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Development of an allele-mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era

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Abstract

The allelic diversity of a collection of 4046 rice accessions was assessed using 15 neutral SSR markers distributed throughout the genome. A total of 482 alleles were detected; the average allelic richness was 32.1 alleles per locus. Using a heuristic approach, an allele-mining set was successfully developed on the basis of SSR marker data. 162 accessions of the allele-mining set, accounting for about 4.0% of the entire collection, captured all of the alleles (482) retained in the entire collection, which showed 100% coverage of alleles with minimum redundancy. As a result of validation of this heuristic approach using another 14 SSR markers associated with starch, 70% of the total alleles and 83% of the restricted alleles (allele frequency > 0.05%) were captured in this allele-mining set. The results showed that the heuristic approach meets the condition as an allele-mining set even when applied to another specific set of markers related to starch synthesis in the same entire and allele-mining set. The newly developed methodology for developing allele-mining sets can be used in other crop species. By retaining all alleles of the entire collection, this allele-mining set will be useful for future studies on introducing unused useful alleles into elite rice varieties by breeders in the post-genomic era.

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Acknowledgments

This study was supported by Biogreen 21 project (Grant 20080401034058) of the Rural Development Administration (RDA) and a grant (Code 200803101010415) from the National Academy of Agricultural Science, RDA, Republic of Korea. This research was also supported by the 2008 KU Brain Pool of Konkuk University for Dr. Zhao Weiguo.

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Authors and Affiliations

  1. Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 340-802, Republic of Korea

    Weiguo Zhao, Jong-Wook Chung & Yong-Jin Park

  2. Institute of Resource Sciences, Kongju National University, Yesan, 340-702, Republic of Korea

    Weiguo Zhao, Jong-Wook Chung & Yong-Jin Park

  3. Jiangsu University of Science and Technology, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, 212018, Zhenjiang, Jiangsu, China

    Weiguo Zhao

  4. National Academy of Agricultural Science, RDA, 249, Suwon, 441-707, Republic of Korea

    Gyu-Taek Cho, Kyung-Ho Ma & Jae-Gyun Gwag

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  1. Weiguo Zhao
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  2. Gyu-Taek Cho
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Correspondence to Yong-Jin Park.

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Zhao, W., Cho, GT., Ma, KH. et al. Development of an allele-mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era. Mol Breeding 26, 639–651 (2010). https://doi.org/10.1007/s11032-010-9400-x

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