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Workshop Explores Journey Through Complex Wheat Genome

A number of ASPB members were among 63 scientists who participated in a workshop on wheat genome sequencing sponsored by the U.S. Department of Agriculture and National Science Foundation, November 10–11, 2003, in Crystal City, Virginia. ASPB staff also attended.

The workshop provided a forum for scientists to share findings and advice on research conducted on wheat, corn, rice, Arabidopsis, and other plants. Bikram Gill of Kansas State University, who coordinated the workshop, noted that advice offered at the workshop could help in developing a strategy for sequencing the wheat genome. The genome workshop on this major food crop, which feeds much of the world, generated international interest: Eighteen of the 63 participating scientists hailed from 12 foreign countries.

Participants noted that wheat constitutes 17 percent of all crop acreage and is a staple of 40 percent of the world’s population, providing 20 percent of the calories consumed. To meet human demands by 2050, Gill noted that grain production needs to increase at an annual rate of 2 percent. According to Gill, this means that significant advances in the understanding of the wheat plant and grain biology must occur to increase absolute yield as well as protect the crop from 25 percent loss from biotic (e.g., pests) and abiotic stresses (e.g., heat, frost, drought, and salinity).

Sequencing is a widely accepted mechanism for obtaining the knowledge required to overcome significant challenges facing the growing of a crop such as wheat, because it leverages similar work from other crops and plants. Gill added that sequencing of the wheat genome is feasible because of the abundance of cytogenetic, molecular, and human resources and the successes in sequencing several other plant and animal genomes. Research indicates that the wheat genome, at 16,000 Megabase pairs (Mbp), is likely to be the largest genome ever to be sequenced and will provide a model for structure–function changes that accompany polyploidy, a phenomenon that is common among plants.

Dave Van Sanford explained that a wheat sequence would provide perfect markers for difficult traits, harness genetic diversity, enhance quality, increase yield in drought prone areas, and help design varieties for sustainable food production. Given the polyploid nature of wheat and its economic significance, the available information argues strongly for the hexaploid genome to be the main target for a wheat genome project, with supporting analyses coming from related cereals such as rice, Brachypodium, barley, and diploid and tetraploid wheat, Gill added.

ASPB members Jeff Bennetzen, Cathy Whitelaw, and Joachim Messing provided detailed assessments of the shotgun sequencing of the maize genome. The sequencing of products from methyl filtration (MF) and high Cot (HC) fractionation procedures are providing gene sequences that are being integrated into two Mb BAC assemblies compiled for the maize genome. The assembly of the maize genome uses the rice genome as a template for confirming mega-contigs, as well as using detailed genetic maps.

Lincoln Stein and ASPB members Takuji Sasaki and Robin Buell emphasized the importance of detailed genetic maps to guard against false assemblies of BAC contigs that are based only on fingerprinting procedures (even if these use high-resolution analytical procedures).

Bennetzen and Dick McCombie noted that shotgun sequencing could produce a draft sequence but that this draft could be completed only by the further analysis of a BAC contig assembly across the entire genome. Buell emphasized the importance of determining full-length complementary DNA (cDNA) sequences soon to help interpret drafts of the genome sequence. Work on full-length cDNA sequences in wheat in Japan and China was reported by ASPB member Yasunari Ogihara and Jizeng Jia, respectively.

A number of countries and their scientific representatives (Rudi Appels, Australia; Daryl Somers and ASPB member Bill Crosby, Canada; Jizeng Jia, China; Jaroslav Dolezel, Czech Republic; Boulos Chalhoub and Francis Quetier, France; Nils Stein, Germany; S. Nagarajan, India; Albino Maggio, Italy; Yasunari Ogihara, Japan; ASPB member Anna-Maria Botha-Oberholster, South Africa; ASPB member Beat Keller, Switzerland; and Ian Bancroft, United Kingdom) at the workshop indicated their commitment to focusing on certain regions of the genome, with the aim of joining their sequencing efforts into a larger wheat genome–sequencing project, according to Gill.

This staged approach would build on the resources already established by large investments in the United States and other countries and contribute to specific new pilot projects established in the United States. Gill noted that leadership in the wheat genome project is crucial, because contributions from large projects also must integrate contributions from smaller projects to establish an international effort and ensure that accurate sequencing–interpretation is provided to extend the sequence of a particular region of the genome.

Gill said there was a strong consensus among the workshop participants for a sequencing project in hexaploid wheat because of its economic importance, its historic role as a polyploid genetic model, the availability of extensive genetic and molecular resources, and a large and vibrant global wheat genetics community.

The wheat genome workshop evolved from an earlier stakeholders’ workshop sponsored by USDA and coordinated by ASPB that was held November 14, 2002, on plants and pest biology. Gill was one of the 45 participants at the stakeholders’ workshop, where he advocated sequencing of the wheat genome.