ARS | Publication request: De novo SNP discovery and development of an interspecific cotton genome map using a simplified genotyping-by-sequencing (GBS) approach

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Abstract Only
Publication Acceptance Date: September 1, 2012
Publication Date: N/A

Technical Abstract: Recent developments in next-generation sequencing (NGS) technology have lowered the cost of sequencing per base and enabled whole genome re-sequencing, genome-wide association studies, and for some species, unprecedented discovery of molecular markers. For species with large, complex genomes, genotyping-by-sequencing (GBS) of reduced representation libraries has emerged as a promising tool for association studies and genomics-assisted breeding. We used a simplified GBS approach to genotype recombinant inbred lines (RILs) of an interspecific cross between Gossypium hirsutum x G. barbadense (TM-1 x 3-79) to discover novel SNPs and develop an interspecific linkage map. The GBS approach presented here provides a powerful tool for developing informative markers in species without a sequenced genome, while also providing a valuable resource for anchoring physical maps and ordering scaffolds from whole genome sequencing projects. The GBS approach will have broad applications in SNP marker-assisted breeding in taxa with limited prior knowledge of the genome or genetic diversity.