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

Authors: ABDELRAHEEM, ABDELRAHEEM - New Mexico State University; KURAPARTHY, VASU - North Carolina State University; Hinze, Lori; STELLY, DAVID - Texas A&M University; WEDEGAERTNER, TOM - Cotton, Inc; ZHANG, JINFA - New Mexico State University

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2021
Publication Date: 5/24/2021
Citation: Abdelraheem, A., Kuraparthy, V., Hinze, L.L., Stelly, D., Wedegaertner, T., Zhang, J. 2021. Genome-wide association study for tolerance to drought and salt tolerance and resistance to thrips at the seedling growth stage in US Upland cotton. Industrial Crops and Products. 169. Article 113645. https://doi.org/10.1016/j.indcrop.2021.113645.
DOI: https://doi.org/10.1016/j.indcrop.2021.113645

Interpretive Summary: Young cotton plants are susceptible to reduced water, excess salt, and physical damage from thrips insects [Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)]. A large group of cotton plants were evaluated to obtain information on the effects of these stresses on cotton growth and development. The objective also was to link these plant responses to regions in the cotton genome. The plants had notable differences in their responses to the three types of stresses. Fifty-three (53) regions of the genome were linked to the drought stress response, 78 regions were linked to the salt stress response, and 8 regions were identified in response to thrips stress. Thirteen clusters were identified where the same region of the genome was linked to multiple stress responses. The results of this study are important to the cotton industry and cotton breeders specifically in that this study represented the first attempt to map thrips resistance regions in the cotton genome, providing important information on stress resistance to identify genomic regions that will be useful for marker-assisted selection (MAS) in cotton.

Technical 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, 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 (11) and 15 QTL were common between tests for DT and ST, respectively. Twenty-three (23) 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.