A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium

Abstract

Sponsored by the National Science Foundation and the U.S. Department of Agriculture, a wheat genome sequencing workshop was held November 10-11, 2003, in Washington, DC. It brought together 63 scientists of diverse research interests and institutions, including 45 from the United States and 18 from a dozen foreign countries (see list of participants at http://www.ksu.edu/igrow). The objectives of the workshop were to discuss the status of wheat genomics, obtain feedback from ongoing genome sequencing projects, and develop strategies for sequencing the wheat genome. The purpose of this report is to convey the information discussed at the workshop and provide the basis for an ongoing dialogue, bringing forth comments and suggestions from the genetics community.

Figure 1.—

Grasses as a single genetic system and recent coevolutionary history of cereals and humans. Grasses originated 55–75 million years ago and now dominate 20% of the land area. The three major cereals (rice, maize, and wheat), which diverged from a common ancestor ∼40 million years ago, provide most of the food for humans. Humans and wheat share a remarkably parallel evolutionary history. About 3 million years ago, humans diverged from apes, and diploid A, B, and D progenitor species of wheat diverged from a common ancestor. About 200,000 years ago, at nearly the same time that modern humans originated in Africa, two diploid grass species hybridized to form polyploid wheat in the Middle East. Humans domesticated wheat ∼15,000 years ago in the fertile crescent (modern-day Iraq and parts of Turkey, Syria, and Iran), marking the dawn of modern civilization. Comparative genetic and genomic studies during the last 10 years revealed extensive synteny among major cereals, and the concept of grasses as a single genetic system emerged. The genome sequence of rice (420 Mb) is nearly completed, and it will serve as the anchor genome to promote gene discovery in all cereals. However, recent data suggest that most domestication-driven, agronomic, and end-use traits, as well as those genes involved in landmark speciation events such as polyploidy, are crop and species specific. The emerging view is that DNA sequence information of all key species is essential for investigating grasses as a single genetic system. Maize (2500 Mb) genome sequencing is underway, and wheat (16,000 Mb) genome sequencing was discussed at the workshop. Figure courtesy of W. J. Raupp, based on discussions with P. F. Byrne, Colorado State University, Fort Collins, with additional data from Huang et al. (2002).

Figure 2.—

By 1915, botanists had described three classes of cultivated wheats; the one-seeded monococcum (2x), the two-seeded emmer (4x), and the dinkel (6x). The one-seeded wild relative of monococcum was reported in Greece and Anatolia between 1834 and 1884. The two-seeded wild relative of emmer was discovered by Aaronsohn in 1910 in Lebanon, Syria, Jordan, and Israel. Therefore, it was well accepted, as Candolle had suggested in 1886, that since wild wheats grow in the Euphrates basin, wheat cultivation must have originated there. Between 1918 and 1925, T. Sakamura and his student H. Kihara at Hokkaido University in Japan and K. Sax at Harvard University reported their classic studies on the genetic architecture of the three groups of wheats. They analyzed meiosis in wheat species and hybrids and were the first to establish the basic chromosome number of seven and document polyploidy in the wheat group. This was an exciting observation and established polyploidy as a major macrospeciation process and wheat as a polyploid genetic model. This method of delineating species evolutionary relationships on the basis of chromosome-pairing affinities in interspecific hybrids came to be called the genome-analyzer method. These hybrids of course could also be exploited in plant breeding for interspecific gene transfers as well as in an approach of shuttle genetics where, for example, genetic mapping can be done in diploid wheat and aneuploid mapping in polyploid wheat. Chromosome figures from Zhang (2002).

Figure 3.—

Chromosome bin mapping of wheat genes that founded human civilization. In the 1950s, E. R. Sears developed aneuploid stocks and identified and mapped many of the unique genes that make wheat humankind's most important crop plant. These included gluten genes (Gli and Glu) that impart bread-making qualities; grain color (R), texture (Ha), and starch compostion (Wx) genes that greatly impact different market classes; photoperiod (Ppd) and vernalization (Vrn) genes that make wheat the most widely adapted plant; durable disease resistance genes (Sr2 and Lr34) and QTL (Qfhs); domestication genes (Tg, Q, s1, C, Rht, Hd, B1, B2); male sterility (ms, Ms), and restorer genes (Rf); and genes regulating polyploid meiosis (Ph1 and Ph2) and abiotic stress (Alt1, Fr, Kna, or; for more details, check out the Catalog of Gene Symbols for Wheat: http:// wheat.pw.usda.gov/ggpages/wgc/98/). In the 1970s, euchromatic and heterochromatic regions were identified in the wheat genome, and a standard karyotype was developed. Deletion stocks were developed in the 1990s. Over 10,000 unigenes, including most of the above-mentioned genes and hundreds of QTL, were mapped in chromosome bins (http://wheat.pw.usda.gov/index.shtml). Because of the abundance of genetic resources, several genes unique to wheat such as Lr21 (Huang et al. 2003), Lr10 (Feuillet et al. 2003), Pm3 (Yahiaoui et al. 2004), Vrn (Yan et al. 2003, 2004), and Q (Faris et al. 2003) have been isolated by map-based cloning. Wheat karyotype after Gill et al. (1991).