ARS | Publication request: Development of Single Nucleotide Polymorphism Markers via Sequence-based Genotyping in Cotton (Gossypium spp)

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2012
Publication Date: N/A

Technical Abstract: High-throughput single nucleotide polymorphism (SNP) genotyping has become the dominant approach to genomic analysis and genetic manipulation in many crop plants. In cotton (Gossypium spp), however, only a very limited number of loci and a dearth of information have been generated from SNP genotyping platforms and made publicly available to researchers. Recently we used a simplified genotyping-by-sequencing (GBS) approach to simultaneously identify and map novel SNP loci with a recombinant inbred line (RIL) mapping population derived from an interspecific cross between TM-1 (G. hirsutum standard) and 3-79 (G. barbadense standard). SNP loci were validated and aligned to a draft sequence of the D-genome diploid cotton G. raimondii, whose progenitor is considered to be the contributor of the D-subgenome of the economically important fiber producing tetraploid cotton species (G. hirsutum and G. barbadense). Our studies demonstrated that the GBS approach is a simple and cost-effective methodology for marker discovery and mapping, and can readily be applied to new genome map development and other molecular investigations in cotton. An example of the mapping and use of sequence-based markers for traits of interest to perform marker assisted selection is also presented.