Identification of main and epistatic QTLs and QTL through environment interactions for eating and cooking quality in Iranian rice

Breeding new rice varieties with high Eating and Cooking Quality (ECQ) characteristics is an important goal in rice breeding programs. To this end, 242 Recombinant Inbred Lines (RILs) of two populations derived from Alikazemi/IR67017-180-2-1-2 and Alikazemi/Saleh crosses were evaluated in two environments. The main and epistatic QTLs and QTL × Environment (Q × E) interactions were analyzed using the Mixed-Model-based Composite Interval Mapping method. A total of 17 main QTLs with additive effects were mapped on 6 rice chromosomes, including 6 QTLs for Amylose Content, 5 QTLs for Gelatinization Temperature and 6 QTLs for Gel Consistency. Seven QTLs were found on chromosome 6 associated with a common RM4128 marker (close to the Alk locus) influencing the ECQ characteristics with favorable alleles from the common female parent. Five QTL clusters were identified on chromosome 6, 7, 8, and 9, suggesting that the co-located QTLs with pleiotropic effects may control ECQ traits. A major QTL cluster was found for AC and GC between RM4128 and RM549 markers close to the Alk locus on chromosome 6, which is in the vicinity of another QTL located in RM587-RM4128 interval. 13 QTL pairs were identified to have a significant epistatic, Additive × Additive effects involved in controlling ECQ traits. A small phenotypic variation was found for the epistatic QTLs and Q × E interactions, suggesting the complexity of ECQ inheritance traits in rice. Further comprehensive studies and validation of the detected QTLs could be useful for marker-assisted selection to improve grain quality in rice.