Structure and Function of the Cotton Genome: An Integrated Analysis of the Genetics, Development and Evolution of the Cotton Fiber

作为世界领先的天然纤维，棉花是美国和全球经济的主要贡献者，为纺织制造业提供了约55%的纤维。在美国，具有重要商业价值的棉花是一种异源四倍体（AD）品种，它是由一种源自非洲-亚洲的旧大陆“A”基因组品种与一种新大陆“D”基因组二倍体的种间杂交进化而来的。纤维本身实际上是单细胞毛发（毛状体），长度从17毫米到50毫米不等，具体取决于物种。一个垂直整合的跨学科团队已经成立，以阐明赋予纤维独特的农业重要特性的基因的组织、结构和功能，并确定多倍体在纤维进化中所起的作用。具体的研究目标分为三个相互关联和互补的方向：功能基因组学、结构基因组学和比较生物学。结合纤维est的产生，利用DNA微阵列技术评估基因级联和信号通路在A或D二倍体棉纤维发育中的功能作用。全球遗传和表达分析将同时进行，使用独特的纤维发育突变体和纤维数量性状位点（qtl）的近等基因系。为了进行长期的基因功能研究，将开发用于棉花基因敲除群体的亲本系。结构基因组学部分将通过绘制与纤维突变体和qtl相关的纤维发育过程中差异表达的新型纤维est，将纤维基因与物理图谱联系起来。利用一种专为多倍体量身定制的新技术，将鉴定含有来自四倍体单个亚基因组的等位基因的“alloBACs”，以进行比较分析。基于表达模式和与qtl或突变位点的接近性，与纤维发育相关的基因将进行详细的比较分析，以在分子水平上深入了解纤维的进化基础。以下无效假设将被检验：(1)同源序列在异源多倍体化后独立进化；(2)序列进化速率在二倍体和多倍体中是相等的。将结构、功能和进化方法结合起来，阐明棉纤维的分子和进化基础，将为公共部门提供大量的新资源，用于基础和应用研究目的。这个多学科团队的科学努力有望为植物生长发育的基本细胞过程、形态变化的进化基础和多倍体的功能意义提供新的见解。因此，加强对这一复杂农业性状的了解，对棉花和其他重要作物品种在产量和质量方面的遗传改良具有很大的希望。

As the world's leading natural fiber, cotton is a major contributor to the U.S. and global economy, providing about 55% of the fiber used in textile manufacturing. The commercially-important cottons in the USA are allotetraploid ("AD") species that evolved from the interspecific hybridization of an Old World "A"-genome species of African-Asian origin with an endemic, New World "D"-genome diploid. The fibers themselves are actually single-celled hairs (trichomes) that range in length from ~17 to 50 mm, depending on the species. A vertically integrated, interdisciplinary team has been assembled to elucidate the organization, structure and function of genes that impart unique agriculturally-important properties to the fiber and to determine what role polyploidy has played in the evolution of the fiber.The specific research objectives are divided into three inter-related and complementary approaches: Functional Genomics, Structural Genomics, and Comparative Biology. In combination with the generation of fiber ESTs, the functional role of gene cascades and signaling pathways in developing cotton fibers derived from A or D diploid species will be assessed using DNA microarray technology. Global genetic and expression analyses will be performed in parallel using a unique collection of fiber developmental mutants and near-isogenic lines for fiber Quantitative Trait Loci (QTLs). For long-term gene function studies, parental lines for generating a gene knockout population in cotton will be developed. The structural genomics component will focus on linking fiber genes to the physical map by mapping novel fiber ESTs that are differentially expressed during fiber development in relation to fiber mutants and QTLs. Using a new technique tailored to polyploids, "alloBACs" containing the alleles from the individual subgenomes of the tetraploid will be identified for comparative analysis. Genes implicated in fiber development on the basis of expression patterns and the proximity to QTLs or mutant loci will be subjected to detailed comparative analysis to gain insight into the evolutionary basis of the fiber at the molecular level. The following null hypotheses will be tested: (1) homeologous sequences have evolved independently subsequent to allopolyploidization; and (2) rates of sequence evolution are equivalent in diploids and polyploids.The novel integration of structural, functional and evolutionary approaches to elucidate the molecular and evolutionary basis of the cotton fiber will generate vast new resources that will be available to the public sector for basic and applied research purposes. The scientific endeavors of this multi-disciplinary team are expected to provide new insight into fundamental cellular processes in plant growth and development, the evolutionary basis of morphological change, and the functional significance of polyploidy. Thus, enhanced understanding of this complex agricultural trait holds great promise for the genetic improvement of cotton and other important crop species in terms of production and quality.