SUMMARY

We recently initiated a large genome resequencing project (led by Josh Udall, with Daojun Yuan and Thiru Ramaraj) funded by the National Science Foundation Plant Genome Program.  In this project, we are addressing biological questions of broad relevance to polyploid plant genomes, while at the same time generating detailed information on genomic and phylogeographic patterns of diversity in wild and domesticated cotton, advancing our capacity to utilize an expanded gene pool for cotton improvement.

A comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV).