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

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

doi:10.1038/s41598-021-85909-9

Cited by 7 publications

(6 citation statements)

References 46 publications

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“…Zanthoxylum (Rutaceae) is one of the most important economic and medicinal tree species in southwestern China and some regions of Asia, such as Japan, South Korea, India, Pakistan, Nepal and so on [ 23 , 24 ]. Due to the special numbing taste of its fruits, it is a very famous and essential ingredient in Sichuan hot-pot in China, and is often used to flavour some delicious dishes in many countries [ 25 , 26 ]. Zanthoxylum armatum DC., commonly named green prickly ash, is not only enriched in special numbing substances, but also has a special fragrance, and the colour of its fruit is green, all of which contribute to its increasing popularity in recent public diets [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum

et al. 2022

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Background Multiprotein bridging factor 1 (MBF1) is a crucial transcriptional coactivator in animals, plants, and some microorganisms, that plays a necessary role in growth development and stress tolerance. Zanthoxylum armatum is an important perennial plant for the condiments and pharmaceutical industries, whereas the potential information in the genes related to stress resistance remains poorly understood in Z. armatum. Results Herein, six representative species were selected for use in a genome-wide investigation of the MBF1 family, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Citrus sinensis, Ginkgo biloba, and Z. armatum. The results showed that the MBF1 genes could be divided into two groups: Group I contained the MBF1a and MBF1b subfamilies, and group II was independent of the MBF1c subfamily.. Most species have at least two different MBF1 genes, and MBF1c is usually an essential member. The three ZaMBF1 genes were respectively located on ZaChr26, ZaChr32, and ZaChr4 of Zanthoxylum chromosomes. The collinearity were occurred between three ZaMBF1 genes, and ZaMBF1c showed the collinearity between Z. armatum and both P. trichocarpa and C. sinensis. Moreover, many cis-elements associated with abiotic stress and phytohormone pathways were detected in the promoter regions of MBF1 of six representative species. The ERF binding sites were the most abundant targets in the sequences of the ZaMBF1 family, and some transcription factor sites related to floral differentiation were also identified in ZaMBF1c, such as MADS, LFY, Dof, and AP2. ZaMBF1a was observed to be very highly expressed in 25 different samples except in the seeds, and ZaMBF1c may be associated with the male and female floral initiation processes. In addition, expression in all the ZaMBF1 genes could be significantly induced by water-logging, cold stress, ethephon, methyl jasmonate, and salicylic acid treatments, especially in ZaMBF1c. Conclusion The present study carried out a comprehensive bioinformatic investigation related to the MBF1 family in six representative species, and the responsiveness of ZaMBF1 genes to various abiotic stresses and phytohormone inductions was also revealed. This work not only lays a solid foundation to uncover the biological roles of the ZaMBF1 family in Z. armatum, but also provides some broad references for conducting the MBF1 research in other plants.

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Section: Introductionmentioning

confidence: 99%

“…armatum is planted as the second most important medicinal species in Pakistan [ 32 ]. The fruit pulp of Zanthoxylum could be extended to treat skin diseases, toothache, fever, and stomach ache [ 24 , 26 , 30 ]. Plant-based medications are a high proportion of prescription used in regions of health care scarcity [ 33 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum

et al. 2022

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“…Consequently, we determined the presence or absence of asexual reproduction by setting the value of conservation at nearly 40% as the criterion. It should be noted that a similar value of conservation was also used as a criterion for clonal propagation in a study of Japanese pepper that used de novo analysis of RAD-Seq data 28 .…”

Section: Resultsmentioning

confidence: 99%

“…No reports exist on the genetic relationships and intraspecific diversity of A. macrostemon using either traditional or high-throughput methods. Encouraged by our research group's previous successes with RAD-Seq or ddRAD-Seq in analyzing various species, including loquat 26 , 27 , Japanese pepper 28 , citrus 29 – 31 , and firefly 32 , we are inspired to apply this knowledge to the study of A. macrostemon .…”

Section: Introductionmentioning

confidence: 99%

RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Probowati,

Koga,

Harada

et al. 2023

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Allium macrostemon Bunge, commonly referred to as "no-biru" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using RAD-Seq. Our analyses distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, groups A and B showed clear evidence of bulb propagation, while group C did not. Group C formed four subgroups: C1, C2, C3, and C4. Hybridization between subgroup C1 and either group A, B, or both, resulted in the emergence of subgroups C2, C3, and C4. Thus, groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status.

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“…Although there are several such lineages, it was not known whether each of these lineages is genetically distinct from the others. Therefore, our research group has previously conducted a genome-level classification of cultivated and wild species of Japanese pepper in various regions of Japan using RAD-Seq (Restriction Site Associated DNA Sequencing) [ 21 ] and has found that each lineage can be identified at the DNA level. The next challenge is to analyze and identify the differences in the properties of these different lineages.…”

Section: Introductionmentioning

confidence: 99%

Classification of Japanese Pepper (Zanthoxylum piperitum DC.) from Different Growing Regions Based on Analysis of Volatile Compounds and Sensory Evaluation

et al. 2022

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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.

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

Cited by 7 publications

References 46 publications

Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum

Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum

RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Classification of Japanese Pepper (Zanthoxylum piperitum DC.) from Different Growing Regions Based on Analysis of Volatile Compounds and Sensory Evaluation

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