Quantitative Trait Locus Analysis of Drought and Salt Tolerance in an Introgressed Recombinant Inbred Line Population of Upland Cotton.

Drought and salt tolerances are complex traits, which are controlled by multiple genes along with environmental factors and their interactive effect. Drought and salt stresses are an important problem in cotton production in the Southwest USA and can result in significant yield loss in Upland cotton (Gossypium hirsutum L.). G. barbadense L. (source of Pima cotton) carries desirable traits such as tolerance to abiotic and biotic stress along with high fiber quality. However, the transfer of drought and salt tolerance from Pima to Upland cotton has been unsuccessful, due to hybrid breakdown in the interspecific segregating generations. Thus, introgression lines with genes transferred from Pima to Upland cotton may overcome the issues in interspecific hybrid breakdown. In this study, four replicated tests were conducted in the greenhouse for drought and salt tolerance along with another test conducted in the field for drought tolerance in an Upland recombinant inbred line population that has a stable introgression from Pima cotton. The objectives of the study were to investigate the genetic basis of drought and salt tolerance and to identify genetic markers associated with drought and salt tolerance. A total of 1044 polymorphic loci were used to construct the genetic map including SSR, SNP and AFLP-RGA markers, spanning 2368 cM. This population along with two parents was evaluated for morpho-physiological, yield and fiber quality traits. Our results showed that drought under greenhouse and field conditions and salt stress in the greenhouse reduced cotton plant growth at the seedling stage, and decreased lint yield and fiber quality traits. A total of 131 quantitative trait loci (QTL) for salt and drought tolerance were detected on most of cotton chromosomes, explaining 5.69 to 22.65 % of the phenotypic variation. Among these, 7 common QTL were detected under both drought and salt stress conditions. This study has provided reliable and stable QTL under multiple tests that will be useful to understand the genetic basis of drought and salt tolerance and for molecular marker-assisted selection in cotton.