Genome-Wide Resequencing Identification of Loci Associated with Early Maturity in Upland Cotton and Functional Validation of GhGATA9

Early maturity is an important agronomic trait in upland cotton (Gossypium hirsutum L.), contributing to an increased cropping index, avoidance of extreme weather, and facilitation of mechanized cotton production. In this study, 15 early-maturing and 15 late-maturing upland cotton accessions were subjected to whole-genome resequencing to identify genomic regions and key genes associated with early maturity. A total of 2,684,227 high-quality single-nucleotide polymorphisms (SNPs) were identified. Based on the integrated Fst–θπ analysis, 16 genomic regions under selection in the early-maturing group were identified, encompassing 80 selected genes. Functional enrichment analysis showed that these genes were mainly involved in cellular membrane organization, fatty acid metabolism, and biotin metabolism. By further examining genes associated with plant growth and development, flowering regulation, and transcriptional regulation, a key transcription factor gene, Gossypium hirsutum GATA transcription factor 9 (GhGATA9), was identified as a candidate gene associated with early maturity. Virus-induced gene silencing (VIGS) assays showed that silencing GhGATA9 delayed both budding and flowering by 2.4 days, indicating that GhGATA9 may function as a positive regulator of early maturity in upland cotton. These findings provide novel molecular markers and a candidate gene for the molecular breeding of early-maturing cotton varieties.