Drought tolerance is a complicated trait that primarily involves genetic and physiological characteristics. Quantitative trait loci (QTL)-hotspot regions from an upland cotton (Gossypium hirsutum) cultivar (CNH 28I) were introgressed into a Pima cotton (G. barbadense) cultivar (Suvin) with superior fiber properties to increase drought tolerance in Pima cotton. To screen the recombinant inbred lines (RILs) derived from CNH 28I×Suvin, QTL-hotspot regions on different chromosomes were selected for drought-tolerant traits: osmotic pressure (OP), canopy temperature (CT), carbon isotope ratio (CIR), relative water content (RWC), root weight (RW), root length (RL), root tip (RT), root surface area (RSA), and root volume (RV). The cotton genome's 157 simple sequence repeat markers related to drought QTL-hotspots were used to genotype the RILs. RIL population amplified polymerase chain reaction products of the same size as the drought-tolerant parent CNH 28I revealed introgression of QTL-hotspot regions. Sixteen QTLs generated polymorphism in the RIL population and parents, of which five (NAU2557, CIR143b, MUSB0818c, JESPR0205, and BNL1053) were associated with CIR, five (NAU2474, BNL3594b, BNL2884, BNL3259, and BNL1153b) with OP, four (JESPR230c, BNL3347, MUSS096a, CI061b) with RV, one (BNL3173b) with RWC, and one (BNL1705) with RL. Using the physiological metrics of RWC, CT, chlorophyll, and fiber length, six improved lines with drought-tolerant characteristics and fiber length were chosen by genotyping and phenotyping.
