Skip to main content
SpringerLink
Log in

Genetic diversity and population structure of Chinese Cherry revealed by chloroplast DNA trnQ-rps16 intergenic spacers variation

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Chinese Cherry, generally referring to Prunus pseudocerasus Lindl. species, is one of the most economically important domestic fruit tree in China. To effectively preserve and sustainably utilize this species, a study in genetic diversity and population structure was carried out by the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacers. Polymorphism was calculated among the 200 individuals from 7 local and 10 wild populations across its geographical range in China. The results showed that (1) Total genetic variation in species level was poor (h = 0.478, π = 0.0018). But in the wild populations, it was much higher than that in the local populations (h = 0.565, π = 0.0021 vs. h = 0.152, π = 0.0006). (2) Low levels of genetic differentiation (FSC = 0.19595, P = 0.000), genetic distance (0.00000–0.00297), as well as pairwise Fst value among populations were detected. These results, combined with the insignificant gene genealogy pattern and neutrality tests indicate that Chinese Cherry has relatively low levels of genetic diversity and insignificant population structure. Coancestry might be a combined effect of the reduction in effective population size with the recent demographic bottlenecks and mating systems. The pronounced seed dispersal abilities and relatively high rates of gene exchange are supported by the limited genetic differentiation among populations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Bio Evol 16:37–48

    Article  CAS  Google Scholar 

  • Birky CWJR (1988) Evolution and variation in plant chloroplast and mitochondrial genomes. In: Gottlieb LD, Jain SK (eds) Plant evolutionary biology. Chapman and Hall, London, pp 23–53

    Chapter  Google Scholar 

  • Cai YL, Li S, Cao DW, Qian ZQ, Zhao GF, Han MY (2006) Use of amplified DNA sequences for the genetic analysis of the cherry germplasm. Acta Horticulturae Sinica 33:249–254

    CAS  Google Scholar 

  • Caiedo AL, Schaal BA (2004) Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Mol Ecol 15:1871–1882

    Article  Google Scholar 

  • Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescence theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959–969

    PubMed  CAS  Google Scholar 

  • Devos N, Tyteca D, Raspé O, Wesselingh RA, Jacquemart AL (2003) Pattern of chloroplast diversity among western European Dactylorhiza species (Orchidaceae). Plant Syst Evol 243:85–97

    Article  CAS  Google Scholar 

  • Donnelly P, Tavare S (1986) The ages of alleles and a coalescent. Adv Appl Probab 18:1–19

    Article  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online l:47–50

    Google Scholar 

  • Forster P, Bandelt HJ, Röhl A (2004) Network 4.2.0.1. Software available free at www.fluxus-engineering.com. Fluxus Technology Ltda

  • Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709

    PubMed  CAS  Google Scholar 

  • Fujii T, Nishida M (1997) High sequence variability in the mitochondrial DNA control region of the Japanese flounder Paralichthys olivaceus. Fisheries Sci 63:906–910

    CAS  Google Scholar 

  • Glémin S, Bazin E, Charlesworth D (2006) Impact of mating systems on patterns of sequence polymorphism in flowering plants. P R Soc B-Biol Sci 273:3011–3019

    Article  Google Scholar 

  • Huang XJ, Chen T, Liang QB, Chen J, Wang XR, Tang HR (2011) Preliminary evaluation on the economic characters of 14 cherry germplasms. South China Fruits 40:15–18

    Google Scholar 

  • Huang XJ, Wang XR, Chen T, Chen J, Tang HR (2012) Research progress of genetic diversity in Cerasus pseudocerasus and their wild relative populations, and utilize progress of cultivation resources. J Fruit Sci (In press)

  • Hurka H, Friesen N, German DA, Franzke A, Nenffer B (2012) ‘Missing link’ species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Mol Ecol 21:1223–1238

    Article  PubMed  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, NewYork, pp 21–132

