**2.1. Identification of SNP markers by second generation sequencing and transcriptome analysis**

#### *2.1.1. SNPs*

In order to obtain intravariety DNA polymorphic regions required for developing a hop variety identification technique, we attempted searching for SNPs in a large amount of sequence data obtained using NGS. We focused on the transcriptome because transcriptome analysis requires about 100-times less data processing than whole-genome analysis, thereby reducing the lead time and cost. Besides, according to our calculation, there are already available data for as many as 15000 SNPs in the transcriptome analysis; the data size, however, is smaller than that for the whole-genome analysis. Thus, we performed an intravariety SNP analysis, using this technique, based on the assumption that SNPs required for the identifica‐ tion of many varieties could be obtained, thereby.
