Twenty-one hop varieties from Europe and the United States were successfully identified by DNA analysis, based on single nucleotide polymorphisms (SNPs; including insertion/deletion sequences) as identification markers. Several dozen megabases of transcriptome sequencing data were obtained by next-generation sequencing of samples from three hop varieties and compared to search for the regions containing SNPs. Consequently, four SNP-rich regions were selected as candidates for exploring identification markers in the hop varieties. Sequence data from these regions in all the tested varieties were obtained by the normal Sanger method and compared for the SNPs present. Combination of these SNPs could work well for identification of the 21 hop varieties. Moreover, the mixture of two varieties could be correctly evaluated by using this method. Hop pellet samples of two different varieties were mixed in various ratios and DNA sequencing was carried out. As a result, 5% contamination of a different variety could be detected by examining the electropherogram of the SNP positions. More quantitative methods for mixture evaluation could be expected using DNA techniques, such as quantitative real-time PCR. Because this SNP-based identification method utilizes the DNA sequence itself, it could be a reproducible tool for accurate identification of the hop varieties.
Part of the book: Next Generation Sequencing