Japanese pepper, Zanthoxylum piperitum, is native to Japan and has four well-known lineages (Asakura, Takahara, Budou, and Arima), which are named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four lineages. Single nucleotide variant analysis was used to classify the plants into eight groups: the Asakura and Arima lineages each had two groups, the Takahara and Budou lineages each had one group, and two additional groups were present. In one Asakura group and two Arima groups, the plants were present in agricultural fields and mountains, thus representing the early stage of domestication of the Japanese pepper. The second Asakura lineage group was closely related to plants present in various areas, and this represents the second stage of domestication of this plant because, after early domestication, genetically related lineages with desirable traits spread to the periphery. These results demonstrate that domestication of Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless lineage being considered a subspecies of Japanese pepper.

The Japanese pepper (Zanthoxylum piperitum DC.) is an attractive plant that is highly palatable and benefits human health. There are several lineages of pepper plants in Japan. However, the classification of each lineage by analyzing its volatile compounds and studies on the effects of differences in volatile compounds on human flavor perception have not been performed in detail. Herein, we conducted gas chromatography (GC) and GC/mass spectrometry (GC/MS) analysis of volatile compounds and sensory evaluation of flavor by an analytical panel using 10 commercially available dry powdered Japanese pepper products from different regions. GC and GC/MS analysis detected limonene, β-phellandrene, citronellal, and geranyl acetate as the major volatile compounds of Japanese peppers. The composition of volatile compounds showed different characteristics depending on the growing regions, and cluster analysis of composition classified the products into five groups. The sensory evaluation classified the products into four groups, and the results of both classifications were in good agreement. Our results provide an important basis for proposing cooking and utilization methods that take advantage of the unique characteristics of each lineage based on scientific evidence.

Japanese pepper, Zanthoxylum piperitum, is native to Japan and has four famous varieties: Asakura, Takahara, Budou, and Arima, named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four varieties. The analysis of the single nucleotide variants was used to classify the plants into eight groups: each of the Asakura and Arima varieties has two groups, each of the Takahara and Budou varieties has one group, and two additional groups are present. In one group of the Asakura varieties and two groups of the Arima varieties, the plants were present in agricultural fields and mountains, representing the early stage of domestication of the Japanese pepper. The second group of the Asakura varieties was of genetically close plants present in various areas, which represents the second stage of domestication of this plant because, after early domestication, genetically related varieties of excellent traits spread to the periphery. These results demonstrate that the domestication of the Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless variety being considered a subspecies of the Japanese pepper.