Whole-Genome Analysis of Mahsuri Rice and Its Blast-Resistant Mutant for Understanding Resistance Mechanisms

Rice blast disease, caused by the pathogenic fungus Magnaporthe oryzae, poses a significant threat to global rice production, particularly impacting the high-value Mahsuri variety cultivated in Malaysia. Despite the extensive genetic diversity within Oryza sativa germplasm that offers a potential source of resistance, genome-level variations in distinguished resistant and susceptible Mahsuri genotypes remain unexplored. Addressing this gap, the present study employed whole-genome resequencing to elucidate the molecular basis of blast resistance in Mahsuri rice. Whole-genome sequences of a blast-resistant Mahsuri Mutant and its susceptible parent genotype were generated, a total of 116 million reads, with sequencing coverage of 23.91X and 21.76X, respectively. Bioinformatic analyses using SAMtools identified single-nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) between the two rice lines, with comparative genomic analysis against the Japonica reference genome revealing a higher variant count in the Mahsuri mutant (4,096,071) than in the parent (4,024,223). Notably, 178,622 SNPs were detected within exonic regions, underscoring their potential impact on protein function and their association with enhanced blast resistance observed in the mutant line. Further genomic analysis identified unique SNPs in several key candidate genes associated with blast resistance, including Pit, Pi64, Pish, Pi21, Piz, Pikm and Pi-ta, providing valuable molecular markers for marker-assisted selection. This comprehensive genomic analysis deepens our understanding of the genetic architecture underlying blast resistance in Mahsuri rice, facilitating more precise and efficient identification of candidate genes to accelerate breeding programs aimed at developing resilient rice varieties for sustainable cultivation in Malaysia and beyond.