BackgroundMicronaire is a comprehensive index reflecting fineness and maturity of cotton fibers. It is one of the important internal quality indicators of cotton fibers and is closely related to the use value of cotton fibers. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the underlying genetic architecture at the genomic level is not yet clear. The aim of this study was to use GWAS to dissect the genetic mechanism underlying the micronaire trait in 83 representative upland cotton lines grown in multiple environments.ResultsThe GWAS of micronaire was conducted using 83 upland cotton accessions and the Cotton 63K Illumina Infinium SNP array. A total of 11 quantitative trait loci (QTLs) on 10 chromosomes for micronaire were detected. Among these 11 QTLs, 27 genes with specific expression patterns were identified and selected. One novel QTL, qFM-A12-1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on the strong, direct LD relationships between the significantly related SNPs and the gene and a haplotype block analysis. GhFLA9 was highly expressed during secondary wall thickening at 20-25 days post-anthesis (DPA). Its expression level was significantly higher in low-micronaire line (Msco-12) than in high-micronaire line (Chuangyou-9).ConclusionsThis study provides a genetic reference for the genetic improvement of cotton fiber micronaire (FM) and lays a foundation for the functional verification of GhFLA9.