Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Development Of PCR-Based Markers From Fiber ESTs And BAC-End Sequences For The Construction Of A Consensus Cotton Genetic Map.

Mauricio Ulloa¹ , James E. Frelichowski¹ , Michael Palmer² , Young-H Park³ , Magdy S. Alabady⁴ , Thea A. Wilkins⁴ , John Yu⁵ , Russ Kohel⁵ , Roy Cantrell⁶ , Dorrie Main² , Jeffrey P. Tomkins² , David Stelly⁷ , Allen Van Deynze⁴

¹  USDA-ARS, W.I.C.S Research Unit, Cotton Enhancement Program, Shafter, CA

²  Clemson Univ, Genomic Institute, Clemson, SC

³  Sakata Seed America Inc., Salinas, CA (current address)

⁴  Department of Plant Sciences, University of California, Davis, CA

⁵  USDA-ARS, College Station, TX

⁶  Cotton Incorporated, Cary, NC

⁷  Texas A&M University, College Station, TX, USA

Despite ongoing efforts by the cotton community, cotton genomics is in its infancy as a high- density PCR-based molecular map for marker-assisted breeding in the public domain is still lacking. A new set of SSRs and SNPs were identified from cotton fiber genes (EST) and BAC-end sequences. We tested a total of 1,232 EST-derived SSR markers, of which 1,019 MUSS and MUCS (83%) successfully amplified PCR products from a survey panel of six Gossypium species, of which 202 (19.8%) were polymorphic between Gossypium hirsutum and Pima (G. barbadense) cottons. Of 1316 primer pairs flanking SSR sequences designed from 2603 BAC-end sequences, 1164 MUSB (88%) successfully amplified DNA from three species and 365 (21%) were polymorphic between TM-1 (Upland) and 3-79 (Pima). A consensus genetic map is under development which will include some of the new 234 markers, as well as BNL, JESPR, and CIR markers. Similarly, primers were designed for SNP discovery either on the 3’ end of ESTs or across predicted introns; they were screened for amplification, copy number (using SSCP) and polymorphism using sequencing of DNA pools. Over 400 primers have been tested to-date with 60% amplifying single copy loci, of which 60% have SNPs (1-7 SNPs/amplicons) in our panel. SSR markers have been assigned to 23 of 26 cotton chromosomes from hypoanueploid deficiency analysis and previously mapped SSR markers. The placement of BAC-end markers into the genetic map will contribute to the development of a consensus map and enable the physical alignment of the cotton genome.