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

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.