Skip to main content
SpringerLink
Log in

Study on chloroplast DNA diversity of cultivated and wild pears (Pyrus L.) in Northern China

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

Abstract

Eight pairs of chloroplast DNA (cpDNA) universal primers selected from 34 pairs were used to assess the genetic diversity of 132 pear accessions in Northern China. Among them, six amplified cpDNA fragments showed genetic diversity. A total of 24 variable sites, including 1 singleton variable site and 23 parsimony informative sites, as well as 21 insertion-deletion fragments, were obtained from the combined cpDNA sequences (5309–5535 bp). Two trnL-trnF-487 haplotypes, five trnL-trnF-413 haplotypes, five rbcL haplotypes, six trnS-psbC haplotypes, eight accD-psaI haplotypes and 12 rps16-trnQ haplotypes were identified among the individuals. Twenty-one haplotypes were identified based on the combined fragments. The values of nucleotide diversity (Pi), average number of nucleotide differences (k) and haplotype diversity (Hd) were 0.00070, 3.56408 and 0.7960, respectively. No statistical significance was detected in Tajima’s D test. Remarkably, the important cpDNA haplotypes and their representing accessions were identified clearly in this study. H_19 was considered as one of the ancient haplotypes and was a divergent centre. H_16 was the most common haplotype of the wild accessions. H_2 was the haplotype representing the most pear germplasm resources (46 cultivars and two wild Ussurian Pear accessions), followed by haplotype H_5 (30 cultivars, two wild Ussurian Pear accessions and four sand pears in outgroups) representing the cultivars ‘Dangshan Suli’ and ‘Yali’, which harbour the largest and the second largest cultivation areas in China. More importantly, this study demonstrated, for the first time, the supposed evolution routes of Pyrus based on cpDNA divergence in the background of pear phylogeny in Northern China.

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
Fig. 6

Similar content being viewed by others

References

  • Bao L, Chen K, Zhang D, Cao Y, Yamamoto T, Teng Y (2007) Genetic diversity and similarity of pear cultivars native to East Asia revealed by SSR (simple sequence repeat) markers. Genet Resour Crop Evol 54:959–971

    Article  CAS  Google Scholar 

  • 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 116:374–380

    Article  CAS  Google Scholar 

  • Bell R, Quamme H, Layne R, Skirvin R (1996) Pears. In: Janick J, Moore JN (eds) Fruit breeding, vol 1: tree and tropical fruits. Wiley, New York, pp 441–514

    Google Scholar 

  • Cao Y (2014) Pear varieties in China. China Agriculture Press, Beijing (in Chinese)

    Google Scholar 

  • Cao Y, Liu F, Gao Y, Jiang L, Wang K, Ma Z, Zhang K (2007) SSR analysis of genetic diversity of pear cultivars. Acta Horticulturae Sinica 34:305–310 (in Chinese)

    CAS  Google Scholar 

  • Cao Y, Tian L, Gao Y, Liu F (2012) Genetic diversity of cultivated and wild Ussurian Pear (Pyrus ussuriensis Maxim.) in China evaluated with M13-tailed SSR markers. Genet Resour Crop Evol 59:9–17

    Article  CAS  Google Scholar 

  • Challice J, Westwood M (1973) Numerical taxonomic studies of the genus Pyrus using both chemical and botanical characters. Bot J Linn Soc 67(2):121–148

    Article  Google Scholar 

  • Chang Y, Cao Y, Zhang J, Tian L, Dong X, Zhang Y, Qi D (2014) Studies on genetic diversity of pear germplasm resources in Liaoning province of China based on chloroplast DNA analysis. Acta Horticulturae Sinica 41(7):1307–1316 (in Chinese)

    CAS  Google Scholar 

  • Clegg M, Zurawski G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman and Hall, New York, pp 1–13

    Chapter  Google Scholar 

  • Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659

    Article  CAS  PubMed  Google Scholar 

  • Cornuet J, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin J, Estoup A (2014) DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30(8):1187–1189

    Article  CAS  PubMed  Google Scholar 

  • Demesure B, Sodzi N, Petit R (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4:129–134

    Article  CAS  PubMed  Google Scholar 

  • Downie S, Palmer J (1992) Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman and Hall, New York, pp 14–35

    Chapter  Google Scholar 

  • Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19:11–15

    Google Scholar 

  • Doyle J, Davis J, Soreng R, Garvin D, Anderson M (1992) Chloroplast inversion and the origin of the grass family (Poaceae). Proc Natl Acad Sci U S A 89:7722–7726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dumolin-Lapegue S, Pemonge M, Petit R (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 6:393–397

    Article  CAS  PubMed  Google Scholar 

  • He Z, Wu B, Yang Q (2011) Identification of Pyrus sinkiangensis and classification discussion of ‘Korla pear’. Shanxi Fruits 5:36–39 (in Chinese)

