抄録
Cottonseeds are rich in proteins with high nutritional value. In this study, a genome-wide association study involving six methods was performed to dissect the genetic architecture of the cottonseed protein content (CPC) in Upland cotton (Gossypium hirsutum L.). The CPC exhibited typical characteristics of a quantitative trait. The six methods revealed 1, 4, 4, 31, 10, and 30 CPC-related quantitative trait nucleotides (QTNs), among which 17 were detected by at least two methods. Notably, TM40095 on A12 and TM59869 on D06 were detected by three methods, thus being considered stable QTNs. Five QTN-by-environment interactions (QEIs) and 29 QTN-by-QTN interactions (QQIs) were detected. The regions flanking the SNPs of two stable QTNs, five QEIs, and four significant QQIs included 49, 174, and 269 candidate genes, respectively. A functional enrichment analysis indicated that 12 and 48 non-redundant genes related to the two stable QTNs and five QEIs, respectively, were associated with significantly enriched functions. Moreover, eight protein (gene)–protein (gene) interactions were predicted. According to RNA-seq expression data, GH_D06G1049 (related to QTNs) and GH_A06G1663, GH_D13G0601, and GH_A05G0236 (related to QEIs) were preferentially expressed in multiple ovule tissues, suggesting that they may contribute to seed protein synthesis and accumulation. These findings provide new clues regarding the genetic basis of CPC and may accelerate the molecular breeding of cotton with ideal protein content.
