Introducing IGROW and the project on sequencing of the wheat genome.


Update on IGROW (International Genome Research On Wheat). [p. 15-16]

Bikram S Gill, Wheat Genetics Resource Center, Plant Pathology Department, Kansas State University, Manhattan, KS 66506-5502, USA.

I introduced IGROW in the 2002 Annual Wheat Newsletter (48:14-15). I shall begin by reiterating the vision of IGROW, which is to

-- create a knowledge base on the genetics, genomics and biology of wheat plant,
-- sustain wheat genetic and genomic infrastructure and resources, and
-- serve as a platform for all wheat stakeholders.

Our immediate, urgent goal is to generate a global physical map and 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 2004.

Several important milestones were reached during this time interval. IGROW held its first ever public workshop on 15 January, 2005, in the Sunrise Room, Town & Country Convention Center, San Diego, CA, as a part of the Plant and Animal Genome XIII Conference held annually and attended by thousands of scientists from several dozen countries (The IGROW workshop abstracts can be viewed at the PAG website: http://www.intl-pag.org/13/). The wheat genetics community has to be congratulated for their enthusiasm, because the workshop room was overflowing. I presented the white paper on IGROW, reiterating the deliberations and decisions presented in the Genetics article (see Gill et al. 2004). Jaroslav Dolezel, Boulos Chalhoub, and Catherine Feuillet made a joint presentation entitled 'Targeted approaches to decipher the complex genome of wheat'. They have made significant progress in making a BAC-contig physical map of 3B using a flow-sorted library (Safer et al. 2004). Jan Dvorak updated progress of the physical map of Ae. tauschii, which can be reviewed at the project website: http://wheat.pw.usda.gov/PhysicalMapping. Daniel Peterson reviewed 'Gene-enrichment strategies for analysis of the wheat gene space', including recent research in wheat (Lamoureux et al. In press). Yasunari Ogihara reviewed the 'Wheat transcriptome project in Japan'. Robin Buell reviewed The Institute for Genomics Research (TIGR) efforts on the 'Development of a bioinformatics pipeline for wheat genome annotation'. Readers are encouraged to visit the TIGR wheat website: http://www.tigr.org/tdb/e2k1/tae1/.

The public workshop was followed by an informal workshop in the evening. Following updates of the genome projects from different countries, most of the discussion was devoted to the mission statement and the organizational aspects of an international wheat genome sequencing project. In the ensuing months and many discussions later, an International Wheat Genome Sequencing Consortium (IWGSC or WGSC) was organized and formally launched at the ITMI workshop meeting in Bozeman, MT (28 May-1 June, 2005). The WGSC website (http://www.wheatgenome.org), has all relevant documents and information. Membership is open to anyone interested in wheat genome sequencing, and application forms can be downloaded from the website.

So we have ITMI and IGROW, and now WGSC ? Confused, yes, and you are not alone, but I will make an attempt to rationalize . ITMI provides an umbrella for all Triticeae research, and IGROW is an umbrella for all genetics and genome research on wheat (check out the ten areas of emphasis of IGROW at website: http://www.ksu.edu/igrow/IGROW_history.html). The WGSC will provide leadership specifically for securing funding and coördination of research for the physical maping and sequencing of the wheat genome. This is going to be a very challenging endeavor, and we all need to be working as a team to make it a success. There is no doubt in my mind that such a project will have huge impact on wheat breeding and end-use research so that the wheat plant we all love continues to play a preëminent role in human nutrition and caloric intake as well as a model for polyploidy research.

Of course, it is always a pleasure to update the awarding of new and ongoing wheat genomics projects to the wheat genetics community. Some good news from the NSF-Crop Genome Research Program as one wheat genomics grant was awarded to J.L. Bennetzen and K.M. Devos (University of Georgia, Athens), and P.J. SanMigul (Purdue University, W. Lafayette, IN) for sample sequencing of the Chinese Spring wheat genome. Mark Sorrells and colleagues won an award from the USDA-NRI for 'Mapping expression profiles of genes controlling seed dormancy in wheat' using microarrays. However, this level of funding is totally inadequate considering the size of the wheat genetics community, and we need to work hard at garnering a bigger piece of the pie, both from NSF and USDA-NRI.

