Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fiber length, lint percentage, and Fusarium wilt resistance.

Sea Island cotton (Gossypium barbadense) is the source of the world's finest fiber-quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits, and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fiber quality, yield, disease resistance, maturity, and plant architecture. The highest number of associated loci was for fiber quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, i.e., disease resistance, fiber length, fiber strength, and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fiber quality (fiber length and fiber strength), and high lint-percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance, and separately improved fiber-quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.