Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri

•Samba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior grain and cooking qualities.•Genome of SM was decoded and comparative genomic analysis using SNP-Seek and EnsemblPlantsv40 database revealed many novel alleles for grain quality.•Novel stop-gain mutations identified at several known loci, which may explain the observed weak biotic stress tolerance of SM.•Novel missense SNPs were mapped to genes that are associated with as many as 62 metabolic pathways.•Genomic resources described here are potentially useful in breeding programs for improved SM for grain quality and stress tolerance. Samba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior ‘eating and cooking qualities’ (ECQs), and ‘grain size and shape’ (GSS) traits. However, SM is found to be relatively stress susceptible and the link between grain quality and stress response remained unknown. We have investigated the genetic basis of the underlying mechanism of these traits in SM through whole genome sequencing and comparative genome analysis with IRGSP v1.0 as the reference genome. SNPs/INDELs analysis of 946 known QTLs related to ECQs, GSS and ‘stress tolerance and resistance’ (STR) reveal unique variants associated with insoluble starch biosynthesis and hydrolysis. Besides, variants in genes (22) associated with different stress signal transduction pathways as well as others involved in the formation of GSS have been identified. Comparative analysis with rice SNP-Seek database uncovered 861 SNPs with a unique third allele in SM rice in which 24 SNPs are missense. In addition, comparison with EnsemblPlants v40 rice variants uncovered 37,218 novel SNPs/INDELs in the SM genome. Of those, 1,767 SNPs are of missense type spanning across 1,283 genes. Specifically, 8 novel stop-gain variants were found in protein kinase-2 precursors, disease-related protein-2, WRKY37 TF, bHLH094, bHLH, NB-ARC, and two leucine-rich repeats domain-containing protein. Combined effects of these variants may possibly have relevance to the biotic and abiotic stress response of SM rice. Our study uncovered many allelic variants in candidate genes that serve as a resource for deploying them in breeding strategies to improve ECQs, GSS and stress tolerance.