The origin, diversity, and domestication of tetraploid cotton (G. hirsutum L. and G. barbadense L.)

Genome resequencing of cotton germplasm can uncover the natural history of cotton from its origination to its domestication. Numerous accessions were selected from the USDA collection for resequencing with high coverage, including wild, feral, and cultivar tetraploid and diploid cotton. A comprehensive variation map of more than 900 G. hirsutum and G. barbadense accessions has been constructed, including SNPs and InDels. SNPs were used to create a phylogenetic tree, illuminate population structure, and identify putative introgression regions. Four main groups of G. hirsutum were identified (domesticated, Landrace 1, Landrace 2, and wild) while three groups were identified in G. barbadense. The cultivars of G. hirsutum appear to be derived from a single landrace, suggesting a single domestication event. The two genomes were scanned for regions of domestication (pi and Fst) and putative selective sweeps were identified. Our new understanding of genetic variation in the cotton genome will assist cotton breeders' efforts to improve the fiber quality, disease resistance, and yield of modern cotton varieties.