Skip to main content

Advertisement

Log in

A range wide geographic pattern of genetic diversity and population structure of Castanea mollissima populations inferred from nuclear and chloroplast microsatellites

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Understanding geographical pattern of genetic diversity and population structure is of great importance for formulating conservation and utilization strategies. In this study, we investigated the genetic diversity and population structure of 28 natural populations of Castanea mollissima in China using eight nuclear and six chloroplast microsatellite makers (nSSRs and cpSSRs). Populations from central China harbored the highest genetic diversity at both nSSR and cpSSR markers (nSSR: H E = 0.705; cpSSR: H = 0.461). The standardized measure of genetic differentiation estimated as G′ ST was 0.447 for nSSR and 0.803 for cpSSR, respectively. The GST-based pollen to seed flow ratio is 3.043, indicating that pollen flow is not extensive among C. mollissima populations. No obvious population genetic structure by geographical locations was found by STRUCTURE analysis based on nSSR data, and similarly, no signal of phylogeographic structure was detected for cpSSR analysis. Five boundaries defining zones of maximum genetic differences within the network of the C. mollissima populations were found, and the locations of those barriers were consistent with those of four mountains, i.e., Daloushan Mountain, Dabashan Mountain, Wushan Mountain, and Qingliangfeng Mountain, indicating that those mountains might act as genetic barriers obstructing the genetic exchange among natural C. mollissima populations. These results provide valuable baseline data for conservation and utilization of this species.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Anagnostakis SL (1992) Measuring resistance of chestnut trees to chestnut blight. Can J For Res 22:568–571

    Article  Google Scholar 

  • Barakat A, DiLoreto D, Zhang Y, Smith C, Baier K, Powell W, Wheeler N, Sederoff R, Carlson J (2009) Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 9:51

    Article  PubMed  Google Scholar 

  • Bohonak A (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93:153–154

    Article  PubMed  CAS  Google Scholar 

  • Burnham CR (1988) The restoration of the American chestnut: Mendelian genetics may solve a problem that has resisted other approaches. Am Sci 76:478–487

    Google Scholar 

  • Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  PubMed  CAS  Google Scholar 

  • Crawford NG (2010) SMOGD: software for the measurement of genetic diversity. Mol Ecol Resour 10:556–557

    Article  PubMed  Google Scholar 

  • Crow JF (2002) Perspective: here's to Fisher, additive genetic variance, and the fundamental theorem of natural selection. Evolution 56:1313–1316

    PubMed  Google Scholar 

  • Dane F, Lang P, Huang HW, Fu Y (2003) Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America. Heredity 91:314–321

    Article  PubMed  CAS  Google Scholar 

  • Deguilloux MF, Dumolin-Lapègue S, Gielly L, Grivet D, Petit R (2003) A set of primers for the amplification of chloroplast microsatellites in Quercus. Mol Ecol Notes 3:24–27

    Article  CAS  Google Scholar 

  • Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem bull 19:11–15

    Google Scholar 

  • Duminil J, Fineschi S, Hampe A, Jordano P, Salvini D, Vendramin GG, Petit RJ (2007) Can population genetic structure be predicted from life-history traits? Am Nat 169:662–672

    Article  PubMed  Google Scholar 

  • Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11:2571–2581

    Article  PubMed  CAS  Google Scholar 

  • El Mousadik A, Petit R (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Mol Ecol 5:547–555

    Article  PubMed  CAS  Google Scholar 

  • Ennos R (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72:250–259

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • Fineschi S, Taurchini D, Villani F, Vendramin G (2000) Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern European countries. Mol Ecol 9:1495–1503

    Article  PubMed  CAS  Google Scholar 

  • Fontaine C, Lovett P, Sanou H, Maley J, Bouvet J (2004) Genetic diversity of the shea tree (Vitellaria paradoxa CF Gaertn), detected by RAPD and chloroplast microsatellite markers. Heredity 93:639–648

    Article  PubMed  CAS  Google Scholar 

  • Goodman SJ (1997) R ST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol Ecol 6:881–885

    Article  CAS  Google Scholar 

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9. 3). Available from http://www2.unil.ch/popgen/softwares/fstat.htm

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

    Article  Google Scholar 

  • Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638

    PubMed  CAS  Google Scholar 

  • Hu LJ, Uchiyama K, Shen HL, Saito Y, Tsuda Y, Ide Y (2008) Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across north-east China. Ann Bot 102:195–205

