Bikram S. Gill, the Wheat Genetics Resource Center, Plant Pathology Department, Kansas State University, Manhattan, KS 66506-5502, USA.
I introduced IGROW in the 2002 Annual Wheat Newsletter (Vol. 48). I shall begin by reiterating the vision of IGROW, which is to
Our immediate, urgent goal is to generate a draft sequence of the gene-rich regions of the wheat genome. Many people on behalf of IGROW have been very active in support of this mandate. I would like to update the activities of IGROW since mid-summer of 2003.
One of the important milestones was a workshop on 9-11 November, 2003, in Washington D.C. on wheat genome sequencing sponsored by the USDA and NSF. This workshop was preceded by a wheat genomics session in Italy during the 10th International Wheat Genetics Symposium, 1-5 September, 2003. At the 10th International Wheat Genetics Symposium, participating scientists from almost 50 countries were enthusiastic about the IGROW mission. The workshop in Washington D.C. was attended by over 60 participants from 12 countries. The workshop produced a blueprint of an international plan for the physical mapping and sequencing the gene-rich regions of the wheat genome, and the report has been accepted for publication in Genetics (Gill et al., In press). The nine-point plan of action is as follows:
1. Construct an accurate, sequence-ready, global physical (BAC-contig) map anchored to the high-resolution genetic and deletion maps of the 21 chromosomes (see item 4 below) of hexaploid wheat genotype Chinese Spring.
2. Explore the use of flow-sorted chromosome- and arm-specific libraries towards the assembly of the global physical map and in preparation for the sequencing of the gene containing regions of homoeologous chromosome groups.
3. Identify genomic sequence tags (GSTs) using gene-enrichment procedures such as hi-C0t or methyl filtration, expressed sequence tags (ESTs), and full-length cDNAs of 2x, 4x, and 6x wheat for an accurate estimation of the wheat unigene set.
4. Leverage rice sequence and wheat-rice gene synteny, comparative genetics, and wheat unigenes towards the development of high-resolution genetic and deletion maps of the 21 chromosomes of Chinese Spring wheat.
5. Identify a random set of 100 gene-containing BACs from the physical map, and another 100 random BACs for sample sequencing, which will provide a test of the gene-rich model and allow refining the technology for assembling sequences with a high repetitive sequence content. Sample sequencing of BACs from different ploidy wheats and genotypes should also be undertaken.
6. Integrate bioinformatics at every step for project management, data analysis, improved methods of sequence annotation, and dissemination of data.
7. Engage all wheat stakeholders, and educational institutions (K-12), globally, especially in developing countries, and locally in all aspects of the research, technology transfer, manpower training, and promotion of science.
8. Maintain all data, materials, and resources in the public domain and free of IPR.
9. Organize an international steering committee to coordinate and execute all aspects of the wheat genome-sequencing project.
The IGROW workshop report was discussed in follow-up meetings of the U.S. wheat workers in Kansas City (February 2004) and at the ITMI workshop in Minneapolis (May 2004). Now, the urgent need is to mobilize the U.S. and the international wheat genetics community for the funding of one or more internationally coordinated pilot projects on wheat genome sequencing. A pilot wheat chromosome group-3 consortium project has been prepared and work has already begun in France (C. Feuillet, personal communication) on the construction of a chromosome-3B physical map using a flow-sorted BAC library. Selective sequencing of specific chromosome regions of Chinese Spring wheat and/or 2x, 4x, and 6x wheat genotypes has been initiated (Boulous and Appels, personal communications). I traveled to India (December 2003-January 2004) and had meetings with Dr. Mangla Rai, DG-ICAR, New Delhi and Drs. Nagarajan and Singh of Indian Agricultural Research Institute (IARI)-New Delhi, and a project has been prepared for India's participation in the IGROW project. I also traveled to Japan at the invitation of Japan International Research Centre for Agricultural Sciences (Dr. Ban) and discussed the IGROW project with the Japan Wheat Sequencing group (Y. Ogihara, coordinator) and to Canada at the invitation of Mark Jordan to attend Agriculture and Agri-Food Canada genomics meetings in Ottawa (June 2004) to update them on IGROW activities.
Of course, it is always a pleasure to updates on the awarding of new and ongoing wheat genomics projects to the wheat genetics community. Unfortunately, no new wheat genomics grant was funded in the recent round of NSF-Crop Genome Research Program Awards. The news was better from the USDA-NRI, where sizeable grants were funded on genomic analysis of major QTL in wheat for scab (PI: Jim Anderson, University of Minnesota, St. Paul), yield (PI: Kulvinder Gill, Washington State University, Pullman), and frost (PI: Kim Campbell USDA-ARS Washington State University, Pullman). The results of the recently concluded, 4-year project funded by the NSF involving 10 universities on the 'Structure and function of the expressed portion of the wheat genomes' (lead PI: Cal Qualset, University of California, Davis) (http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi) will be published in a series of papers in special volume of Genetics (September 2004). As a result of this project and ongoing work elsewhere, wheat now ranks number one in plants with over 500,000 ESTs (http:/www.ncbi.nlm.nih.gov/dbEST) and also is the most densely mapped genome with over 20,000 EST loci mapped on the 21 chromosomes of wheat (see project website). Updating the NSF-funded project entitled 'Insular organization of the D genome of wheat' (lead PI: Jan Dvorak, University of California, Davis), a BAC-contig map of the D genome of wheat consisting of 13,647 BAC-contigs and 4,000 singletons has been constructed (project website: http://wheat.pw.usda.gov/PhysicalMapping). Dvorak is a PI on another NSF-funded virtual center project at UC-Davis on wheat SNPs, a new generation of markers. Shahryar Kianian (North Dakota State University, Fargo) is the lead PI on an NSF-funded proposal that will establish a virtual center in wheat mutagenesis and functional genomics at NDSU (project website: http://wire.ndsu.nodak.edu/DEALING/seedtrack.php). Jorge Dubcovsky (University of California, Davis) is a lead PI on a USDA-IFAFS project entitled 'Bringing Genomics to the Wheat Fields,' which involves most of the public-breeding programs in the U.S. (project website: http://maswheat.ucdavis.edu/Production.htm). Congratulations to these PIs for winning awards from the highly competitive NSF Crop Genome Research and USDA-NRI plant genome programs. The abovementioned proposals are not only producing resources for the wheat genetics and breeding community, but have done much to bolster the position of wheat as a genetic mode for polyploidy research.
On a final note, in addition to the cloning of the Lr21 and Vern1 genes reported last year, papers were published in the autumn of 2003 on the cloning of Lr10 and Pm3 genes from the laboratory of Beat Keller (Feuillet et al. 2003; Yahiaoui et al. 2004). Congratulations to the Dubcovsky laboratory for their paper on the cloning of VRN2 gene that was published in Science (Yan et al. 2004) and commentary on the paper by Jean Marx (2003).