Submitted to: Genetics and Molecular Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/20/2014
Publication Date: 2/13/2015
Publication URL: http://handle.nal.usda.gov/10113/60678
Citation: Li, J., Sun, Y., Liu, H., Wang, Y., Jia, Y., Xu, M. 2015. Natural variation of rice blast resistance gene Pi-d2. Genetics and Molecular Research. 14(1):1235-1249. doi.org/10.4238/2015.February.13.2. Interpretive Summary: Rice blast is one of the most threatening diseases worldwide. We examined the origins of rice disease resistance genes by taking a closer look at one major rice blast resistance gene, Pi-d2. DNA sequence variation of this gene was found in 35 cultivated rice, Oryza sativa, and 6 wild rice accessions. Pi-d2 was found in accessions of O. rufipogon, a putative progenitor of cultivated rice, suggesting that Pi-d2 originated in wild rice before the formation of subgroups in cultivated rice. This study validated the theory that wild rice is a source of novel resistance to blast disease. These findings will help us discover critical portions of resistance genes and allow us to develop novel strategies for controlling blast disease.
Technical Abstract: Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (TEJ), tropical japonica (TRJ) and aromatic (ARO), and 6 accessions of wild rice varieties, Oryza nivara and O. rufipogon were analyzed. A total of 13 nucleotide differences were found in the open reading frame (ORF) of Pi-d2. Translation of these ORFs revealed nine variants three of which were novel Pi-d2 variants. Variants H2 and H5 were identified in accessions of cultivated rice and O. nivara. H1, H3, H4, H6, and H8 were only identified in cultivated rice. H2 and H5 were the common type of IND and O. nivara, H8 was the common type of TRJ and AUS, H6 was the specific type of AUS, H3 was the specific type of ARO. H7 and H9 were specific haplotypes of O. nivara and O. rufipogon, respectively. These findings demonstrate that Pi-d2 variants are useful indicators for each subgroup and Pi-d2 is an ancient gene that existed before speciation of rice subgroups.