Mapping main and epistatic effects and environmental interactions of QTLs for cooking and eating quality traits of rice in a recombinant inbred lines population

Amylose content (AC), gelatinazation temperature (GT) and viscosity profile (from the rapid visco analazer curve) are primary indices for evaluating eating and cooking qualities of rice grain. The main objective of this research was to characterize the genetic parameters including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs) that are involved in the control of these traits. The experimental data were collected from a recombinant inbred lines (RILs) population derived from a cross between two Iranian varieties, Hashemi and Nemat during three years (2009-2011). A genetic linkage map consisting of 171 microsatellite markers was constructed and QTL analysis performed using QTLNETWORK 1.2 resolved the genetic components into main effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 18 main-effect QTLs for the ten traits, most of them were on chromosome 6. QEs interaction were significant in seven main-effect QTLs and R2 ae ranged from 0.09 to 8.14% for each trait. Seventeen digenic interactions involving 34 loci were detected for the ten traits, and two pairs of epistatic QTLs were involved in QEs. Six QTL clusters were detected on chromosome 6 that three of them corresponding to the Wx locus and one of them corresponding to the Alk locus. Results of current research showed that some of cooking and eating quality traits are controlled by two regions on chromosome 6, Wx and Alk loci regions. The markers linked to these two genes can be used for marker assisted selection in breeding programmes.