    Google Scholar 

  • Iketani H, Manabe T, Matsuta N, Akihama T, Hayashi Y (1998) Incongruence between RFLPs of chloroplast DNA and morphological classification in east Asian pear (Pyrus spp). Genet Resour Crop Evol 45:533–539

    Article  Google Scholar 

  • Jing Z (1989) The origin and development of Pingguoli. Northern Horticulture 1:21–22 (in Chinese)

    Google Scholar 

  • Katayama H, Ogihara Y (1996) Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Curr Genet 20:527–581

    Google Scholar 

  • Katayama H, Uematsu C (2003) Comparative analysis of chloroplast DNA in Pyrus species: physical map and gene localization. Theor Appl Genet 106:303–310

    Article  CAS  PubMed  Google Scholar 

  • 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 Evol 54:1573–1585

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Kelchner S, Clark L (1997) Molecular evolution and phylogenetic utility of the chloroplast rpII6 intron in Chusquea and the Bambusoideae (Poaceae). Mol Phylogenet Evol 8:385–397

    Article  CAS  PubMed  Google Scholar 

  • Kimura T, Iketani H, Kotobuki K, Matsuta N, Ban Y, Hayashi T, Yamamoto T (2003) Genetic characterization of pear varieties revealed by chloroplast DNA sequences. J Hortic Sci Biotechnol 78:241–247

    Article  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  PubMed  Google Scholar 

  • Liu Y (2006) Research on chloroplast DNA diversity of genus pear in China. Master Dissertation. Capital Normal University, Beijing. (in Chinese)

  • 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

    Article  Google Scholar 

  • 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(2):433–441

    Article  Google Scholar 

  • Lu F, Zhang Y (2009) Taxonomic status identification of Ping guo pear by AFLP molecular marker. J Anhui Agric Sci 37:1937–1938 (in Chinese)

    Google Scholar 

  • Lu J, Wu J, Zhang S, Wu H, Zhang Y (2011) Genetic diversity and polygentic relationship among pears revealed by SSR analysis. J Nanjing Agric Univ 34(2):38–46 (in Chinese)

    CAS  Google Scholar 

  • Ma Y, Zhang Y (2009) The application of RAPD in status identification of ‘Pingguoli’. Chin Agric Sci Bull 25:71–73 (in Chinese)

    Google Scholar 

  • Ma B, Niu J, Pan L, Feng J, Lu X (2004a) Study on the genetic relationships among 18 pear cultivars by RAPD. J Fruit Sci 21(6):521–525 (in Chinese)

    Google Scholar 

  • Ma B, Niu J, Wu Z, Tan W (2004b) Molecular markers analysis of main cultivars relationship between Pyrus in Xinjiang. J Shihezi Univ (Nat Sci) 22(2):97–102 (in Chinese)

    CAS  Google Scholar 

  • Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M et al (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 8(10):e77022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nei M, Li W (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Palmer J, Jorgensen R, Thompson W (1985) Chloroplast DNA variation and evolution in Pisum; patterns of change and phylogenetic analysis. Genetics 109:195–213

    CAS  PubMed  PubMed Central  Google Scholar 

  • Parani M, Lakshmi M, Ziegenhagen B, Fladung M, Senthilkumar P, Parida A (2000) Molecular phylogeny of mangroves VII PCR-RFLP of trnS-psbC and rbcL gene regions in 24 mangrove and mangrove-associate species. Theor Appl Genet 100:454–460

    Article  CAS  Google Scholar 

  • Parducci L, Szmidt A (1999) PCR-RFLP analysis of cpDNA in the genus Abies. Theor Appl Genet 98:802–808

    Article  CAS  Google Scholar 

  • Petit R, Kremar A, Wagner D (1993) Geographic structure of chloroplast DNA polymorphisms in European oaks. Theor Appl Genet 87:122–128

    Article  CAS  PubMed  Google Scholar 

  • Pu F, Wang Y (1963) Pomology of China. Pears, vol 3. Shanghai Science and Technology Press, Shanghai (in Chinese)

    Google Scholar 

  • Pu F, Lin S, Song W, Chen R, Li X (1985) Research on the karyotypes of Pyrus in China I. Plant Sci J 3(4):381–387 (in Chinese)

    Google Scholar 

  • Pu F, Lin S, Chen R, Song W, Li X (1986) Research on the karyotypes of Pyrus in China II. Acta Horticulturae Sinica 13(2):87–90 (in Chinese)

    Google Scholar 

  • Qu Z, Pan J, Shan Z (1990) The log of Beijing fruit tree. Beijing Press, Beijing, pp 239–240 (in Chinese)

    Google Scholar 

  • Qu B, Jin X, Chen Y, Liu H, Wang P (2001) RAPD analysis of germplasm resources in Pyrus. Acta Horticulturae Sinica 28:460–462 (in Chinese)

