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Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara

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Abstract

The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species.

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Acknowledgments

We thank Dr. Akito Kaga, National Institute of Agrobiological Sciences of Japan, for his technological assistance in sequencing. Hai-Fei Zhou thanks JIRCAS of Japan for supporting his stay in National Institute of Agrobiological Sciences of Japan. This study was supported by the National Basic Research Program of China (2007CB815704) and National Natural Science Foundation of China (30430030, 30121003) and JIRCAS of Japan.

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Authors and Affiliations

  1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China

    Hai-Fei Zhou, Xiao-Ming Zheng, Ruo-Xun Wei & Song Ge

  2. The Research Institute for Development (IRD), Montpellier, France

    Gerard Second

  3. National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan

    Duncan A. Vaughan

  4. Graduate School, Chinese Academy of Sciences, 100039, Beijing, China

    Song Ge

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  1. Hai-Fei Zhou
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  2. Xiao-Ming Zheng
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  5. Duncan A. Vaughan
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Correspondence to Song Ge.

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Communicated by T. Sasaki.

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Zhou, HF., Zheng, XM., Wei, RX. et al. Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara . Theor Appl Genet 117, 1181–1189 (2008). https://doi.org/10.1007/s00122-008-0855-7

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