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SNPs discovery and CAPS marker conversion in soybean

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Abstract

To discover new SNPs and develop an easy assay method in soybean, we compared the high-throughput pyrosequencing ESTs with whole genome sequences in different soybean varieties and identified 3899 SNPs. Transitions were found to be much more frequent than transversions in these SNPs. We found that SNPs were widely distributed in the soybean genome, targeting numerous genes involved in various physiological and biochemical processes influencing important agronomic traits. A set of 16 SNPs were validated in nine soybean varieties, and seven SNPs were converted into CAPS. From functional gene association analysis, the marker CAPS282 on the 3′-UTR of gene Glyma07g03490 was identified as associated with 100-seed weight in soybean. The SNP discovery and CAPS markers conversion system developed in this study is fast and cost effective, and holds great promise for molecular-assisted breeding of soybean.

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Acknowledgments

Soybean genome sequence data were produced by the U.S. Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community, and we thank them. The project was supported by the National High-Technology Program (2006AA100104, 200008AA10Z153, 2009ZX08009-032B), the Key Research Plan of Heilongjiang Province (GA06B103), and the Innovation Research Group of NEAU (CXT004).

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Authors and Affiliations

  1. College of Life Science, Northeast Agricultural University, 150030, Harbin, Heilongjiang, People’s Republic of China

    Yongjun Shu, Yong Li, Zhenlei Zhu, Xi Bai, Hua Cai, Wei Ji & Yanming Zhu

  2. College of Life Science and Technology, Harbin Normal University, 150025, Harbin, Heilongjiang, People’s Republic of China

    Yongjun Shu

  3. State Key Lab of Agrobiotechnology and Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong, NT, People’s Republic of China

    Dianjing Guo

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  1. Yongjun Shu
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  2. Yong Li
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  3. Zhenlei Zhu
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  4. Xi Bai
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  5. Hua Cai
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  6. Wei Ji
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  7. Dianjing Guo
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  8. Yanming Zhu
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Correspondence to Yanming Zhu.

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Yongjun Shu and Yong Li contributed equally to this work.

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Shu, Y., Li, Y., Zhu, Z. et al. SNPs discovery and CAPS marker conversion in soybean. Mol Biol Rep 38, 1841–1846 (2011). https://doi.org/10.1007/s11033-010-0300-2

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  • DOI: https://doi.org/10.1007/s11033-010-0300-2

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