Genome-wide association screening and verification of potential genes associated with defoliation rate induced by defoliant in upland cotton

Defoliant sensitivity is an important trait of machine-picked cotton that directly affects the defoliation efficiency and the quality of machine-picked cotton fibers. Identification of the genetic components underlying defoliant sensitivity in upland cotton (Gossypium hirsutum L.) is highly important. In this study, the defoliation rate (DR) of 328 re-sequenced upland cotton accessions after 5 days of defoliant treatment was evaluated at two locations for two years in four environments; the results showed a great variation among the accessions, and the phenotype were normally distributed. A genome-wide association study (GWAS) was subsequently performed with resequencing data and defoliation rate data. As a result, two quantitative trait loci (QTL) related to defoliation rate were identified, qDS-A05 and qDS-A06, among which, qDS-A06 was identified in three environments. By combining linkage disequilibrium (LD) analysis, haplotype analysis, and expression analysis, a key candidate gene for DR was identified in qDS-A06, which was named GhDS-A06. This gene encodes a carboxylate clamp (CC)-tetratricopeptide repeat (TPR) protein, and is likely involved in the development of the abscission zone according to the reference of the function of TPR proteins in tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana L.). Additionally, the favorable haplotype frequency of GhDS-A06 varied among diverse areas of cotton growing in China, and the favorable haplotype frequency in northwestern China was much greater than that in other regions, which suggested that the favorable haplotype GhDS-A06 was artificially selected during breeding for machine-harvested cotton in northwestern China. The findings in the study not only provide genetic insights into defoliant sensitivity in upland cotton but also offer an ideal target for molecular breeding of defoliant sensitivity improved machine-harvested cotton plants.