Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2013
Publication Date: 10/26/2013
Publication URL: http://handle.nal.usda.gov/10113/60739
Citation: Li, J., Sun, Y., Liu, H., Wang, Y., Jia, Y., Xu, M. 2013. Genetic variation and evolution of the Pit blast resistance locus in rice. Genetic Resources and Crop Evolution. 61:473-489. DOI 10.1007/s10722-013-0051-8. Interpretive Summary: Studying the origin of rice blast resistance genes can guide the identification of genetic resources that possess novel resistance genes that can be used in breeding. In this study, we genetically sequenced the rice blast resistance gene Pit in 26 rice varieties including 9 accessions of wild rice relatives. We demonstrated that the five different rice subpopulations carry different Pit haplotypes. The resistant Pit allele was commonly found in wild rice relatives suggesting that Pit is an ancient gene existing before the formation of rice subgroups. This study validated the concept that wild rice relatives harbor resistant genes that need to be intensively explored as a resource for developing improved rice cultivars.
Technical Abstract: Resistance (R) gene Pit in rice, encodes a protein with nucleotide binding sites-leucine rich repeat domain (NBS-LRR), prevents infections by strains of M. oryzae in a gene for gene manner. Here, we analyzed the open reading frame (ORF) of Pit in 26 varieties including Aus (AUS), indica (IND), temperate japonica (TEJ), tropical japonica (TRJ), aromatic (ARO) subgroups of Oryza sativa, and nine accessions of wild rice relatives including O. nivara and O. rufipogon from different growing areas. Twenty-one nucleotide differences were found within the ORFs of 35 accessions. Translation of these ORFs revealed a total of 11 Pit variants, seven of which were novel. Furthermore, variant H1 was identified in O. sativa and O. nivara; H2 and H10 were identified in O. sativa and O. rufipogon. H3, H4, and H11 were only found in O. sativa. H11 was the common type of TEJ and ARO; H3 and H4 was the specific type of TRJ and IND, respectively. H5, H6, and H7 were specific haplotypes of O. nivara, while, H8 and H9 were specific haplotypes of O. rufipogon. These results suggest that Pit is an ancient gene that existed before the divergence of rice subgroups.