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Patterns of nucleotide diversity in wild and cultivated rice

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Abstract

There are few reports of the patterns of polymorphism in the non-coding regions of plant genomes. In this study, we explored nucleotide diversity and linkage disequilibrium (LD) in 47 non-coding regions on chromosome 4 of wild and cultivated rice. The cultivated rice retained about 70% of the diversity of wild rice, which was verified by coalescent simulations with one population bottleneck for 198 combinations of duration and population sizes. Multi-locus likelihood analysis showed that the severity of the bottleneck ranged from 2.25 to 3.33, with an average value of 2.70; i.e., the diversity found in the cultivated rice could be explained by a founding population of 2,700 individuals if the initial domestication event occurred over a period of 1,000 years. LD decreased more rapidly in wild rice than in cultivated rice within 10 kb, and the LD observed in cultivated rice was increased at 100–140 kb by comparison with wild rice. The patterns of LD indicated the possibility of a haplotype block in cultivated rice but not in wild rice.

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Abbreviations

LD:

Linkage disequilibrium

SNP:

Single nucleotide polymorphism

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Acknowledgments

We thank Yang Gao for helpful suggestions on LD decay analysis, and Hongbin Lin for assistance with coalescent simulation. This work was supported by the Project of Conservation and Utilization of Agricultural Wild Plants of the Ministry of Agriculture of China, 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. State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Genetics and Breeding, China Agricultural University, 100193, Beijing, China

    Xianran Li, Lubin Tan, Zuofeng Zhu & Chuanqing Sun

  2. National Centre for Evaluation of Agricultural Wild Plants (Rice), 100193, Beijing, China

    Xianran Li, Lubin Tan, Zuofeng Zhu & Chuanqing Sun

  3. Laboratory of Crop Heterosis and Utilization, Ministry of Education, 100193, Beijing, China

    Xianran Li, Lubin Tan, Zuofeng Zhu & Chuanqing Sun

  4. Beijing Key Laboratory of Crop Genetic Improvement, 100193, Beijing, China

    Xianran Li, Lubin Tan, Zuofeng Zhu & Chuanqing Sun

  5. Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 101300, Beijing, China

    Haiyan Huang, Ying Liu & Songnian Hu

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  1. Xianran Li
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  2. Lubin Tan
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Correspondence to Chuanqing Sun.

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Li, X., Tan, L., Zhu, Z. et al. Patterns of nucleotide diversity in wild and cultivated rice. Plant Syst Evol 281, 97–106 (2009). https://doi.org/10.1007/s00606-009-0191-7

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