Evaluating Blast Resistance of Huang-Huai Geng/Japonica Varieties Using Intragenic Markers

Huang-Huai rice region is the second largest product area of high-quality geng/japonica (GJ) rice in China. Improving blast resistance of rice varieties with resistance genes is the most effective, economical and environmentally friendly manner to reduce the loss caused by the outbreaks of rice blast (Magnaporthe oryzae). Although many resistance genes have been cloned, the improvement of blast resistance is proceeding slowly. In order to facilitate genetic improvement of blast resistance, we performed haplotype analysis of 26 blast resistance loci using 40 rice accessions with high-quality genome sequence, and identified unique variations for each functional gene. Based on identified unique variations, we provided a set of intragenic markers for 24 genomic loci, including 35 markers developed and 7 markers reported in previous studies. Subsequently, we conducted genotyping of resistance genes in 130 GJ varieties approved in Huang-Huai region, and revealed that the functional types of two genes, BRG8 and PICI1, were fixed in all GJ varieties, while the functional types of another eight genes, namely Pi64, bsr-d1, Pi21, ROD1, Pi2, Pi9, Pi36 and Pb2, were not carried by any GJ variety. In addition, the functional types of seven genes, Pi35, Pigm, Pid4, Pik, Pikm, Piks and Pijx, were carried by the minority of varieties, or few varieties. Finally, we evaluated panicle blast resistance of 96 GJ varieties to a mix of six representative blast isolates. The majority showed high susceptibility, while the variety ‘Shengdao 138’ displayed the highest resistance. Analysis of resistance genes and panicle blast of tested GJ varieties demonstrated that genes Pizt, Pid3 and Pid2 contributed to partial resistance. Collectively, this study provided a set of intragenic markers for 24 blast resistance loci, a clear view of resistance genes carried by Huang-Huai GJ varieties, and the variety ‘Shengdao 138’ showing high panicle resistance, which could be of great use in genetic improvement of GJ varieties in Huang-Huai rice region, and maybe GJ varieties in other rice regions worldwide.