Comparative Evolutionary Genomics of Cotton

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The convergence of modern genomic approaches with other areas of biology holds great promise for insights into central problems in development and evolution. One of the more vexing challenges has been to unravel the complex relationship between morphological and developmental change and evolutionary processes at the molecular level. In this project morphological, evolutionary, and genomic approaches will be integrated in an analysis of the genetic basis of the developmental transformations that occurred during cotton fiber evolution. By dissecting distinct stages in this morphological series, unparalleled insight will be gained into the genes involved in evolutionary transformations of cotton fiber during: (a) divergence among wild species; (b) early stages of domestication; (c) modern crop improvement; and (d) chromosome doubling. Cotton is unique in that four different species were independently domesticated from different wild ancestors, two each in the Old World and New Worlds. The former have two sets of chromosomes (they are "diploid") whereas this number is doubled (they are "polyploid") in the latter. By including all of these species, the research will detail the comparative genetics of plant domestication and the extent to which parallel selection has led to convergent or parallel patterns of gene expression change. In addition, the experiments will shed new light on the intriguing hypothesis that genome doubling has led to novel avenues for crop improvement. Additional experiments will reveal the patterns of genome size change among species that vary several-fold in genome size, and lead to insights regarding the molecular mechanisms responsible for this evolutionary change. In addition this project will contribute significantly to enhancement of the world's leading textile fiber through the development of important tools and resources necessary for long-term sustainability. These include an expanded set of expressed sequence tagged genes ("ESTs"); a "fingerprint map" for the cotton genome; an improved resource of bacterial artificial chromosomes ("BACs") for ready cloning of important cotton genes and other uses; and detailed information on gene expression for key stages in cotton fiber development. Human resources will also be developed, with special emphasis given to members of historically under-represented groups, through myriad connections to undergraduate and graduate education, K-12 and outreach efforts, and scientific exchanges.