Functional and Sequence Analysis of Fiber Development in Allotetraploid Cotton

Functional and Sequence Analysis of Fiber Development in Tetraploid Cotton

PI: Z. Jeffrey Chen (The University of Texas at Austin)

Co-PIs: Foo Cheung (The J. Craig Venter Institute), Candace H. Haigler (North Carolina State University), Brian E. Scheffler (Alcorn State University) and David M. Stelly (Texas A & M University)

Cotton is the largest source of natural textile fiber and a major oilseed crop. Each cotton fiber is a highly elongated seed hair with a secondary wall composed of almost pure cellulose. The large numbers (~20,000 per seed) and nearly synchronous development of cotton fiber cells make them an excellent model system to study plant cell differentiation, expansion, and wall biosynthesis. Analysis of fibers provides genomic information about leaf trichomes, seed fibers, xylem elements, and other cells with thick walls. The cotton genus Gossypium is also a model for research on plant genome evolution and polyploidy. The study of genetic and epigenetic effects on duplicate genes and genomes will ultimately lead to trait improvement. The project goals are to identify cotton genes and regulatory sequences that are important to fiber cell development and cellulose biosynthesis. Contemporary genomic resources will be developed for sequencing, assembling, and annotating the genomes of two major cultivated tetraploid species (G. hirsutum and G. barbadense), also known as Upland and Pima cotton, respectively. New sequencing technology will be used to identify gene expression changes at key stages of fiber development in Upland and Pima cotton. Conserved and unique genes as well as allele-specific expression patterns associated with fiber quality traits will be comparatively analyzed in cotton and in related genera. The function of cotton genes will be tested through genome wide screens in Arabidopsis and in mutants in cotton. Using sequencing-based fingerprinting techniques, a high-resolution integrated physical map will be developed as a community resource and as a sequencing template for tetraploid cotton.

Improving cotton fiber yield and quality will provide a sustainable alternative to petroleum-based synthetic fibers. Most crops are of polyploid origin, so methods and principles being developed from this project will also advance other crops with complex and polyploid genomes. Improved comprehension of fiber development and cellulose and wall biosynthesis will broadly impact research on biomass crops and biofuel production. Genomic sequence and gene expression data will be made available through public data depositories, including GenBank, Gene Expression Ominibus (GEO), National Center for Biotechnology Information (NCBI), and the J. Craig Venter Institute (JCVI). Plant and seed materials will be distributed through the website for cotton resources, (CottonDB). Innovative and scalable education and training modules in plant genomics, biotechnology, and bioinformatics will be developed for middle and high schools, two year colleges and undergraduate institutions in the Mississippi Delta. The effectiveness of education and outreach will be enhanced through cooperation with USDA-ARS K-12 outreach services and augmented by close collaborations with two Historically Black Colleges and Universities (HBCUs), namely, Alcorn State University and Mississippi Valley State University.