Expression-based genotyping of the rice blast resistance genes in the elite maintainer line Yixiang1B

Rice blast caused by Magnaporthe oryzae poses a major threat to rice production worldwide. Utilization of resistance is the most effective and economic means to control the disease. An elite maintainer line Yixiang1B (Y1B) has been widely exploited in three-line hybrid rice breeding. However, it remains unclear which blast resistance gene or genes contribute to its resistant phenotype. In this work, we found that a novel functional Pid2 allele is critical for the Y1B’s resistance against rice blast pathogen. First, we confirmed that Y1B is resistant to a number of M. oryzae isolates, with a resistance frequency of 65%. Then, we exploited expression-based approach to genotype the cloned rice blast resistance genes. Transcripts from Pid2 , Pid3 , Pib , Pi36 , Pi5 and Pia were readily detected in Y1B upon M. oryzae infection. Sequencing analyses detected many SNPs in these genes, except that Pib had no substitution and Pid2 contained two tandem base-pair mutations at the nucleotide positions 1997 and 1998 leading to the H666R substitution. Knocking-down Pid2_Y1B via RNAi in Y1B resulted in susceptibility. In contrast, over-expression of Pid2_Y1B in a blast-susceptible accession led to enhanced resistance to M. oryzae . Therefore, Pid2_Y1B is the main contributor to the rice blast resistance in Y1B. Taken together, we identified a functional resistance allele of Pid2 that can be utilized as a resource in rice blast resistant breeding programs.