Genome-wide association study reveals novel genes on different chromosomal positions regulating boll weight in upland cotton ( Gossypium hirsutum L.)

The boll weight (BW) is the most decisive yield component character and is utilized as a key index for selection in various cotton improvement programs. In the current study, 1260 accessions of cotton with a diverse genetic background were assessed for boll weight across four different environments (two locations for each environment) in China. A genome-wide association study (GWAS) was performed to mine novel single nucleotide polymorphisms (SNPs) controlling boll weight characteristics. A total of 1,122,352 SNPs were identified in association with boll weight across multiple environments, of which 138 were designated as key SNPs, harboring significantly higher association peaks for the all chromosomes on the basis of log10 P value (− log10 ≥ 6). Among 53 significant associations related to BW development across environments were identified. Six genes in the vicinity of these key SNPs (Pentatricopeptide repeat-containing protein PCMP-E76 ) , Trihelix transcription factor ASIL2, Auxin-responsive protein SAUR50, Floral homeotic protein AGAMOUS ( AG ) , Piriformospora indica-insensitive protein 2 ( PII-2 ) , and LOB domain-containing protein 16 ( LBD16 ) exhibited higher expression patterns. These identified BW-related key SNPs and candidate genes could prove to have potential for influencing BW development in upland cotton. The outcome of the current study will serve as a base for further mechanistic research focused on the exploitation of BW for accelerated cotton improvement.