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Genetic variation of NBS-LRR class resistance genes in rice lines

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Abstract

The use of plant disease resistance (R) genes in breeding programs needs an understanding of their variation patterns. In our current study, we investigated the polymorphisms of 44 NBS-LRR class R-genes among 21 rice cultivars and 14 wild rice populations. Our data suggested that there were four basic types of variations: conserved, diversified, intermediate-diversified, and present/absent patterns. Common characteristics at a locus of conserved R-genes were: copy-number uniformity, clear divergence (long branches) with other paralogs, and highly identical alleles. On the other hand, copy-number variability, a nearly equal and non-zero branch lengths, and high levels of nucleotide diversity were observed at the loci of highly diversified R-genes. Research suggests that the ratio of diverse alleles to the total number of genes at a locus is one of the best criteria to characterize the variation pattern of an R-gene. Our data suggested that a significant genetic reduction was detected only in four present/absent R-genes, compared with the variation observed in wild rice. In general, no difference was detected between wild rice and cultivars, japonica and indica rice, or between lines from different geographic regions. Our results also suggested that R-genes were under strong selection, which shaped R-gene variation patterns.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (30570987 and 30470122), pre-program for NBRPC (2005CCA02100), 111 project and SUR grant from IBM to D.T., Y.H. or J.Q.C.

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Authors and Affiliations

  1. State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, 210093, China

    Sihai Yang, Tingting Gu, Chunyu Pan, Zhumei Feng, Jing Ding, Jian-Qun Chen & Dacheng Tian

  2. Jiangsu Province & Chinese Academy of Science, Institute of Botany, Nanjing, 210014, China

    Yueyu Hang

Authors
  1. Sihai Yang
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  2. Tingting Gu
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  3. Chunyu Pan
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  4. Zhumei Feng
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  5. Jing Ding
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  6. Yueyu Hang
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  7. Jian-Qun Chen
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  8. Dacheng Tian
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Corresponding authors

Correspondence to Jian-Qun Chen or Dacheng Tian.

Additional information

Communicated by D. A. Lightfoot.

Sihai Yang and Tingting Gu contributed equally to this work.

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Yang, S., Gu, T., Pan, C. et al. Genetic variation of NBS-LRR class resistance genes in rice lines. Theor Appl Genet 116, 165–177 (2008). https://doi.org/10.1007/s00122-007-0656-4

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  • DOI: https://doi.org/10.1007/s00122-007-0656-4

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