Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

A Set Of Informative Markers Designed Specifically For Breeding Cotton

Allen Van Deynze¹ , Thea Wilkins² , Kevin Stoffel¹ , Mike Lee¹ , David Stelly³ , Alex Kozik¹

¹  University of California, 1 Shields Ave, Davis, CA, 95616

²  Texas Tech University, Plant and Soil Science, Lubbock, TX 79409

³  Texas A&M University, College Station, TX, USA

The variation in current cotton (Gossypium hirsutum) germplasm is narrow within breeding programs. The result is slow advancement, especially for traits 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 few varieties. We previously reported on the optimum genomic regions to base SNP discovery for high-throughput genotyping in cotton breeding lines. We have taken advantage of this knowledge and assembled the G. arboreum and G. raimondii EST sequences to develop a strategy to discover SNPs relevant to cotton breeding germplasm. We have screened over 1900 loci for SNPs, and indels across a standard panel representing US cotton germplasm, as well as crossable species. Primers were prescreened for duplication using SSCP. They are then prescreened for polymorphism in breeding lines using pooled sequencing. Putative polymorphic loci are then sequenced individually and scored. We have identified 164 polymorphic loci yielding 370 SNPs in G. hirsutum and 1466 SNPs across all species. This highly informative dataset will be presented and made publicly available for breeding.