Nematode-resistance loci in Upland cotton genomes are associated with structural differences

Abstract Reniform and root-knot nematodes are two of the most destructive pests of conventional Upland cotton, Gossypium hirsutum L., and continue to be a major threat to cotton production in semi-arid regions of the southern United States and Central America. Fortunately, natural tolerance to these nematodes has been identified in Pima cotton varieties (G. barbadense) and several Upland varieties (G. hirsutum), which has led to a robust breeding program that has successfully introgressed and stacked these independent resistant traits into several Upland cotton lines with superior agronomic traits, e.g. BAR 32-30 and BARBREN-713. This work identifies the genomic variations that have been bred into these nematode tolerant lineages by comparing their respective genomes to the last susceptible parental line Phytogen PSC355 (PSC355) in order to identify nematode resistant loci. We discover several large genomic differences within marker regions that harbor resistance genes and expression mechanisms shared by the resistant lines with respect to the susceptible parental line. This work emphasizes the utility of whole genome comparisons as a means of elucidating large and small differences by lineage.