Statistical Inference of Selection and Divergence of the Rice Blast Resistance Gene Pi-ta

The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of d...

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Published inG3 : genes - genomes - genetics Vol. 4; no. 12; pp. 2425 - 2432
Main Authors Amei, Amei, Lee, Seonghee, Mysore, Kirankumar S, Jia, Yulin
Format Journal Article
LanguageEnglish
Published England Genetics Society of America 21.10.2014
Subjects
binding sites
blast disease
crops
cultivars
disease resistance
Disease Resistance - genetics
domestication
evolution
genes
Genes, Plant
genomics
Haplotypes
introgression
Investigations
Markov Chains
Monte Carlo Method
Oryza - genetics
Oryza rufipogon
Oryza sativa
Phylogeny
Plant Diseases - genetics
Plant Proteins - classification
Plant Proteins - genetics
sequence analysis
statistical analysis
wild rice
United States
NBS-LRR
Poisson random field
evolution
resistance gene
Pi-ta
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Summary:The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study, we applied a recently developed statistical method, time-dependent Poisson random field model, to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our study suggests that the Pi-ta gene may have more recently introgressed into cultivated rice, indica and japonica, and U.S. weedy rice from the wild species, O. rufipogon. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, U.S. cultivars and U.S. weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site and leucine-rich repeat domain, 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.
Bibliography:http://handle.nal.usda.gov/10113/60682
http://dx.doi.org/10.1534/g3.114.014969
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ISSN:2160-1836
2160-1836
DOI:10.1534/g3.114.014969