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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #306547

Research Project: Using Genetic Approaches to Reduce Crop Losses in Rice Due to Biotic and Abiotic Stress

Location: Dale Bumpers National Rice Research Center

Title: Statistical inference of selection and divergence of rice blast resistance gene Pi-ta

Author
item AMEI, AMEI - University Of Nevada
item LEE, SEONGHEE - Samuel Roberts Noble Foundation, Inc
item MYSORE, KIRANKUMAR - Samuel Roberts Noble Foundation, Inc
item Jia, Yulin

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/6/2014
Publication Date: 10/21/2014
Publication URL: http://handle.nal.usda.gov/10113/60682
Citation: Amei, A., Lee, S., Mysore, K.S., Jia, Y. 2014. Statistical inference of selection and divergence of rice blast resistance gene Pi-ta. Genes, Genomes, Genetics. 4:2425-2432.

Interpretive Summary: Rice blast disease, caused by Magnaporthe oryzae, is one of the most destructive diseases of rice. Over 100 major and minor resistance genes have been identified but only 22 have been cloned. The resistance gene Pi-ta has been effectively used to control rice blast disease worldwide. A few recent studies have described the possible evolution of Pi-ta in cultivated and weedy rice, the latter a noxious weed. However, evolutionary statistics used for the studies are too limited to understand selection and divergence of Pi-ta during crop domestication. In this study, we applied a new statistical method to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our data suggest that the Pi-ta gene may have recently been established in cultivated rice and US weedy rice. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, US cultivars, and US weedy rice. We also found that the DNA sequences of two regions of the Pi-ta gene are commonly found among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.

Technical Abstract: The resistance gene Pi-ta has been effectively used to control rice blast disease worldwide. A few recent studies have described the possible evolution of Pi-ta in cultivated and weedy rice. However, evolutionary statistics used for the studies are too limited to precisely understand selection and divergence of Pi-ta during crop domestication. In this study, we applied a new statistical method, time-dependent Poisson random field model to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our data suggest that the Pi-ta gene may have recently introgressed into cultivated rice, indica and japonica, and US weedy rice. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, US cultivars, and US weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site (NBS) and leucine-rich repeat domain (LRD), are highly conserved among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.