    Article  PubMed  Google Scholar 

  • Huang HW (1998) Review of current research of the world Castanea species and importance of germplasm conservation of China native Castanea species. J Wuhan Bot Res 16:171–176

    Google Scholar 

  • Huang HW, Dane F, Kubisiak TL (1998) Allozyme and RAPD analysis of the genetic diversity and geographic variation in wild populations of the American chestnut (Fagaceae). Am J Bot 85:1013–1021

    Article  PubMed  CAS  Google Scholar 

  • Huang HW, Dane F, Norton JD (1994) Allozyme diversity in Chinese, Seguin and American chestnut (Castanea spp.). Theor Appl Genet 88:981–985

    Article  Google Scholar 

  • Jump AS, Penuelas J (2005) Running to stand still: adaptation and the response of plants to rapid climate change. Ecol Lett 8:1010–1020

    Article  Google Scholar 

  • Kubisiak TL, Hebard F, Nelson CD, Zhang J, Bernatzky R, Huang HW, Anagnostakis S, Doudrick R (1997) Molecular mapping of resistance to blight in an interspecific cross in the genus Castanea. Phytopathology 87:751–759

    Article  PubMed  CAS  Google Scholar 

  • Lang P, Huang HW (1999) Genetic diversity and geographic variation in natural populations of the endemic Castanea species in China. Acta Bot Sin 41:651–657

    CAS  Google Scholar 

  • Liu YC (2000) Flora geography of national wild conservative plants in Chongqiong. J Southwest China Norm Univ (Nat Sci) 25:439–447

    Article  Google Scholar 

  • Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12:228–237

    Article  Google Scholar 

  • Magri D, Vendramin GG, Comps B, Dupanloup I, Geburek T, Gömöry D, Latałowa M, Litt T, Paule L, Roure JM (2006) A new scenario for the Quaternary history of European beech populations: palaeobotanical evidence and genetic consequences. New Phytol 171:199–221

    Article  PubMed  CAS  Google Scholar 

  • Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197

    Article  Google Scholar 

  • Manni F, Guerard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Hum Biol 76:173–190

    Article  PubMed  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Marinoni D, Akkak A, Bounous G, Edwards KJ, Botta R (2003) Development and characterization of microsatellite markers in Castanea sativa (Mill.). Mol Breeding 11:127–136

    Article  CAS  Google Scholar 

  • Martín MA, Mattioni C, Molina JR, Alvarez JB, Cherubini M, Herrera MA, Villani F, Martín LM (2012) Landscape genetic structure of chestnut (Castanea sativa Mill.) in Spain. Tree Genet Genomes 8:127–136

    Article  Google Scholar 

  • Martin MA, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers. Tree Genet Genomes 6:735–744

    Article  Google Scholar 

  • Martins K, Chaves L, Vencovsky R, Kageyama P (2011) Genetic structure based on nuclear and chloroplast microsatellite loci of Solanum lycocarpum A. St. Hil. (Solanaceae) in Central Brazil. Genet Mol Res 10:665–677

    Article  PubMed  CAS  Google Scholar 

  • Mattioni C, Cherubini M, Micheli E, Villani F, Bucci G (2008) Role of domestication in shaping Castanea sativa genetic variation in Europe. Tree Genet Genomes 4:563–574

    Article  Google Scholar 

  • Monmonier MS (1973) Maximum-difference barriers: an alternative numerical regionalization method*. Geogr Anal 5:245–261

    Article  Google Scholar 

  • Ministry of environmental protection (2011) China national biodiversity conservation strategy and action plan. China Environmental Science Press, Beijing

    Google Scholar 

  • Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York

    Google Scholar 

  • Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170

    Article  PubMed  CAS  Google Scholar 

  • Newton A, Allnutt T, Dvorak W, Del Castillo R, Ennos RA (2002) Patterns of genetic variation in Pinus chiapensis, a threatened Mexican pine, detected by RAPD and mitochondrial DNA RFLP markers. Heredity 89:191–198

    Article  PubMed  CAS  Google Scholar 

  • Ohsawa T, Tsuda Y, Saito Y, Ide Y (2011) The genetic structure of Quercus crispula in northeastern Japan as revealed by nuclear simple sequence repeat loci. J Plant Res 124:645–654

    Article  PubMed  Google Scholar 

  • Parker IM, Gilbert GS (2004) The evolutionary ecology of novel plant-pathogen interactions. Annu Rev Ecol Evol Syst 35:675–700

