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Microsatellite Analysis of Genetic Variation and Population Genetic Differentiation in Autotetraploid and Diploid Rice

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Abstract

Genetic diversity and population genetic structure of autotetraploid and diploid populations of rice collected from Chengdu Institute of Biology, Chinese Academy of Sciences, were studied based on 36 microsatellite loci. Among 50 varieties, a moderate to high level of genetic diversity was observed at the population level, with the number of alleles per locus (A e) ranging from 2 to 6 (mean 3.028) and polymorphism information content ranging from 0.04 to 0.76 (mean 0.366). The expected heterozygosity (H e) varied from 0.04 to 0.76 (mean 0.370) and Shannon’s index (I) from 0.098 to 1.613 (mean 0.649). The autotetraploid populations showed slightly higher levels of A e, H e, and I than the diploid populations. Rare alleles were observed at most of the simple sequence repeat loci in one or more of the 50 accessions, and a core fingerprint database of the autotetraploid and diploid rice was constructed. The F-statistics showed genetic variability mainly among autotetraploid populations rather than diploid populations (F st = 0.066). Cluster analysis of the 50 accessions showed four major groups. Group I contained all of the autotetraploid and diploid indica maintainer lines and an autotetraploid and its original diploid indica male sterile lines. Group II contained only the original IR accessions. Group III was more diverse than either Group II or Group IV, comprising both autotetraploid and diploid indica restoring lines. Group IV included a japonica cluster of the autotetraploid and diploid rices. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between autotetraploid and diploid varieties. This analysis indicated that the gene pools of diploid and autotetraploid rice were somewhat dissimilar, as variation exists that distinguishes autotetraploid from diploid rices. Using this variation, we can breed new autotetraploid varieties with some important agricultural characters that were not found in the original diploid rice varieties.

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Acknowledgments

The authors are grateful to Mr. Ye Yan, Chaolong Gao, and Chuanmin Zeng for their excellent technical assistance. The authors are also grateful to the editor and anonymous reviewers and professional colleagues for critical comments and help on the presentation of the manuscript. Also, special thanks go to the Chinese Academy of Sciences for funding this research.

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Authors and Affiliations

  1. Department of Agriculture, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, P.R. China

    Li Luan, Xing Wang, Wen-Bo Long, Yu-Hua Liu, Sheng-Bin Tu, Fan-Lun Kong & Mao-Qun Yu

  2. Department of Biology, Sichuan University, Chengdu, 610041, P.R. China

    Zhan-Peng Zhao

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  1. Li Luan
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  2. Xing Wang
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  3. Wen-Bo Long
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  7. Fan-Lun Kong
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Correspondence to Sheng-Bin Tu.

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Luan, L., Wang, X., Long, WB. et al. Microsatellite Analysis of Genetic Variation and Population Genetic Differentiation in Autotetraploid and Diploid Rice. Biochem Genet 46, 248–266 (2008). https://doi.org/10.1007/s10528-008-9156-8

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  • DOI: https://doi.org/10.1007/s10528-008-9156-8

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