Comparative Evolutionary Genomics of Cotton

现代基因组学方法与生物学其他领域的融合为洞察发展和进化中的中心问题带来了巨大的希望。更令人烦恼的挑战之一是在分子水平上解开形态和发育变化与进化过程之间的复杂关系。在这个项目中，形态、进化和基因组方法将结合在一起，分析棉纤维进化过程中发生的发育变化的遗传基础。通过解剖这一形态系列的不同阶段，将获得无与伦比的洞察力，了解参与棉花纤维进化转化的基因：(A)野生物种之间的分化；(B)驯化的早期阶段；(C)现代作物改良；(D)染色体加倍。棉花的独特之处在于，四个不同的物种是从不同的野生祖先那里独立驯化出来的，东半球和新大陆各有两个。前者有两组染色体(它们是“二倍体”)，而后者的染色体数目是两倍(它们是“多倍体”)。通过包括所有这些物种，这项研究将详细说明植物驯化的比较遗传学，以及平行选择在多大程度上导致了基因表达变化的收敛或平行模式。此外，这些实验将阐明一个有趣的假设，即基因组加倍导致了作物改良的新途径。其他实验将揭示基因组大小变化数倍的物种之间的基因组大小变化模式，并导致对导致这种进化变化的分子机制的洞察。此外，该项目将通过开发长期可持续性所需的重要工具和资源，为加强世界领先的纺织纤维做出重大贡献。其中包括一套扩大的表达序列标签基因(“EST”)；棉花基因组的“指纹图谱”；改进的细菌人工染色体资源(“BAC”)，以便随时克隆重要的棉花基因和其他用途；以及关于棉纤维发育关键阶段的基因表达的详细信息。还将开发人力资源，通过与本科生和研究生教育、K-12和外联工作以及科学交流的各种联系，特别重视历史上代表性不足的群体的成员。

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.