Genomic insights into genetic improvement of upland cotton in the world’s largest growing region

Upland cotton (Gossypium hirsutum L.) is the world’s most essential fiber-producing crop. The Xinjiang Uygur autonomous region is the largest cotton-growing region on our planet; superior local environments, unique cultivation management measures, and excellent cotton cultivars have ensured its irreplaceable role. However, the origin of the higher yield production and elite fiber quality observed with genetically improved upland cotton cultivars in this region remains largely unknown. Here, we resequenced 486 accessions with ~10.51-fold coverage and identified approximately 4.49 million SNPs with which to evaluate population variation. Considering population kinship and phenotypic differences in terms of fiber-related traits, biotic and abiotic stress tolerance, and seed germination parameters, we present that cultivars in the northwest inland region (NIR) are largely different from those grown in other regions of China (OTHER). NIR accessions featured significantly higher average values for fiber length (FL) and strength (FS), and also better drought tolerance. Moreover, a huge divergence in genomic variation (SNPs) was identified between the two groups, with 1967 genes in NIR and 1538 in OTHER accessions harboring nonsynonymous, stop gain, or stop loss SNPs. Through a genome-wide association study, we detected 502 significant associated loci: 210 across all accessions, 182 in OTHER, and 110 in NIR. A large number exhibited specific trait associations between different cotton-growing regions, accelerating differential yield production and fiber quality in their respective local environments. Our results shed substantial light on the genomic basis of genetic improvement mechanisms, provide a foundation for genetic manipulation and molecular selection towards cotton improvement, and will enable further breeding improvement analysis of polyploid plants. •A large-scale investigation of cotton accessions from the world’s largest growing region, Xinjiang, and other regions.•Illuminates the distinct genomic kinship between Xinjiang cultivars and other accessions.•Cultivars from Xinjiang have better yield traits and fiber quality than others when grown in Xinjiang.•Divergent loci have been identified in Xinjiang and other accessions respectively.