Four genome assemblies of new wild Gossypium hirsutum accessions from the Yucatan Peninsula, the center of domestication

Abstract

Gossypium hirsutum is a leading source of natural cotton fiber, accounting for most of the market share. While domestication and improvement have led to significant gains in fiber quantity and quality, the narrow germplasm base of modern cultivars creates vulnerabilities, including to emerging pests. Wild populations provide a reservoir for genetic diversity that may be valuable in identifying and transferring resistance or stress-adaptation alleles to modern breeding lines. Here we report four new genome assemblies of G. hirsutum representing distinct populations from its center of diversity in Yucatan, Mexico. These chromosome-level assemblies are highly contiguous and structurally similar to existing G. hirsutum genomes; however, comparative analyses highlight their distinctiveness, suggesting they form a valuable reservoir of untapped diversity. Preliminary analyses of nucleotide-binding leucine-rich repeat (NLR) immune receptor genes underscore this variation, suggesting presence-absence variation may exist among populations. These findings demonstrate the potential of these new genomic resources for discovery of novel disease resistance alleles and, generally, for expanding the narrow germplasm base of the modern cotton cultivars.