Genome-wide association mapping of seed shape-related traits in cotton using SSR markers

Abstract Background Cotton is a significant crop for fiber production; however, seed shape-related traits have been less investigated in comparison to fiber quality. Comprehending the genetic foundation of traits associated with seed shape is crucial for improving the seed and fiber quality in cotton. Results A total of 238 cotton accessions were evaluated in four different environments over a period of two years. Traits including thousand grain weight (TGW), aspect ratio (AR), seed length, seed width, diameter, and roundness demonstrated high heritability and significant genetic variation, as indicated by phenotypic analysis. The association analysis involved 145 simple sequence repeats (SSR) markers and identified 50 loci significantly associated with six traits related to seed shape. The markers MON_DPL0504aa and BNL2535ba were identified as influencing multiple traits, including aspect ratio and thousand grain weight. Notably, markers such as HAU2588a and MUSS422aa had considerable influence on seed diameter and roundness. The identified markers represented an average phenotypic variance between 3.92% for seed length and 16.54% for TGW. Conclusions The research finds key loci for seed shape-related traits in cotton, providing significant potential for marker-assisted breeding. These findings establish a framework for breeding initiatives focused on enhancing seed quality, hence advancing the cotton production.