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Background Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments. Results GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL,  qFM-A12–1 , included 12 significant SNPs, and  GhFLA9  was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene.  GhFLA9  was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis. The expression level of  GhFLA9  was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9). Conclusions This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of  GhFLA9.

Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)