rice, paddy 121.87
Wheat 192.64
.


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.

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, Developer
Claire Hebbard, Outreach