Genome-wide association study reveals the genetic basis of microelement concentration in cottonseed

Cottonseed is rich in microelements that are beneficial for human health. However, research on microelement concentrations in cottonseed remains limited. The distributions of manganese (Mn), copper (Cu), and zinc (Zn) concentrations in cottonseeds were analyzed across multiple years and locations using a genetic population of 276 cotton accessions. The results revealed that cottonseed microelement concentrations were primarily influenced by genetic factors. Correlation analysis indicated significant relationships among Mn, Cu, and Zn, although the strengths of these correlations varied across regions and years. In addition, Mn, Cu, and Zn play distinct roles in cotton production; Cu is positively correlated with fiber yield, whereas Zn is predominantly negatively associated with fiber quality traits. A GWAS identified 34 significant SNPs on 15 chromosomes distributed within 22 QTLs that potentially influenced microelement concentrations in cottonseeds. Notably, the SNP locus i14125Gh was found to be associated with both Cu and Zn, and the candidate gene Gh_A12G1265 was screened, suggesting its potential role in co-regulating their concentrations. In addition, the candidate gene Gh_D07G0953 was related to Cu concentration. This study provides valuable SNP information, candidate genes, and new insights to support the development of cotton varieties with enhanced microelement concentrations. • The Mn, Cu, and Zn concentrations in cottonseeds of 276 accession were determined. • The trait of microelement concentration in cottonseeds was primarily influenced by environmental factors. • The application of GWAS identified 22 QTLs for microelement concentration in cottonseeds. • Haplotype analysis identified two potential candidate genes related to microelement concentration.