Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Sampling Nucleotide Diversity In Cotton

Allen Van Deynze , Kevin Stoffel

  University of California, Davis, CA, USA,95616

The United States planted 14.1 million acres of cotton in 2002 and accounted for 33% of worldwide cotton exports (USDA Economics and StatisticsSystem 2003). Maintaining and improving fiber quality is critical to the US cotton industry. The variation in current cotton (Gossypium hirsutum) germplasm is narrow within breeding programs. The result is slow advancement in traits, especially those that are controlled by many genes and are highly influenced by the environment, such as fiber quality. Yet cotton has many sexually-compatible relatives with an abundance of novel fiber characteristics. DNA markers are a tool that can be used to efficiently identify and manipulate genes and recover desired genetic backgrounds. Although there is an abundance of genomic and EST sequence (genes) being accumulated in cotton, most are derived from one or two varieties. We surveyed a set of 139 primers designed from BAC-end, SSR genomic sequences, 5’, coding and 3’ EST regions. We amplified and sequenced single copy products in 12 cotton genotypes. Our results establish the optimum regions to sample sequences for polymorphism and locus specificity. This research is the first systematic approach to SNP discovery in cotton, outlining the best approach for large scale SNP discovery programs. This project establishes the infrastructure to develop and evaluate markers for traits including fiber quality genes in cotton