Genetic diversity and population structure of blast resistance genes in Thai upland rice germplasm

Rice blast is the most devastating disease of rice (Oryza sativa L.) causing yield losses worldwide. It had been shown that partially resistant rice varieties are a useful way to control rice blast disease. Landraces are a rich source of traits governing resistance/ tolerance to biotic and abiotic stresses. Therefore, 94 upland rice varieties were used to assess the genetic diversity and population structure of nine major rice blast resistance genes (Pib, Pid2, Pigm(t), Pi9, Pi-36(t), Pi54, Pi1, Pi-2(t), and Pita). The allele frequencies of the nine major R genes varied from 4.26% to 72.34%. The 94 varieties contained a range of one to seven genes with a blast resistance allele. One variety (12CR071) had the maximum seven blast resistance genes. The polymorphism information content (PIC) value among varieties varied from 0.0815 (R36STS CAPS) to 0.5000 (pB8) with an average of 0.3784 indicating moderate genetic diversity for rice blast resistance in upland rice varieties. Cluster analysis grouped 94 varieties into two major clusters. Population structure was analyzed to understand the evolution of blast resistance genes in rice. The population structure classified the upland rice into two distinct subpopulations. Interestingly, analysis of molecular variance (AMOVA) showed that much of the variability was found within subpopulation (95%), indicating a high gene exchange between the two subpopulations. In addition, eight varieties of upland rice and two control varieties were evaluated against leaf rice blast disease using four isolates of Pyricularia oryzae. The results showed that four upland rice varieties were resistant to all isolates used. Disease reactions were negatively correlated with the genotype scores of Pib, Pigm(t), Pi54, Pi-2(t), and Pita. In addition, based on the spearman rank correlation analysis, it revealed that the Pigm(t) were positively correlated to the leaf blast resistance. These findings provide important information for new sources of resistance genes for designing future breeding program of leaf blast resistant rice varieties.