Journal of Molecular Evolution

, Volume 68, Issue 4, pp 393–402

Genetic Signature of Rice Domestication Shown by a Variety of Genes

Authors

  • Yuanli Zhang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Jiao Wang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Xiaohui Zhang
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
  • Jian-Qun Chen
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of BiologyNanjing University
Article

DOI: 10.1007/s00239-009-9217-6

Cite this article as:
Zhang, Y., Wang, J., Zhang, X. et al. J Mol Evol (2009) 68: 393. doi:10.1007/s00239-009-9217-6

Abstract

Cultivated rice was domesticated from common wild rice. However, little is known about genetic adaptation under domestication. We investigated the nucleotide variation of both cultivated rice and its wild progenitors at 22 R-gene and 10 non–R-gene loci. A significant regression was observed between wild rice and rice cultivars in their polymorphic levels, particularly in their nonsynonymous substitutions (θa). Our data also showed that a similar proportion (approximately 60%) of nucleotide variation in wild rice was retained in cultivated rice in both R-genes and non–R-genes. Interestingly, the slope always was >1 and the intercept always >0 in linear regressions when a cultivar’s polymorphism was x-axis. The slope and intercept values can provide a basis by which to estimate the founder effect and the strength of artificial direct selection. A larger founder effect than previously reported and a strong direct-selection effect were shown in rice genes. In addition, two-directional selection was commonly found in differentiated genes between indica and japonica rice subspecies. This kind of selection may explain the mosaic origins of indica and japonica rice subspecies. Furthermore, in most R-genes, no significant differentiation between cultivated and wild rice was detected. We found evidence for genetic introgression from wild rice, which may have played an important role during the domestication of rice R-genes.

Keywords

Genetic variationNBS-LRR genesTwo-directional selection

Supplementary material

239_2009_9217_MOESM1_ESM.doc (229 kb)
(DOC 229 kb)
239_2009_9217_MOESM2_ESM.ppt (3.4 mb)
(ppt 3489 kb)
239_2009_9217_MOESM3_ESM.ppt (2.8 mb)
(ppt 2911 kb)

Copyright information

© Springer Science+Business Media, LLC 2009