Tree Genetics & Genomes

, 14:89 | Cite as

Genetic structure of cultivated Zanthoxylum species investigated with SSR markers

  • Yang Hu
  • Lu Tian
  • Jingwei Shi
  • Jieyun Tian
  • Lili Zhao
  • Shijing FengEmail author
  • Anzhi WeiEmail author
Original Article
Part of the following topical collections:
  1. Population structure


Zanthoxylum is an economically and ecologically important genus of the Rutaceae family, of which Z. bungeanum and Z. armatum have a long history of cultivation in China. However, how the natural processes such as selection and drift and agriculture practices have influenced the genetic variation of cultivated Zanthoxylum species during long-term domestication remains elusive. Herein, we determined the population genetic structure of current widely cultivated Zanthoxylum species, Z. bungeanum and Z. armatum. Microsatellite markers revealed a high level of genetic variation and significant genetic differentiation for both species despite Z. bungeanum showed higher genetic diversity than Z. armatum. AMOVA indicated that most of the genetic variation exists within individuals rather than among provenances for both species. Population structure analyses generated three distinct groups within the entire accessions. All Z. bungeanum accessions were distinguished into two major geographic groups, north and south groups, with Qinling Mountains as the main geographic barrier to gene flow while a significant genetic differentiation was observed between cultivated and wild Z. armatum accessions. Mantel test of Z. bungeanum displayed a significant correlation between genetic and geographic distances within each inferred group but no correlation between genetic and geographic distance was observed when comparing genetic and geographic distances focusing only on pairwise of north vs. south provenances, ruling out the hypothesis that gene flow between north and south provenances followed an isolation-by-distance model. Our research provided a fundamental genetic profile that will improve the conservation and responsible exploitation of the extant germplasm of Zanthoxylum.


Genetic structure SSR markers Zanthoxylum 



This work was supported by the promotion projects (Northwest A&F University) grant (TGZX2016-08). We also thank the anonymous reviewers for their comments and suggestions on the manuscript.

Supplementary material

11295_2018_1300_MOESM1_ESM.xlsx (18 kb)
Table S1 Information and genetic diversity of Z. bungeanum and Z. armatum provenances with SSR markers (XLSX 17 kb)
11295_2018_1300_MOESM2_ESM.xls (86 kb)
Table S2 The raw data of SSR markers (XLS 85 kb)


