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.
