A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton

The number and location of mapped quantitative trait loci (QTL) depend on genetic populations and testing environments. The identification of consistent QTL across genetic backgrounds and environments is a pre-requisite to marker-assisted selection. This study analyzed a total of 661 abiotic and biotic stress resistance QTL based on our previous work and other publications using the meta-analysis software Biomercator. It identified chromosomal regions containing QTL clusters for different resistance traits and hotspots for a particular resistance trait in cotton from 98 QTL for drought tolerance under greenhouse (DT) and 150 QTL in field conditions (FDT), 80 QTL for salt tolerance in the greenhouse conditions (ST), 201 QTL for resistance to Verticillium wilt (VW, Verticillium dahliae), 47 QTL for resistance to Fusarium wilt (FW, Fusarium oxysporum f. sp. vasinfectum), and 85 QTL for resistance to root-knot nematodes (RKN, Meloiodogyne incognita) and reniform nematodes (RN, Rotylenchulus reniformis). The traits used in QTL mapping for abiotic stress tolerance included morphological traits-plant height and fresh and dry shoot and root weights, physiological traits-chlorophyll content, osmotic potential, carbon isotope ratio, stomatal conductance, photosynthetic rate, transpiration, canopy temperature, and leaf area index, agronomic traits-seedcotton yield, lint yield, boll weight, and lint percent, and fiber quality traits-fiber length, uniformity, strength, elongation, and micronaire. The results showed that resistance QTL are not uniformly distributed across the cotton genome; some chromosomes carried disproportionally more QTL, QTL clusters, or hotspots. Twenty-three QTL clusters were found on 15 chromosomes (c3, c4, c5, c6, c7, c11, c14, c15, c16, c19, c20, c23, c24, c25, and c26). Moreover, 28 QTL hotshots were associated with different resistance traits including one hotspot on c4 for Verticillium wilt resistance, two QTL hotspots on c24 for chlorophyll content measured under both drought and salt stress conditions, and three other hotspots on c19 for the resistance to Verticillium wilt and Fusarium wilt, and micronaire under drought stress conditions. This meta-analysis of stress tolerance QTL provides an important foundation for cotton breeding and further studies on the genetic mechanisms of abiotic and biotic stress resistance in cotton.