Broad spectrum blast resistance alleles in newly developed Malaysian rice (Oryza sativa L.) genotypes

Rice blast, caused by Magnaporthe oryzae, is a destructive disease. A total of 23 rice genotypes, were screened using a set of 51 simple sequence repeats SSR/ InDel markers and 51 single nucleotide polymorphic (SNP) markers to evaluate the sequence variation. Six newly identified Malaysian isolates of M. oryzae were used for blast screening. The resistant genotypes, consisting of Pongsu Seribu 2, O. rufipogon accessions, Tetep and IR64 had a resistant disease score of 2/3 showing minimal symptoms of blast. In contrast, Mahsuri and MR264 were the most susceptible and had a disease score of 5. In total, 11 sequence variations and two putative haplotype blocks, were observed in the SNP data representing Pi54 and Pita. The SNPs for Pita and Pi54 revealed the presence of resistant alleles that generated reproducible and aggressive calls based on the Sequenom data, but when screened with SSR and INDel markers showed poor correspondence to phenotype effects. Therefore, SNPs for Pi54 and Pita were found to be the most reliable for marker-assisted selection. The blast-resistant alleles identified in this study indicate that they are involved in the defence response against diverse isolates and play a role in putative broad spectrum resistance.