Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq

Maddumage Dona Ginushika Priyadarsh Premarathne,Nami Fukutome,Nobuo Ibaragi,Yukio Nagano,Fumiyo Hayakawa,Atsushi J Nagano,Hisataka Mizuno,Kazuaki Yamasaki

doi:10.1038/s41598-021-85909-9

Abstract

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.

Highlights

Zanthoxylum piperitum is native to Japan and southern Korea
Double digest Restriction-site associated DNA sequencing (RAD-Seq) generated more than 11.9 gigabases of data for a total of 235.2 million raw single-end 51-bp reads
Our study classified Zanthoxylum piperitum into several groups based on DNA sequences and geographic information

Summary

Introduction

Zanthoxylum piperitum is native to Japan (except for Ryukyu) and southern Korea. In Japan, it is mainly used for culinary purposes. A typical feature of this lineage is the absence of spines For this reason, the spineless plant is called the Asakura lineage in Japan. The Arima lineage, known as the Rokko lineage, is another Japanese pepper lineage found in Kobe City in southern Hyōgo Prefecture The flowers of these plants are typically used as ingredients in Arima cuisine. The Takahara lineage is grown in Takayama City in northern Gifu Prefecture These plants are grown at high altitudes 800 m above sea level, in contrast to the other lineages, which are cultivated on the plains. The Budou lineage (Budou means “grape” in Japanese) is categorised based on its morphology This lineage is cultivated mainly in Kainan City, Wakayama Prefecture.

Methods

Results

Conclusion