  1. Amar MH, Biswas MK, Zhang ZW, Guo WW (2011) Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Sci Hort 128:220–227CrossRefGoogle Scholar
  2. Artaria C, Maramaldi G, Bonfigli A, Rigano L, Appendino G (2011) Lifting properties of the alkamide fraction from the fruit husks of Zanthoxylum bungeanum. Int J Cosmetic Sci 33:328–333CrossRefGoogle Scholar
  3. Bao W, Wuyun T, Li T, Liu H, Jiang Z, Zhu X, Du H, Bai Y (2017) Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies. PLoS One 12:e0188685CrossRefPubMedPubMedCentralGoogle Scholar
  4. Ben-Ayed R, Sans-Grout C, Moreau F, Grati-Kamoun N, Rebai A (2014) Genetic similarity among Tunisian olive cultivars and two unknown feral olive trees estimated through SSR markers. Biochem Genet 52:258–268CrossRefPubMedGoogle Scholar
  5. Bressan EA, Briner Neto T, Zucchi MI, Rabello RJ, Veasey EA (2014) Genetic structure and diversity in the Dioscorea cayenensis/D. rotundata complex revealed by morphological and isozyme markers. Genet Mol Res 13:425–437CrossRefPubMedGoogle Scholar
  6. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 21:550–570Google Scholar
  7. Cheng J, Lee X, Theng BKG, Zhang L, Fang B, Li F (2015) Biomass accumulation and carbon sequestration in an age-sequence of Zanthoxylum bungeanum plantations under the grain for green program in karst regions, Guizhou province. Agric For Meteorol 203:88–95CrossRefGoogle Scholar
  8. Deng HP, Xu J, Chen F, Song QZ (2008) Morphological and molecular identification on genetic diversity of Zanthoxylum armatum var. novemfolius. Acta Bot Boreal Occident Sin 28:2103–2109Google Scholar
  9. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  10. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  11. Feng S, Yang T, Liu Z, Chen L, Hou N, Wang Y, Wei A (2015) Genetic diversity and relationships of wild and cultivated Zanthoxylum germplasms based on sequence-related amplified polymorphism (SRAP) markers. Genet Resour Crop Ev 62:1193–1204CrossRefGoogle Scholar
  12. Feng S, Liu Z, Chen L, Hou N, Yang T, Wei A (2016) Phylogenetic relationships among cultivated Zanthoxylum species in China based on cpDNA markers. Tree Genet Genome 12:45CrossRefGoogle Scholar
  13. Feng S, Zhao L, Liu Z, Liu Y, Yang T, Wei A (2017) De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development. Sci Rep-UK 7:16754CrossRefGoogle Scholar
  14. Huang C (1997) Flora Reipublicae Popularis Sinicae In: Delectis florae reipublicae popularis sinicae agendae academiae sinicae edita. Science Press, Beijing, pp 8–10Google Scholar
  15. Innocenzo M, Francesca S, Enzo P (2009) Evaluation of olives cultivated in southern Italy by simple sequence repeat markers. Hort Science 44:582–588Google Scholar
  16. Kamvar ZN, Tabima JF, Grünwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. Peer j 2:e281CrossRefPubMedGoogle Scholar
  17. Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecol Resour 15:1179–1191CrossRefGoogle Scholar
  18. Kumar V, Kumar S, Singh B, Kumar N (2014) Quantitative and structural analysis of amides and lignans in Zanthoxylum armatum by UPLC-DAD-ESI-QTOF–MS/MS. J Pharmaceut Biomed 94:23–29CrossRefGoogle Scholar
  19. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  20. Lassois L, Denancé C, Ravon E, Guyader A, Guisnel R, Hibrand-Saint-Oyant L, Poncet C, Lasserre-Zuber P, Feugey L, Durel CE (2016) Genetic diversity, population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers. Plant Mol Biol Rep 34:827–844CrossRefGoogle Scholar
  21. Laucou V, Lacombe T, Dechesne F, Siret R, Bruno J-P, Dessup M, Dessup T (2011) High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theor Appl Genet 122:1233–1245CrossRefPubMedGoogle Scholar
  22. Li WJ, Yang TX (2013) Zanthoxylum bungeanum, Sanqin press. In: Xi’anGoogle Scholar
  23. Lumaret R, Ouazzani N (2001) Plant genetics - ancient wild olives in Mediterranean forests. Nature 413:700CrossRefPubMedGoogle Scholar
  24. Mantel N (2002) The detection of disease clustering and a generalized regression approach. Cancer Res 59:377–381Google Scholar
  25. Nagai H, Yoshida T, Kamiya K, Yahara T, Tachida H (2009) Development and characterization of microsatellite markers in Zanthoxylum ailanthoides (Rutaceae). Mol Ecol Resour 9:667–669CrossRefPubMedGoogle Scholar
  26. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research – an update. Bioinformatics 28:2537–2539CrossRefPubMedPubMedCentralGoogle Scholar
  27. Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15CrossRefGoogle Scholar
  28. R Core Team D (2013) R: A language and environment for statistical computing, vol 14. R Foundation for Statistical Computing, Vienna, Austria., pp 12–21Google Scholar
  29. Rana TS, Narzary D, Ohri D (2010) Genetic diversity and relationships among some wild and cultivated species of Chenopodium L. (Amaranthaceae) using RAPD and DAMD methods. Curr Sci 98:840–846Google Scholar
  30. Rana JC, Chahota RK, Sharma V, Rana M, Verma N, Verma B, Sharma TR (2015) Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers. Tree Genet Genomes 11:821CrossRefGoogle Scholar
  31. Soto-Cerda BJ, Maureira-Butler I, Muñoz G, Rupayan A, Cloutier S (2012) SSR-based population structure, molecular diversity and linkage disequilibrium analysis of a collection of flax (Linum usitatissimum L.) varying for mucilage seed-coat content. Mol Breeding 30:875–888CrossRefGoogle Scholar
  32. Takanori Y, Hisako N, Tetsukazu Y, Hidenori T (2010) Genetic structure and putative selective sweep in the pioneer tree, Zanthoxylum ailanthoides. J Plant Res 123:607–616CrossRefGoogle Scholar
  33. This P, Jung A, Boccacci P, Borrego J, Botta R (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458CrossRefPubMedGoogle Scholar
  34. Victory E, Glaubitz J, Rhodes O, Woeste K (2006) Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites. Am J Bot 93:118–126CrossRefGoogle Scholar
  35. Wang H, Pan G, Ma QG, Zhang JP, Pei D (2015) The genetic diversity and introgression of Juglans regia and Juglans sigillatain Tibet as revealed by SSR markers. Tree Genet Genomes 11:804Google Scholar
  36. Yang Q, Cao WD, Zhou XX, Cao W, Xie YH, Wang SW (2014) Anti-thrombotic effects ofα-linolenic acid isolated from Zanthoxylum bungeanum maxim seeds. BMC Complement Altern Med 14:348CrossRefPubMedPubMedCentralGoogle Scholar
  37. You YM, Zhou M, Lu HJ, Gasper G-S, Cheng YJ, Liu X (2015) Sanshool from Zanthoxylum L. induces apoptosis in human hepatocarcinoma HepG2 cells. Food Sci Biotechnol 24:2169–2175CrossRefGoogle Scholar
  38. Zeng J (2000) The origin and geographical distribution of Chinese prickly ash. Agr Hist China 4:68–75Google Scholar
  39. Zhang Y, Wang D, Li Y, Zhou D, Zhang J (2014) Purification and characterization of flavonoids from the leaves of Zanthoxylum bungeanum and correlation between their structure and antioxidant activity. PLoS One 9:e105725CrossRefPubMedPubMedCentralGoogle Scholar
  40. Zheng HX, Li ZQ, XUE HD, Wang DW, Sun Y (2011) RAPD analysis of the germplasm resources of Zanthoxylum bungeanum. J Northwest For Univ 26:96–100Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.College of ForestryNorthwest A&F UniversityYanglingChina
  2. 2.Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingChina
  3. 3.College of Life ScienceNorthwest A&F UniversityYanglingChina

Personalised recommendations