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De novo sequencing of seed transcriptome and development of genic-SSR markers in common buckwheat (Fagopyrum esculentum)

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Abstract

Large-scale identification of simple sequence repeat (SSR) markers has not been reported in the genus Fagopyrum due to a lack of genomic resources. High-throughput transcriptomic sequencing can provide a rich resource for development of genic-SSR markers. In our study, the immature seeds transcriptome of common buckwheat (Fagopyrum esculentum) was sequenced using the Illumina HiSeq™ 2000 platform. We obtained a total of 21 million paired-end reads after filtering. The reads were assembled into 54,947 transcripts with an average length of 1235 bp. In total, 46,126 (83.95%) transcripts showed significant hits to known proteins or domains. Among these, 43,647 (79.43%) transcripts was assigned at least one gene ontology (GO) term. A total of 12,677 (23.07%) transcripts were mapped to the 141 Kyoto Encyclopedia of Genes and Genome (KEGG) pathways. Overall, 2326 transcripts contained at least one SSR with a frequency of one SSR per 1.17 kb. Mono-nucleotide repeats were the most abundant type (45.48%) followed by tri-nucleotide repeats (35.17%). Of the 150 SSRs chosen randomly, 36 markers showed polymorphism among 24 common buckwheat accessions, and 141 genic-SSRs (94.0%) were transferable to tartary buckwheat. A low level of genetic diversity was found among 35 registered tartary buckwheat varieties in China assessed using 31 polymorphic SSR markers. Genic-SSR markers developed herein will be valuable for construction of linkage maps, genetic diversity studies, and marker-assisted selection in Fagopyrum species.

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Author notes

  1. Taoxiong Shi and Ruiyuan Li contributed equally to this work.

Authors and Affiliations

  1. Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China

    Taoxiong Shi, Qijiao Chen, Yue Li, Fan Pan & Qingfu Chen

  2. Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, 550001, China

    Ruiyuan Li

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  1. Taoxiong Shi
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  4. Yue Li
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Correspondence to Qingfu Chen.

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Shi, T., Li, R., Chen, Q. et al. De novo sequencing of seed transcriptome and development of genic-SSR markers in common buckwheat (Fagopyrum esculentum). Mol Breeding 37, 147 (2017). https://doi.org/10.1007/s11032-017-0743-4

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