Mapping of Main and Epistatic QTLs and QTL by Environment Interaction for Rice Grain Yield and Yield Components Under Well Watered and Drought Stress Conditions

Quantitative trait loci (QTLs) controlling yield and yield components were identified by using a F₅ population of 150 lines from a cross between ‘Sepidroud’ (Indica) and ‘Gharib’ (Indica) in normal and stress conditions. Based on the genetic linkage map containing 131 polymorphic SSR and 52 AFLP markers which covered 1063.14 cM of the rice genome with an average distance of 5.81 cM between markers, the main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) for grain yield and its components were analyzed by QTL IciMapping software. Sixteen M-QTLs and three E-QTLs were identified for grain yield and its components in normal condition and 13 M-QTLs and 12 E-QTLs were found in stress condition for these traits including four M-QTLs and four E-QTLs for number of panicle per plant, three M-QTLs and three E-QTLs for grain yield, four M-QTLs and five E-QTLs for number of total spikelet per plant, six M-QTLs and two E-QTLs for number of filled grain per panicle, nine M-QTLs and one E-QTL for grain weight and three M-QTLs for spikelet fertility. The phenotypic variation explained by each M-QTL and E-QTL ranged from 5.86 to 22.87% and 6.64 to 18.86%, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Thirteen M-QTLs and four E-QTLs were identified for the all studied traits. The phenotypic variation explained by each QTL and QTL-by-environment interaction ranged from 0.2 to 10.51% and 0.05 to 13.22%, respectively. As many as 29 M-QTLs were detected to be associated with yield and its components; some of them are being reported for the first time. Seven M-QTLs (qNFGP4, qGW1, qGW3.1, qNTSP1 and qNTSP11) were identified with high phenotypic variance and could be considered to use in marker-assisted selection (MAS) programs for improving yield in rice. Also, the marker RM252, RM1, RM5800, RM202, RM42, E37M59-3 and E37M59-1 had a close linkage with these major QTLs and could be used in marker-assisted selection (MAS) programs.