Genome-wide association study for tolerance to drought and salt tolerance and resistance to thrips at the seedling growth stage in US Upland cotton

Abstract

Upland cotton (Gossypium hirsutum L.) is the most important fiber-producing crop, and its seedlings are sensitive to abiotic and biotic stresses including drought, salt and thrips [Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)]. In this study, an association mapping panel of 376 Upland cotton accessions was evaluated to identify quantitative trait loci (QTL) for thrips resistance in two replicated tests and drought (DT) and salt tolerance (ST) each in three replicated tests. Significant genotypic differences were detected for severity rating-based thrips resistance and morphological traits (including plant height, fresh shoot weight, fresh root weight, dry shoot weight and dry root weight (except for ST), and physiological traits (including chlorophyll content reading, stomatal conductance, photosynthesis rate, transpiration, and leaf temperature) under DT and ST conditions. Heritability estimates were low for physiological traits, moderate for morphological traits measured for both DT and ST and moderate to high for thrips resistance. Based on a genome-wide association study (GWAS) using 26,301 polymorphic SNPs, 53 and 78 QTL were detected for DT and ST, respectively, on all 26 chromosomes except for A02, A04, A06, A12 and D07. Eleven and 15 QTL were common between tests for DT and ST, respectively. Twenty-three of 131 QTL were common between DT and ST. Eight QTL were identified for thrips resistance on five chromosomes (A09, D01, D02, D03 and D11). Thirteen QTL clusters were detected on 11 chromosomes (i.e., A01, A08, D01, D02, D03, D05, D06, D10, D11, D12, and D13). Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance. This study represented the first attempt to map thrips resistance QTL in cotton, providing important information for biotic and abiotic stress resistance to select QTL that will be useful for marker-assisted selection (MAS) in cotton.