Identification of main and epistatic QTLs for grain yield related traits in a recombinant inbred lines population of rice (Oryza sativa L.)

Rice yield as a complex trait is the main target in most rice breeding programs. To map the main and epistatic QTLs controlling grain yield and yield components, an experiment was carried out using a 129 F6 recombinant inbred lines population (IRA population) originated from a cross between Alikazemi / IR67017-180-2-1-2, in 2015 growing season in two locations, Rasht and Tonekabon, Iran.  The experimental design was augmented design arrangment with five check cultivars in randomized complete block design with five replications. Analysis of variance showed that the linkage map consisted of 87 Single Sequence Repeats (SSRs) covering 1356.0 cM of rice genome in 12 linkage groups with an average distance of 15.58 cM spamming two markers. The results of combined analysis of variance for two locations, using composite interval mapping method, identified a total of 13 main QTLs on rice chromosomes for five measured traits. The qTN3 with 13.9% for tiller number per plant, the qFG4 with 11.6% for filled grain per panicle and the qGY6 with 15.6% for grain yield had significant positive additive effect. Furthermore, the qSG1 with 19.9% phenotypivc variation had a negative additive effect on the number of unfilled grain.panicle-1. These finding suggest that these QTLs can be used in rice breeding programs for improving grain yield. The interaction between additive effect (A) of QTLs and environment (E) was significant on grain yield and number of unfilled grain.panicle-1, but it was not significan on other traits. A total of 18 QTL pairs with significant additive × additive (AA) epistatic effect were identified for all traits. The highest epistasic effects were related to grain yield and number of unfilled grain.panicle-1 with six pairs of QTLs for each of these traits. Only one of the epistatic effects between qSG1-2 and qSG6 had significant AAE effect with a R2aae = of 3.4%. In addition, some QTLs were identified as three gene clusters controlling the grain yield, number of tiller.plant-1 and number of filled grain.panicle-1. Furthermore, five microsatellite markers including RM7551, RM8218-RM3417 and RM5302- RM283 0.2 to 5 cM distance from were identified as linked markers with qGY6, qFG4 and qSG1, respectively. These markers can be considered in the marker-assisted rice breeding program.