Cross-Linked Sorghum and Rice Physical Maps as a Foundation for Analyzing Genome Structure, Function, and Variation in C4 Grasses

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Researchers from a vertically integrated "center without walls" will conduct closely coordinated research in structural, functional, and population genomics across leading Poaceae (grass family) seed/grain crops, biomass crops, and major weeds. The grass family stands between humankind and famine, as most calories consumed by humans and livestock derive from sorghum, rice, maize, wheat, sugarcane, millet, and other grasses. Population growth and industrial/residential encroachment on arable land place greater pressure on agriculture to secure higher yields at less cost. Modern capabilities for gene discovery open new doors to intrinsic genetic improvement of crops in a manner that is consistent with responsible stewardship of the biosphere. By utilizing well-established parallels in the organization of genes along the chromosomes of different grass genomes, the small genomes of sorghum and rice will be used to accelerate study and improvement of crops with much larger genomes such as maize and sugarcane. The small Sorghum genome (approximately 760 megabases) is the most logical complement to that of rice (approximately 440 megabases) as a "grass genome template", and is an important bridge to closely related large genome crops such as maize (approximately 2500 megabases) and sugarcane (2500 - 4200 megabases). This project has four major components:Genome organization. Physical maps for the sorghum and rice genomes will be developed that are "cross-linked" to each other and also to other large genome crops. This will accelerate completion of a sequence-ready physical map for rice, and will provide reference points to extrapolate genomic sequence data to sorghum, maize, sugarcane, and other grasses.Genome function. A library of unique expressed sequence tags (ESTs) and corresponding cDNA clones will be developed, with a target of obtaining sequence information for 10,000 different genes, expressed at key stages in the growth and development of the sorghum plant. These resources will be used for many applications, including study of gene expression at key stages of plant growth and development.Population genomics. Both a methodological and intellectual structure for investigating relationships between naturally occurring allelic diversity at the DNA level and morphological/ecogeographic diversity among Sorghum genotypes will be developed as a valuable complement to genetic/physical approaches to the identification of genes responsible for variation in key steps of plant growth and development.Informatics. Software and web-based resources will be developed and implemented to make genomic data rapidly accessible by remote users.This project, together with links to national and international efforts, will yield a well-integrated set of shared resources for intrinsic genetic improvement of both seed/grain and biomass crops that are keystones of agriculture. Sorghum is a leading cereal grain in arid and semi-arid agriculture; ranking fifth in importance among the world' s grain crops. Rice, although a minor U.S. crop, provides more calories to humans worldwide than any other crop. Sugarcane is arguably the world's most valuable crop at approximately $143 billion per year. The sorghum genus also includes one of the world's most aggressive weeds - "Johnsongrass" (S. halepense) - that reduces yields of maize, soybean, cotton and other major crops by up to 45%. Sorghum genomics may lead to new strategies for environmentally benign plant growth regulation, either suppressing the spread of weeds or stimulating dense stands of desirable forage and turf grasses.