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，约占纺织品制造业所用纤维的55%。在美国具有商业重要性的棉花是异源四倍体（“AD”）物种，其从非洲-亚洲起源的旧世界“A”-基因组物种与特有的新世界“D”-基因组二倍体的种间杂交进化而来。纤维本身实际上是单细胞的毛（毛状体），长度从17到50毫米不等，取决于物种。该研究团队是一个垂直整合的跨学科团队，旨在阐明赋予纤维独特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。具体研究目标分为三个相互关联和互补的方法：功能基因组学、结构基因组学和比较生物学。结合纤维ESTs的产生，基因级联和信号通路在来自A或D二倍体物种的棉花纤维发育中的功能作用将使用DNA微阵列技术进行评估。将使用纤维发育突变体和纤维数量性状基因座（QTL）的近等基因系的独特集合平行进行全局遗传和表达分析。对于长期的基因功能研究，将开发用于在棉花中产生基因敲除群体的亲本系。结构基因组学的组成部分将集中在连接纤维基因的物理地图映射新的纤维EST，差异表达纤维发育过程中的纤维突变体和QTL。使用一种专门针对多倍体的新技术，将鉴定出含有来自四倍体的各个亚基因组的等位基因的“异源BAC”，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，与纤维发育有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。将检验以下零假设：（1）同源异型序列在异源多倍体化后独立进化;和（2）序列进化的速率在二倍体和多倍体中是相等的。结构，阐明棉纤维分子和进化基础的功能和进化方法将产生大量新的资源，这些资源将可用于公共部门的基础和应用研究。调查或这个多学科团队的科学努力有望为植物生长和发育的基本细胞过程，形态变化的进化基础以及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大有希望。

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.