Mapping fiber and yield QTLs with main, epistatic, and QTL X environment interaction effects in recombinant inbred lines of upland cotton

Most agronomic traits of cotton (Gossypium hirsutum L.) are quantitatively inherited and affected by environment. The importance of epistasis as the genetic basis for complex traits has been reported in many crops. In this study, a linkage map was constructed by means of a recombinant inbred tine (RIL) population derived from 7235 x TM-1. Main effects, epistatic effects, and environmental interaction effects of quantitative trait loci (QTLs) controlling fiber and yield component traits were determined by mixed linear model based QTL mapping in two to four environments. Sixteen main effect QTLs for 12 traits and 19 digenic interaction QTLs for 12 traits were detected. The amount of variation explained by the QTLs of main effect was larger than the QTLs involved in epistatic interactions. Among seven QTLs having QTL x Environment (QE) interaction effects, five produced significant additive effects and two did not, but only one interaction showed significant additive x additive x environment (AAE) interaction effects. Some QTLs with large effects detected in specific environments could be associated with environmental response elements.