Structural Variation and the Genetic Diversity of Cotton

Allotetraploid cotton species are a vital source of spinnable fiber for textiles. However, the polyploid nature of the cotton genome complicates analyses while raising many evolutionary questions as to the relationships between homoeologous loci. With new whole-genome re-sequencing data from 34 lines of cotton, representing all tetraploid cotton species, we explore the evolution of the cotton genome with greatly improved resolution. Identifying SNPs and structural variants among these 34 lines and their extant diploid relatives, we clarify phylogenetic relationships among tetraploid species, including newly characterized species, and identify introgression between different species of cultivated cotton. We explore the evolution of homoeologs in the A_T- and D_T-genomes and especially the phenomenon of homoeologous conversion. Homoeologous conversion is rare in cotton, perhaps due to the vast difference in chromosome sizes in the two genomes. Several regions of the genome have been introgressed between G. hirsutum and G. barbadense resulting in superior cultivars with putative beneficial alleles from both species and new combinations of alleles. The genotypic data resulting from this study provide a valuable resource for cotton researchers and breeders, who can freely access the data online at CottonGen. Continued efforts will expand the CottonGen database with sequence data from more lines of cotton, providing biological insight and access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.