Mining of Blast Resistance Gene, Pi2 and Its Novel Allelic Variant from Landraces of Rice from Karnataka

Rice blast is one of the important fungal diseases of rice, caused by Magnaporthe oryzae . Rice blast can be effectively managed by the deployment of R-genes. Pi2 (Piz - 5) is one of the major blast resistant genes effective against pathogen populations in various parts of India. In the present study, Pi2 gene was mined from 83 native landraces of rice from Karnataka state, India which revealed the presence of Pi2 in 60 landraces with the frequency of 72.28 %. Further, by using sequencing based allele mining approach, allelic variants of Pi2 from 16 landraces were analysed. High nucleotide variations (InDels) in the middle region of the conserved domain sequence of Pi2 in all variants were obtained. 469 polymorphic sites were observed with a total 570 mutations and 191 InDels among 16 Pi2 variants. Among Pi2 resistant and susceptible variants, 206 mutations with 29 InDel events were observed. Comparative modeling and Ramachandran plot of Pi2 protein variants from resistant and susceptible landraces were studied which revealed the significant differences among them. One potential novel Pi2 allelic variant from landrace Vanasurya was identified for the first time. This novel effective allelic variant can be used in rice breeding programmes to enhance blast resistance.