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Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences

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Abstract

Tartary buckwheat is an important edible crop as well as medicinal plant in China. More and more research is being focused on this minor grain crop because of its medicinal functions, but there is a paucity of molecular markers for tartary buckwheat due to the lack of genomics. In this study, a genome survey was carried out in tartary buckwheat, from which SSR markers were developed for analysis of genetic diversity. The survey generated 21.9 Gb raw sequence reads which were assembled into 348.34 Mb genome sequences included 204,340 contigs. The genome size was estimated to be about 497 Mb based on K-mer analysis. In total, 24,505 SSR motifs were identified and characterised from this genomic survey sequence. Most of the SSR motifs were di-nucleotide (67.14 %) and tri-nucleotide (26.05 %) repeats. AT/AT repeat motifs were the most abundant, accounting for 78.60 % of di-nucleotide repeat motifs. SSR fingerprinting of 64 accessions yielded 49.71 effective allele loci from a total of 63 with the 23 polymorphic SSR primer combinations. Analyses of the population genetic structure using SSR data strongly suggested that the 64 accessions of tartary buckwheat clustered into two separate subgroups. One group was mainly distributed in Nepal, Bhutan and the Yunnan-Guizhou Plateau regions of China; the other group was mainly derived from the Loess Plateau regions, Hunan and Hubei of China and USA. The cluster analysis of these accession’s genetic similarity coefficient by UPMGA methods strongly supported the two subgroup interpretation. However accessions from Qinghai of China could be grouped into either of the two subgroups depending on which classification method was used. This region is at the intersection of the two geographical regions associated with the two subgroups. These results and information could be used to identify and utilize germplasm resources for improving tartary buckwheat breeding.

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Acknowledgments

We would like to thank Professor Donald Grierson, University of Nottingham, UK, for discussion and helping with the manuscript. We would like to thank Germplasm Resources Information Network in the US, Chinese Crop Germplasm Resources Information System and Institute of crop variety resources, Shanxi, China. This work was supported by NSFC (National Natural Science Foundation of China) (No. 31301385, 31471556), Science and Technology Project of Shanxi Province (20150311007-1), the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi (STIP, 2013115), the Basic Facility Platform Project of Shanxi Provincial Department of Science and Technology (2012091004–0103), Shanxi Agricultural University breeding innovation funds (2010028) and the Key Discipline Foundation of Shanxi Province.

Conflicts of Interest

The authors declare no conflict of interest.

Authors’ Contributions

Siyu Hou, Hongying Li and Yuanhuai Han designed the experiments and drafted the manuscript. Zhaoxia Sun , Lijun Zhang, Zhijun Qiao and Bin Wu collected plant materials. Bin Linghu performed the SSR experiments and analyzed the data. Dongmei Xu modified the manuscript.

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Authors and Affiliations

  1. School of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi, 030801, People’s Republic of China

    Siyu Hou, Zhaoxia Sun, Bin Linghu, Dongmei Xu, Bin Zhang, Xingchun Wang, Yuanhuai Han & HongYing Li

  2. Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Institute of Crop Genetic Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, 030031, People’s Republic of China

    Yuanhuai Han, Lijun Zhang & Zhijun Qiao

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

    Bin Wu

  4. Crop Germplasm Resources Research Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, 030031, People’s Republic of China

    Lijun Zhang & Zhijun Qiao

  5. Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Taigu, Shanxi, 030801, People’s Republic of China

    Siyu Hou, Zhaoxia Sun, Bin Zhang, Xingchun Wang, Yuanhuai Han & HongYing Li

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  1. Siyu Hou
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  2. Zhaoxia Sun
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  3. Bin Linghu
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  4. Dongmei Xu
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  5. Bin Wu
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  6. Bin Zhang
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  7. Xingchun Wang
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  8. Yuanhuai Han
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  9. Lijun Zhang
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  10. Zhijun Qiao
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  11. HongYing Li
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Correspondence to HongYing Li.

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Hou, S., Sun, Z., Linghu, B. et al. Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences. Plant Mol Biol Rep 34, 233–241 (2016). https://doi.org/10.1007/s11105-015-0907-5

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  • DOI: https://doi.org/10.1007/s11105-015-0907-5

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