Some exciting news was received in terms of publications reporting on new genomic resources for the wheat community. The results of a 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) (project website: http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi) were published in a series of papers in special volume of Genetics (October 2004). Wheat-rice syntenic maps (TIGR website) are now part of an essential toolkit of every wheat geneticist. Li et al. (2004) generated 2.9 Mb of genomic shotgun sequence and 556 kb of methyl-filtered sequence from Ae. tauschii. Lamoureux et al. (2005) produced 1.4 Mb Cot-filtered genomic sequence of Chinese Spring. So far, over 4 Mb of contiguous wheat sequences consisting of 10-20 kb cosmids to over 200 kb BACs have been reported in the NCBI database. For 2004-05, 2.5 Mb wheat sequences were generated mainly from the laboratories of Justin Faris (five BACs, 0.786 Mb surrounding the tan spot toxin gene, unpublished), Olin Anderson (0.592 Mb surrounding the Glu locus, see Kong et al. 2004; Gu et al. 2004), Beat Keller (0.341 Mb from the Lr10 gene region, see Isidore et al. 2005), Peter Langridge (0.275 Mb from the Ph2 gene region, unpublished), Boulos Chalhoub (0.274 Mb from the Ha locus, see Chantret et al. 2005), and Jorge Dubcovsky (0.235 Mb from the Ha and VRN2 gene regions, see Chantret et al. 2004 and Yan et al. 2004, respectively). The application of TILLING, another useful reverse genetic tool for wheat genome analysis was reported by Slade et al. (2005). This method provides a targeted approach for rapid screening of mutants for a candidate gene. Scofield et al. (In press) reported a VIGS technique to advance functional genomics research in wheat.

References.

  • Chantret N, Cenci A, Sabot F, Anderson O, and Dubcovsky J. 2004. Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol Genet Genomics 1(4):377-86.
  • Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B. 2005. Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17(4):1033-1045.
  • Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, and Sasaki T. 2004. A Workshop Report on Wheat Genome Sequencing; International Genome Research on Wheat (IGROW) Consortium. Genetics 168:1087-1096.
  • Gu YQ, Coleman-Derr D, Kong X, and Anderson OD. 2004. Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four Triticeae genomes. Plant Physiol 135(1):459-70.
  • Isidore E, Scherrer B, Chalhoub B, Feuillet C, and Keller B. 2005. Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res 15:526-536.
  • Kong XY, Gu YQ, You FM, Dubcovsky J, and Anderson OD. 2004. Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat. Plant Mol Biol 54(1):55-69.
  • Lamoureux D, Peterson DG, Liu WL, Fellers JP, and Gill BS. 2005. The efficacy of Cot-based gene enrichment in wheat. Genome (accepted).
  • Li W, Zhang P, Fellers JP, Friebe B, and Gill BS. 2004. Sequence composition, organization and evolution of the core Triticeae genome. The Plant J 40:50-511.
  • Safar J, Bartos J, Janda J, Bellec A, Kubalakova M, Valarik M, Pateyron S, Weiserova J, Tuskova R, Cihalikova J, Vrana J, Simkova H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Dolezel J, and Chalhoub B. 2004. Dissecting large and complex genomes:  flow sorting and BAC cloning of individual chromosome types from bread wheat. Plant J 39:960-968.
  • Scofield SR, Huang L, Brandt AS, and Gill BS. 2005. Development of a virus-induced gene-silencing system for hexaploid wheat and its use in functional analysis of the Lr21-mediated leaf rust resistance pathway. Plant Physiol (In press).
  • Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, and Facciotti D. 2005. A reverse genetic, nontransgenic approact to wheat crop improvement by TILLING. Nature Biotech 23(1):75-81.
  • Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel PJ, Bennetzen JL, Echenique V, and Dubcovsky J. 2004. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640-1644.