A population of recombinant inbred lines (RILs) derived from the cross between Japonica rice Nipponbare (NIP) and Indica rice Zhongjiazao 17 (YK 17) was used to analyse the genomic regions for amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and protein content (PC). Sums of 33 quantitative trait loci (QTLs) were detected on all chromosomes except chromosome 8, 10 and 12, respectively with single QTL explaining 1.56-89.51% of the phenotypic variation. From total, 15 of them were identified in all three environmental conditions. The marker interval RM7158-RM3414 harbours most of the detected QTLs and it may host the Waxy (Wx) gene along with Alk are the major determinant for cooking and eating quality (ECQs). Four QTLs (qAC6, qGT6.2, qPC6 and qPC7) showed highly significant additive x environment interaction providing evidence of environment effect. Moreover, 7 epistatic QTL pairs including 3 for AC, 3 for GT and 1 for PC were also detected. The Wx gene sequencing results showed that the promoter region of Wx gene in YK17 contains three Indels along with two SNPs on Exon 9 and Exon 10 in comparison to NIP. The results confirmed that the Wx gene is the major determinant for cooking and eating quality in rice. These findings can help to develop understanding for the genetic mechanism of ECQs and allelic variation in YK17 Wx gene will be utilized for future grain quality improvement programs. (C) 2019 Friends Science Publishers