Development and characterization of microsatellite primers for <i>Zanthoxylum schinifolium</i> (Rutaceae)

Kim, Young Mi; Jo, Aruna; Jeong, Ji Hee; Kwon, Yong Rak; Kim, Ho Bang

doi:10.3732/apps.1600145

Cited by 6 publications

(6 citation statements)

References 12 publications

(14 reference statements)

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“…2 ), how these processes shaped the current pattern of genetic variation within and between populations remains obscure. A range of previous studies attempted to study the genetic diversity of specific local varieties or species with molecular markers such as isozyme 14 , random amplified polymorphic DNA 15 , 16 , inter simple sequence repeat 15 , 17 , amplified fragment length polymorphism 18 , simple sequence repeat 19 – 22 , and chloroplast DNA 23 , 24 markers. The limited number of polymorphic loci produced by these low-resolution markers hinders genetic research on Zanthoxylum species.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

et al. 2020

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Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

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Section: Introductionmentioning

confidence: 99%

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

et al. 2020

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“…Primers used for ITS2 amplification are F: 5 -ATGCGATACTTGCTGTGAAT-3 and R: 5-GACGCTTCTCCAGACTACAAT-3 . Primers used for ETS amplification are F: 5 -ATAGAGCGCGTGAGTGGTG-3 and R: 5-GACAAGCATATGACTGGATCAA-3 [17]. PCR amplification was conducted in 40 µL volume consisting of 20 µL 2×Taq MasterMix, 0.5 µL each primer, 2.0 µL genomic DNA, and 17.0 µL double-distilled water.…”

Section: Molecular Proceduresmentioning

confidence: 99%

“…Furthermore, these markers are generally unable to resolve more distant evolutionary relationships. Therefore, due to the high level of polymorphism, codominance nature, biparental inheritance, and reproducibility, a mass of SSR markers were developed for Zanthoxylum species [17][18][19]. DNA sequence variation has been are most suitable for inferring evolutionary histories, and SNPs are a rapidly developing source of sequence data from multiple loci.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Feng

Niu

Liu

et al. 2020

Forests

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Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

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“…They found 15 polymorphic and 3 monomorphic microsatellite markers for the genetic study of Z. schinifolium . Furthermore, 3 of the 11 cross-amplified primers could distinguish between two Zanthoxylum species [ 27 ]. Su et al (2022) investigated the developmental mechanism of Z. bungeanum prickles via morphological and multiomic analyses.…”

Section: Introductionmentioning

confidence: 99%

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

Deng,

He,

et al. 2023

CIMB

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Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag–simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

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Development and characterization of microsatellite primers for Zanthoxylum schinifolium (Rutaceae)

Cited by 6 publications

References 12 publications

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

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