Genome-wide association study identifies key loci and candidate genes for seed vigor in upland cotton (

Introduction: Rapid and uniformgermination of cotton seeds is a prerequisite for achieving high and stable yields. Elucidating the molecular mechanisms underlying seed germination will help establish a genetic foundation for improving seed vigor, which is a key agronomic trait. Methods: In this study, seeds from 259 Results and discussion: Using a mixed linear model (MLM), six stable SNPs associated with the germination index (GI), three with germination potential (GP), and six with vigor index (VI) were identified, yielding a total of 15 stably associated SNPs across the three traits in multiple environments. Among them, locus A09:47545163 was repeatedly detected for both the germination index and potential. Using a 500-kb interval as the reference distance for candidate region delineation, 166 candidate genes harboring nonsynonymous mutations were identified. Further integrating GO/KEGG enrichment analysis, genotype effects at significant loci, and gene functional annotation, we prioritized 10 candidate genes that are potentially involved in the formation and regulation of seed vigor in cotton. Meanwhile, public TM-1 transcriptomic expression data provided exploratory supporting evidence for the functional inference of some candidate genes. These findings provide new evidence for elucidating the genetic basis of seed vigor in upland cotton and offer valuable gene resources for the development of high-vigor germplasm and related molecular markers.