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Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites

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Abstract

China is one of the largest centers of genetic diversity of Oryza sativa L. in the world. Using a genetically representative primary core collection of 3,024 rice landraces in China, we analyzed the genetic structure and intraspecific differentiation of O. sativa, and the directional evolution of SSR. The genetic structure was investigated by model-based structure analysis and construction of neighbor-joining phylogenetic tree. Comparison between genetic structure and predefined populations according to Ting’s taxonomic system revealed a hierarchical genetic structure: two distinct subspecies, each with three ecotypes and different numbers of geo-ecogroups within each ecotype. Two subspecies evidently resulted from adaptation to different environments. The different cropping systems imposed on the subspecies led to further differentiation, but the variation within each subspecies resulted from different causes. Indica, under tropical-like or lowland-like environments, exhibited clear differentiation among seasonal ecotypes, but not among soil-watery ecotypes; and japonica showed clear differences between soil water regime ecotypes, but not among seasonal ecotypes. Chinese cultivated rice took on evident directional evolution in microsatellite allele size at several aspects, such as subspecies and geographical populations. Japonica has smaller allele sizes than indica, and this may partly be the result of their different domestication times. Allele size was also negatively correlated with latitude and altitude, and this may be interpreted by different mutation rates, selection pressures, and population size effects under different environments and cropping systems.

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Acknowledgments

We thank Professor Robert A McIntosh, University of Sydney, for suggested revisions to the manuscript. This research was supported by the National Basic Research Program of China (“973” Program, 2004CB117201), Program for Changjiang Scholars and Innovative Research Team in University, and Program of Introducing Talents of Discipline to Universities (111-2-03).

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Authors and Affiliations

  1. Key Laboratory of Crop Genomics & Genetic Improvement of Ministry of Agriculture, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People’s Republic of China

    Dongling Zhang, Hongliang Zhang, Meixing Wang, Junli Sun, Yongwen Qi, Fengmei Wang, Xiangkun Wang & Zichao Li

  2. China National Rice Research Institute, Hangzhou, 310006, People’s Republic of China

    Xinghua Wei

  3. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Longzhi Han

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  1. Dongling Zhang
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  2. Hongliang Zhang
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  3. Meixing Wang
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Correspondence to Hongliang Zhang or Zichao Li.

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Zhang, D., Zhang, H., Wang, M. et al. Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 119, 1105–1117 (2009). https://doi.org/10.1007/s00122-009-1112-4

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