Genetic variations in plant architecture traits in cotton (Gossypium hirsutum) revealed by a genome-wide association study

Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brown-fiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study (GWAS) identified 11 quantitative trait loci (QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02G017510 and Ghir_D02G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02G017510. Ghir_A12G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045 (T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton.