Abstract
Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H T = 0.826). A significant isolation-by-distance value (r = 0.587, P < 0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.
Similar content being viewed by others
References
Bai WN, Liao WJ, Zhang DY (2010) Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia. New Phytol 188:892–901
Bao L, Chen K, Zhang D, Li X, Teng Y (2008) An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers. Sci Hortic-Amst 116:374–380
Bassil N, Postman JD (2010) Identification of European and Asian pears using EST-SSRs from Pyrus. Genet Resour Crop Ev 57:357–370
Caicedo AL, Schaal BA (2004) Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Mol Ecol 13:1871–1882
Calvino CI, Martinez SG, Downie SR (2008) The evolutionary history of Eryngium (Apiaceae, Saniculoideae): rapid radiations, long distance dispersals, and hybridizations. Mol Phylogenet Evol 46:1129–1150
Campbell CS, Evans RC, Morgan DR, Dickinson TA, Arsenault MP (2007) Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): limited resolution of a complex evolutionary history. Plant Syst Evol 266:119–145
Cao YF, Tian LM, Gao Y, Liu FZ (2012) Genetic diversity of cultivated and wild Ussurian pear (Pyrus ussuriensis Maxim.) in China evaluated with M13-tailed SSR markers. Genet Resour Crop Ev 59:9–17
Challice JS, Westwood MN (1973) Numerical taxonomic studies of the genus Pyrus using both chemical and botanical characters. Bot J Linn Soc 67:121–148
Chen K, Abbott RJ, Milne RI, Tian XM, Liu J (2008) Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China. Mol Ecol 17:4276–4288
Clegg MT, Brandon SG Jr, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci U S A 91:6795–6801
Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659
Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959–969
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Duan J, Fu B, Wang B, Yang J, Pang L, Kang H, Li Y (2008) Wild fruit germplasm resources in Shanxi Province (in Chinese). J Fruit Sci 25:1–5
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 10:564–567
Fernie AR, Tadmor Y, Zamir D (2006) Natural genetic variation for improving crop quality. Curr Opin Plant Biol 9:196–202
Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13:167–173
Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1–13
Harpending HC (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66:591–600
Harrison SP, Yu G, Takahara H, Prentice IC (2001) Diversity of temperate plants in east Asia. Nature 413:129–130
Heuertz M, Fineschi S, Anzidei M, Pastorelli R, Salvini D, Paule L, Frascaria-Lacoste N, Hardy OJ, Vekemans X, Vendramin GG (2004) Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol 13:3437–3452
Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913
Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philos T Roy Soc B 359:183–195
Heywood V, Casas A, Ford-Lloyd B, Kell S, Maxted N (2007) Conservation and sustainable use of crop wild relatives. Agr Ecosyst Environ 121:245–255
Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, Johnson JB, Rissler L, Victoriano PF, Yoder AD (2010) Phylogeography's past, present, and future: 10 years after Avise, 2000. Mol Phylogenet Evol 54:291–301
Honnay O, Jacquemyn H, Aerts R (2012) Crop wild relatives: more common ground for breeders and ecologists. Front Ecol Environ 10:121
Iketani H, Manabe T, Matsuta N, Akihama T, Hayashi T (1998) Incongruence between RFLPs of chloroplast DNA and morphological classification in east Asian pear (Pyrus spp.). Genet Resour Crop Ev 45:533–539
Jarvis DI, Hodgkin T (1999) Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Mol Ecol 8:159–173
Katayama H, Adachi S, Yamamoto T, Uematsu C (2007) A wide range of genetic diversity in pear (Pyrus ussuriensis var. aromatica) genetic resources from Iwate, Japan revealed by SSR and chloroplast DNA markers. Genet Resour Crop Ev 54:1573–1585
Katayama H, Tachibana M, Iketani H, Zhang S, Uematsu C (2012) Phylogenetic utility of structural alterations found in the chloroplast genome of pear: hypervariable regions in a highly conserved genome. Tree Genet Genomes 8:313–326
Kato S, Imai A, Rie N, Mukai Y (2013) Population genetic structure in a threatened tree, Pyrus calleryana var. dimorphophylla revealed by chloroplast DNA and nuclear SSR locus polymorphisms. Conserv Genet 14:983–996
Lenne JM, Wood D (1991) Plant diseases and the use of wild germplasm. Annu Rev Phytopathol 29:35–63
Li E, Yi S, Qiu Y, Guo J, Comes HP, Fu C (2008) Phylogeography of two East Asian species in Croomia (Stemonaceae) inferred from chloroplast DNA and ISSR fingerprinting variation. Mol Phylogenet Evol 49:702–714
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452
Linder HP (2008) Plant species radiations: where, when, why? Philos T Roy Soc B 363:3097–3105
Liu J, Sun P, Zheng X, Potter D, Li K, Hu C, Teng Y (2013) Genetic structure and phylogeography of Pyrus pashia L. (Rosaceae) in Yunnan Province, China, revealed by chloroplast DNA analyses. Tree Genet Genomes 9:433–441
Liu J, Zheng X, Potter D, Hu C, Teng Y (2012) Genetic diversity and population structure of Pyrus calleryana (Rosaceae) in Zhejiang province, China. Biochem Syst Ecol 45:69–78
Lo EY, Stefanovic S, Christensen KI, Dickinson TA (2009) Evidence for genetic association between East Asian and western North American Crataegus L. (Rosaceae) and rapid divergence of the eastern North American lineages based on multiple DNA sequences. Mol Phylogenet Evol 51:157–168
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
Maxted N, Scholten M, Codd R, Ford-Lloyd B (2007) Creation and use of a national inventory of crop wild relatives. Biol Conserv 140:142–159
Meilleur BA, Hodgkin T (2004) In situ conservation of crop wild relatives: status and trends. Biodivers Conserv 13:663–684
Miller MP (2005) Alleles in space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. J Hered 96:722–724
Moritz C (1994) Applications of mitochondrial DNA analysis in conservation: a critical review. Mol Ecol 3:401–411
Newton AC, Allnutt TR, Gillies A, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol Evol 14:140–145
Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Mol Ecol 18:1034–1347
Oddou-Muratorio S, Petit RJ, Le Guerroue B, Guesnet D, Demesure B (2001) Pollen- versus seed-mediated gene flow in a scattered forest tree species. Evolution 55:1123–1135
Okubo M, Sakuratani T (2000) Effects of sodium chloride on survival and stem elongation of two Asian pear rootstock seedlings. Sci Hortic-Amst 85:85–90
Petit R, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Muller-Starck G, Demesure-Musch B, Palme A, Martin JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563–1565
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
Pimentel D, Wilson C, McCullum C, Huang R, Dwen P, Flack J, Tran Q, Saltman T, Cliff B (1997) Economic and environmental benefits of biodiversity. Bioscience 47:747–757
Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245
Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16:37–45
Posada D, Crandall KA, Templeton AR (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487–488
Pu F (1988) Study on pear germplasm resources (in Chinese). China Fruits 12:42–46
Pu F, Wang Y (1963) Pomology of China, vol 3. Pears (in Chinese). Shanghai, Shanghai Science and Technology
Qian H, Ricklefs RE (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407:180–182
Qiu YX, Fu CX, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora. Mol Phylogenet Evol 59:225–244
Robbani M, Banno K, Yamaguchi K, Fujisawa N, Liu JY, Kakegawa M (2006) Selection of dwarfing pear rootstock clones from Pyrus betulaefolia and P. calleryana seedlings. J Jpn Soc Hortic Sci 75:1–10
Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608–615
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569
Rubtsov GA (1944) Geographical distribution of the genus Pyrus and trends and factors in its evolution. Am Nat 78:358–366
Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079–1089
Shang F, Wang P, Feng G (1998) Study on the characteristics and causes of formation of plant diversity in the Funiu Mountains transition region (in Chinese). J Henan Univ (Nat Sci) 28:54–60
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562
Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85:1301–1315
Tamura F (2012) Recent advances in research on Japanese pear rootstocks. J Jpn Soc Hortic Sci 81:1–10
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 Biol Evol 665:2731–2739
Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066
Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140:767–782
Teng Y, Tanabe K, Tamura F, Itai A (2002) Genetic relationships of Pyrus species and cultivars native to East Asia revealed by randomly amplified polymorphic DNA markers. J Am Soc Hortic Sci 127:262–270
Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822
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 25:4876–4882
Tian B, Liu R, Wang L, Qiu Q, Chen K, Liu J (2009) Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum. J Biogeogr 36:2148–2155
Wang YL, Li X, Guo J, Guo ZG, Li SF, Zhao GF (2010) Chloroplast DNA phylogeography of Clintonia udensis Trautv. & Mey. (Liliaceae) in East Asia. Mol Phylogenet Evol 55:721–732
Watanabe K, Kajita T, Murata J (2006) Chloroplast DNA variation and geographical structure of the Aristolochia kaempferi group (Aristolochiaceae). Am J Bot 93:442–453
Wuyun T, Ma T, Uematsu C, Katayama H (2013) A phylogenetic network of wild Ussurian pears (Pyrus ussuriensis Maxim.) in China revealed by hypervariable regions of chloroplast DNA. Tree Genet Genomes 9:167–177
Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002a) Simple sequence repeats for genetic analysis in pear. Euphytica 124:129–137
Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002b) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2:14–16
Yao LH, Zheng XY, Cai DY, Gao YA, Wang K, Cao YF, Teng YW (2010) Exploitation of Malus EST-SSRs and the utility in evaluation of genetic diversity in Malus and Pyrus. Genet Resour Crop Ev 57:841–851
Yu T (1979) Taxonomy of the fruit tree in China (in Chinese). China Agriculture, Beijing
Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–989
Zhang J, Zeng Y (2000) Plant diversity and protection of Funiu Mountains (in Chinese). J Henan Univ (Nat Sci) 30:76–81
Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ (2005) Phylogeography of the Qinghai–Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol Ecol 14:3513–3524
Zong Y, Sun P, Niu Q, Teng Y (2013) Distribution situation and assessment of morphological diversity of wild Pyrus betulaefolia in Northern China (in Chinese). J Fruit Sci 30:918–923
Acknowledgments
This work was supported by the National Natural Science Foundation of China (No. 30871690), Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20110101110091), and Specialized Research Fund for Major Science and Technique of Zhejiang Province of China (No. 2012C12904-2).
Data archiving statement
The accD–psaI and trnL–trnF sequences have been submitted to GeneBank and the accession numbers were from KF771383 to KF771402.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by D. Chagné
Electronic supplementary material
Below is the link to the electronic supplementary material.
Fig. S1
Mismatch distribution analysis for 18 populations of Pyrus betulaefolia. The observed number of differences between pairs of haplotypes is plotted with a dashed line. The solid line indicates the expected distribution under a sudden expansion model. (JPEG 1262 kb)
Fig. S2
Haplotype networks of Pyrus betulaefolia constructed in TCS under the 95% statistical parsimony criterion. The nineteen haplotypes H1–H19 are represented by different colors. Small, open circles represent missing haplotypes. Both solid and dot lines represent single mutant events, dot lines showed the resolved loops in the nested clade analysis. Numbers labeled on the branches indicate the locations of mutant nucleotides. (JPEG 2180 kb)
Table S1
(DOC 30 kb)
Rights and permissions
About this article
Cite this article
Zong, Y., Sun, P., Liu, J. et al. Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China. Tree Genetics & Genomes 10, 739–749 (2014). https://doi.org/10.1007/s11295-014-0718-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11295-014-0718-0