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Genome-wide investigation on the genetic variations of rice disease resistance genes

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Abstract

Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93–11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable “artificially selective sweeping” could be detected in a large proportion of the conserved R-genes, a scenario described in the “arms race” co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.

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Acknowledgements

We thank two anonymous reviewers for their insightful advices. This research was supported by NSFC (30570987 and 30470122), SRFDP, Pre-program for NBRPC (2005CCA02100) and SUR grant from IBM to D. T., Y. H. or J.␣Q. C.

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Correspondence to Dacheng Tian.

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Yang, S., Feng, Z., Zhang, X. et al. Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol Biol 62, 181–193 (2006). https://doi.org/10.1007/s11103-006-9012-3

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