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

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