    Google Scholar 

  • Li MM, Cai YL, Qian ZQ, Zhao GF (2009) Genetic diversity and differentiation in Chinese sour cherry Prunus pseudocerasus Lindl., and its implications for conservation. Genet Resour Crop Evol 56:455–464

    Article  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSPv5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  PubMed  CAS  Google Scholar 

  • Liu CJ, Liu MZ (1993) The seed identification of the relics from HouMa copper casting site Shaanxi. (Shaanxi Province archaeology institute) HouMa copper casting sites. Cultural relic press, Beijing

    Google Scholar 

  • Luan SS, Chiang TY, Xun G (2006) High genetic diversity vs. low genetic differentiation in Nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR finger printing. Ann Bot 98:583–589

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nei M, Tajima F (1983) Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105:207–217

    PubMed  CAS  Google Scholar 

  • Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155

    Article  PubMed  CAS  Google Scholar 

  • Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245

    PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425

    CAS  Google Scholar 

  • Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants: problems and prospects. Mol Ecol 7:465–474

    Article  Google Scholar 

  • Shaw J, Lickey BE, Schilling EE, Small LR (2007) Comparison of whole chloroplast genome sequences to choose non-coding regions for phylogenetic studies in angiosperms: the Tortoise and the Hare. Ame J Bot 94:275–288

    Article  CAS  Google Scholar 

  • Song CM, Wen XP, Yang ET (2011) Cherry germplasm from Guizhou Province analyzed by ISSR Markers. Acta Horticulturae Sinica 38:1531–1538

    CAS  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Bio Evol 28:2731–2739

    Article  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Wang FY, Gong X, Hu CM, Hap G (2008) Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation. J Syst Evol 46:l3–l22

    Google Scholar 

  • Wang LY, Abbott RJ, Zheng W, Chen P, Wang YJ, Liu JQ (2009) History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Mol Ecol l8:709–721

    Article  Google Scholar 

  • Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evol 19:395–420

    Article  Google Scholar 

  • Xun G, Luan SS, Hung KH, Hwang CC, Lin CJ, Chiang YC, Chiang TY (2011) Population structure of Nouelia insignis (Asteraceae), an endangered species in southwestern China, based on chloroplast DNA sequences: recent demographic shrinking. J Plant Res 124:221–230

    Article  Google Scholar 

  • Yü DJ, Li CL (1986) Flora of China, vol 38. Science Press, Beijing

    Google Scholar 

  • Yu Y, Downie SR, He X, Deng X, Yan L (2011) Phylogeny and biogeography of Chinese Heracleum (Apiaceae tribe Tordylieae) with comments on their fruit morphology. Plant Syst Evol 296:179–203

    Article  Google Scholar 

  • Yuan QJ, Zhang ZY, Peng H, Ge S (2008) Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Mol Ecol 17:1054–1065

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank the National Natural Science Foundation of China (30971990) and the Key Cultivation Special Project Foundation of Education Department of Sichuan Province (2011A005) for the grant.

Author information

Authors and Affiliations

  1. College of Horticulture, Sichuan Agricultural University, Xinkang Road #46, Ya’an City, 625014, Sichuan, China

    Tao Chen, Hao-ru Tang, Qing Chen, Xiao-jiao Huang & Jiao Chen

  2. Institute of Pomology and Olericulture, Sichuan Agricultural University, Huimin Road #211, Wenjiang, 611130, Chengdu, China

    Xiao-rong Wang & Hao-ru Tang

Authors
  1. Tao Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao-rong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hao-ru Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qing Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiao-jiao Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jiao Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiao-rong Wang.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chen, T., Wang, Xr., Tang, Hr. et al. Genetic diversity and population structure of Chinese Cherry revealed by chloroplast DNA trnQ-rps16 intergenic spacers variation. Genet Resour Crop Evol 60, 1859–1871 (2013). https://doi.org/10.1007/s10722-013-9960-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-013-9960-9

Keywords

Search

Navigation