Plant Molecular Biology

, Volume 62, Issue 1, pp 181–193

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

Authors

  • Sihai Yang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Zhumei Feng
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Xiuyan Zhang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Ke Jiang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Xinqing Jin
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Yueyu Hang
    • Institute of BotanyJiangsu Province & Chinese Academy of Science
  • Jian-Qun Chen
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
Article

DOI: 10.1007/s11103-006-9012-3

Cite this article as:
Yang, S., Feng, Z., Zhang, X. et al. Plant Mol Biol (2006) 62: 181. doi:10.1007/s11103-006-9012-3

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.

Keywords

Disease resistance genesGenomic comparisonRiceVariation

Supplementary material

11103_2006_9012_MOESM1_ESM.pdf (843 kb)
Supplementary material

Copyright information

© Springer Science+Business Media B.V. 2006