    Article  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855

    Article  Google Scholar 

  • Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701

    Article  PubMed  CAS  Google Scholar 

  • Piry S, Luikart G, Cornuet J-M (1999) Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J Hered 90:502–503

    Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Sanguinetti C, Dias NE, Simpson A (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:914–921

    PubMed  CAS  Google Scholar 

  • Sebastiani F, Carnevale S, Vendramin G (2004) A new set of mono-and dinucleotide chloroplast microsatellites in Fagaceae. Mol Ecol Notes 4:259–261

    Article  CAS  Google Scholar 

  • Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787–792

    Article  PubMed  CAS  Google Scholar 

  • Storfer A, Murphy M, Evans J, Goldberg C, Robinson S, Spear S, Dezzani R, Delmelle E, Vierling L, Waits L (2007) Putting the ‘landscape’in landscape genetics. Heredity 98:128–142

    Article  PubMed  CAS  Google Scholar 

  • Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453–464

    Article  PubMed  CAS  Google Scholar 

  • Takahashi T, Tani N, Niiyama K, Yoshida S, Taira H, Tsumura Y (2008) Genetic succession and spatial genetic structure in a natural old growth Cryptomeria japonica forest revealed by nuclear and chloroplast microsatellite markers. Forest Ecol Manag 255:2820–2828

    Article  Google Scholar 

  • Tanaka T, Yamamoto T, Suzuki M (2005) Genetic diversity of Castanea crenata in northern Japan assessed by SSR markers. Breeding Sci 55:271–277

    Article  CAS  Google Scholar 

  • Tsuda Y, Ide Y (2010) Chloroplast DNA phylogeography of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in Japan. J Plant Res 123:343–353

    Article  PubMed  CAS  Google Scholar 

  • Tsuda Y, Sawada H, Ohsawa T, Nakao K, Nishikawa H, Ide Y (2010) Landscape genetic structure of Betula maximowicziana in the Chichibu mountain range, central Japan. Tree Genet Genomes 6:377–387

    Article  Google Scholar 

  • Villani F, Pigliucci M, Benedettelli S, Cherubini M (1991) Genetic differentiation among Turkish chestnut (Castanea sativa Mill.) populations. Heredity 66:131–136

    Article  Google Scholar 

  • Wang J, Gao PX, Kang M, Lowe AJ, Huang HW (2009) Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China. J Biogeogr 36:2156–2164

    Article  Google Scholar 

  • Wang R, Compton SG, Chen X-Y (2011) Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree. Mol Ecol 20:4421–4432

    Article  PubMed  Google Scholar 

  • Wang WT (1992) On some distribution patterns and some migration routes found in the eastern Asiatic region. Acta Phytotaxon Sin 30:1–24

    CAS  Google Scholar 

  • Wang Y, Kang M, Huang HW (2008) Microsatellite loci transferability in chestnut. J Am Soc Hort Sci 133:692–700

    Google Scholar 

  • Wheeler N, Sederoff R (2009) Role of genomics in the potential restoration of the American chestnut. Tree Genet Genomes 5:181–187

    Article  Google Scholar 

  • Xu DY (2003) An analysis of seed plants floral composition in Dabashan Nature Reserve. J Southwest China Norm Univ (Nat Sci) 28:963–968

    Google Scholar 

  • Yamamoto T, Tanaka T, Kotobuki K, Matsuta N, Suzuki M, Hayashi T (2003) Characterization of simple sequence repeats in Japanese chestnut. J Hortic Sci Biotech 78:197–203

    CAS  Google Scholar 

  • Ying JS (2001) Genetic diversity and distribution pattern of seed plants in China. Biodiv Sci 9:393–398

    Google Scholar 

  • Zheng Z (1983) The characteristics of the flora and an outline of the distribution of plants in Hubei Province, People's Republic of China. J Wuhan Bot Res 1:165–175

    Google Scholar 

Download references

Acknowledgments

We thank two anonymous reviewers for their valuable suggestions and critical comments on the earlier version of the manuscript. This project was funded by the National Science Foundation of China (30771479) and key initiative grant of the Chinese Academy of Sciences (KSCX2-YW-N-061).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hongwen Huang.

Additional information

Communicated by A. Kremer

W. Liu and M. Kang contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, W., Kang, M., Tian, H. et al. A range wide geographic pattern of genetic diversity and population structure of Castanea mollissima populations inferred from nuclear and chloroplast microsatellites. Tree Genetics & Genomes 9, 975–987 (2013). https://doi.org/10.1007/s11295-013-0610-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-013-0610-3

Keywords

Navigation