Genome-wide association study reveals the genetic control underlying node of the first fruiting branch and its height in upland cotton (Gossypium hirsutum L.)

Abstract

Improving early maturity in upland cotton (Gossypium hirsutum L.) is an important target in breeding. The node of the first fruiting branch (NFFB) and its height (HNFFB) are two important indexes to measure early maturity in cotton. To facilitate breeding for early maturity traits in upland cotton and reveal the genetic control underlying the two traits, a genome-wide association study was performed using 53,848 high-quality single nucleotide polymorphisms (SNPs) from 77,774 of a recently developed CottonSNP80K array. A total of 55 target trait-associated SNPs were detected, of which 12 SNPs were for NFFB and 43 were for HNFFB. Two SNPs for NFFB and 22 SNPs for HNFFB were repeatedly detected in at least two environments and/or by two models. These 24 SNPs also exhibited high phenotypic contributions of more than 10% and could be used for marker-assisted selection in future breeding programs. Furthermore, 89 candidate genes were identified in the genome sequence of upland cotton. These genes were categorized through Gene Ontology analysis. Gh_A05G1482 might be a potential candidate gene for improving the early maturation of cotton. These findings reveal the genetic control underlying NFFB and HNFFB and provide insight into genetic improvements for early maturity in upland cotton.