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Genome-wide mining, characterization, and development of microsatellite markers in Tartary buckwheat (Fagopyrum tataricum Garetn.)

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Abstract

A large set of potential microsatellites markers covering the entire genome are required for genetic diversity, mapping and functional genomics studies. In this study, a total of 37,572 microsatellites with frequency of 83.25 microsatellites per Mb were mined in the recently sequenced Fagopyrum tataricum. Among these 37,572 microsatellites, most of the microsatellites were di-nucleotide (26,196, 69.72%) and AT/TA repeat motifs were the most abundant (24,742, 65.85%). A total of 26,549 microsatellite markers were designed from the flanking sequences of 37,572 microsatellites and 2643 (9.96%) were genic microsatellite markers. All of these newly-developed microsatellite markers were physically anchored to the eight chromosomes of F. tataricum and the first and high-density physical map was constructed with an average marker density of 58.82 markers per Mb. Amplification efficiency and experimental evaluation of the newly-developed microsatellite markers assessed with 440 markers randomly selected in F. tataricum, showed that these microsatellite markers are highly effective and valuable. The large number of new microsatellite markers and their location on the physical map provided a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in Fagopyrum species.

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Acknowledgements

This study was financially supported by Chinese Postdoctoral Science Foundation (2017M622944), Chongqing Postdoctoral Science Foundation (No. Xm2017176), and Fundamental Research Funds for the Central Universities (No. XDJK2018C051).

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  1. Xiaomei Fang, Kehui Huang and Jiao Nie have contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, People’s Republic of China

    Xiaomei Fang, Kehui Huang, Jiao Nie, Yuanli Zhang, Yuke Zhang, Yingshuang Li, Wenwen Wang, Xin Xu, Renwu Ruan, Xiaohui Yuan, Zhengsheng Zhang & Zelin Yi

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  1. Xiaomei Fang
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Figure S1

The physical map of the 26,549 microsatellite markers of F. tataricum. The eight chromosomes of Tartary buckwheat are arranged from left to right. The background is green color and the blue lines are the positions of microsatellite markers. (PNG 1796 kb)

Figure S2

Dendrograms of 12 Fagopyrum varieties based on the 894 polymorphic loci from the 440 SSR markers (A), 748 loci form inter-genic SSR markers (B), 146 loci from intra-genic SSR markers (C). (PNG 1032 kb)

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Fang, X., Huang, K., Nie, J. et al. Genome-wide mining, characterization, and development of microsatellite markers in Tartary buckwheat (Fagopyrum tataricum Garetn.). Euphytica 215, 183 (2019). https://doi.org/10.1007/s10681-019-2502-6

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