Young-Ho Yoon

Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum)

We report the chloroplast (cp) genome sequence of tartary buckwheat (Fagopyrum tataricum) obtained by next-generation sequencing technology and compared this with the previously reported common buckwheat (F. esculentum ssp. ancestrale) cp genome. The cp genome of F. tataricum has a total sequence length of 159,272 bp, which is 327 bp shorter than the common buckwheat cp genome. The cp gene content, order, and orientation are similar to those of common buckwheat, but with some structural variation at tandem and palindromic repeat frequencies and junction areas. A total of seven InDels (around 100 bp) were found within the intergenic sequences and the ycf1 gene. Copy number variation of the 21-bp tandem repeat varied in F. tataricum (four repeats) and F. esculentum (one repeat), and the InDel of the ycf1 gene was 63 bp long. Nucleotide and amino acid have highly conserved coding sequence with about 98% homology and four genes—rpoC2, ycf3, accD, and clpP—have high synonymous (Ks) value. PCR based InDel markers were applied to diverse genetic resources of F. tataricum and F. esculentum, and the amplicon size was identical to that expected in silico. Therefore, these InDel markers are informative biomarkers to practically distinguish raw or processed buckwheat products derived from F. tataricum and F. esculentum.

Mining of microsatellite markers using next generation sequencing data and its application in genetic relationship analysis of tartary buckwheat (Fagopyrum tataricum Gaertn)

Fagopyrum genus is composed of about 20 species and among them two major species, common buckwheat (F. esculentum) and tartary buckwheat (F. tataricum). SSR markers are only reported in common buckwheat with lower numbers based on enriched repeat libraries and next-generation sequencing (NGS) is a cost-effective alternative. Here we report the development of new cDNA SSR (cSSR) markers characterized from transcriptome sequence data of F. esculentum and F. tataricum using NGS and these cSSR markers were applied for the validation of buckwheat germplasm. From the transcriptome sequences, a total of 8,360 and 6,518 putative cSSR markers were identified in common and tartary buckwheat, respectively, using SSR Locator. Among the cSSR markers, tetra-mer repeats are most abundant and occurred in rates of 54.9 and 37.3% in common and tartary buckwheat, respectively. To test the usefulness of newly developed cSSR markers with previously developed SSR markers based on the SSR motif enrichment library, in analysis of genetic relationship in tartary buckwheat, we selected five representative cSSR markers and applied to investigate the polymorphism of tartary buckwheat germplasm and found these markers can be applied in genetic diversity of germplasm with high polymorphism.