Project Summaries

08-386  Project Manager: D. C. Jones

A HIGH-THROUGHPUT MARKER SYSTEM FOR GENOME-WIDE COTTON RESEARCH

David M. Stelly, Texas AgriLife Research

Extensive use of genome-wide analyses requires that molecular markers, such as single-nucleotide polymorphisms (SNPs), be highly abundant, informative, and extremely cost effective to use once developed.  Earlier public efforts toward development of cotton SNPs have been few and small-scale. In general, the paleo-octaploid nature of Upland and Pima cottons complicates the SNP development; this is exacerbated by the low rates of intraspecific DNA diversity, uneven distributions of SNPs across the genomes and lack of an AD-genome sequence assembly. The distinctness of A and D subgenomes, however, leads to relatively high rates of SNPs between the subgenomes, which are often also seen in contrasts of A and D diploid species' genomes. To differentiate them from genotype-to-genotype SNPs, these have accordingly dubbed "genome-specific polymorphisms" ("GSPs"). The subgenomic specificity of GSPs renders them useful in transcriptomics, genomics and simplifying information from SNPs that involve sequences present in A and D subgenomes. This project is dedicated to providing SNPs, GSPs and related resources such as genome maps and sequence data to the cotton breeding and research community.

 

Project Year: 2012
 

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