    Google Scholar 

  • Qu B, Jin X, Chen Y, Liu H, Wang P (2002) Classification study of Pingguoli in Yanbian area using RAPD markers. Progress Hortic 5:178–182 (in Chinese)

    Google Scholar 

  • Qu B, Jin X, Chen Y, Liu H, Wang P, Zheng D (2003) Classification study of Pingguoli in Yanbian area by using RAPD markers. J Jilin Agric Univ 25:292–295 (in Chinese)

    Google Scholar 

  • Rubtsov G (1944) Geographical distribution of the genus Pyrus and trends and factors in its evolution. Am Nat 78:358–366

    Article  Google Scholar 

  • Sehic J, Garkava-Gustavsson L, Fernández-Fernández F, Nybom H (2012) Genetic diversity in a collection of European pear (Pyrus communis) cultivars determined with SSR markers chosen by ECPGR. Sci Hortic 145:39–45

    Article  CAS  Google Scholar 

  • Shan J, Li J, Luo S, Cheng Q, Li C (2010) Analysis of genetic relationships of pear germplasm resources in Xinjiang based on ISSR and RAPD. Xinjiang Agric Sci 47(9):1714–1721 (in Chinese)

    CAS  Google Scholar 

  • Shen Y, Teng Y, Tanabe K (2006) RAPD analysis for genetic assessment of some cultivars of Pyrus pyrifolia derived from China and Japan. Acta Horticulturae Sinica 33(3):621–624 (in Chinese)

    CAS  Google Scholar 

  • Small R, Ryburn J, Cronn R, Seelanan T, Wendel J (1998) The tortoise and the hare: choosing between non-coding plastome and nuclear ADH sequences for phylogeny reconstruction in recently diverged plant group. Am J Bot 85:1301–1345

    Article  CAS  PubMed  Google Scholar 

  • Swofford D (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland MA. (Program)

  • Taberlet P, Gielly L, Pauton G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Teng Y, Tanabe K, Tamura F, Itai A (2001) Genetic relationships of pear cultivars in Xinjiang, China as measured by RAPD markers. J Hortic Sci Biotechnol 76:771–779

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Urrestarazu J, Royo J, Santesteban L, Miranda C (2015) Evaluating the influence of the microsatellite markerset on the genetic structure inferred in Pyrus communis L. PLoS One 10(9):e0138417

    Article  PubMed  PubMed Central  Google Scholar 

  • Vavilov N (1951) The origin, variation, immunity and breeding of cultivated plants. Chronica Botanica 13:1–366

    Google Scholar 

  • Wang Y (1988) Deciduous fruit tree breeding. Press of Agriculture, Beijing, pp 192–193 (in Chinese)

    Google Scholar 

  • Wu G (1984) The taxonomy of temperate-zone fruit trees in China. Press of Agriculture, Beijing, pp 33–80 (in Chinese)

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet 102:865–887

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002b) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106:9–18

    Article  CAS  PubMed  Google Scholar 

  • Yang H (1985) The application of palynology in the taxonomy of some plants in Pyrus. Fruit Sci 3:2–9 (in Chinese)

    Google Scholar 

  • Yang C (2010) Genetic diversity of cytoplasm heredity in some main cultivars of Pyrus. Master Dissertation. Shihezi University, Xinjiang. (in Chinese)

  • Yang L, Li W, Qu B (2010) The classification discussion of ‘Pingguoli’. J Agric Sci Yanbian Univ 32:73–76 (in Chinese)

    Google Scholar 

  • Yao L, Zheng X, Cai D, Gao Y, Wang K, Cao Y, Teng Y (2010) Exploitation of Malus EST-NSSRs and the utility in evaluation of genetic diversity in Malus and Pyrus. Genet Resour Crop Evol 57:841–851

    Article  CAS  Google Scholar 

  • Yu D (1979) Taxonomy of the fruit tree in China. Agriculture Press, Beijing (in Chinese)

    Google Scholar 

  • Zhang J, Chen Q, Cao Y, Yang X, Fan J, Hu H (2016) Genetic diversty and phylogenetics of pear (Pyrus L.) germplasm resources from Hubei province revealed by chloroplast DNA variation. J Genet Resour 17(4):766–772 (in Chinese)

    Google Scholar 

  • Zong Y, Sun P, Liu J, Yue X, Niu Q, Teng Y (2014) Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China. Tree Genet Genomes 10:739–749

    Article  Google Scholar 

  • Zou L, Zhang X, Zhang Z, Song B, Guo S (1986) Research on genetic relationships of Pyrus based on pollen morphology. Acta Horticulturae Sinica 13(4):219–224 (in Chinese)

    Google Scholar 

Download references

Acknowledgements

The study was sponsored by the National Natural Science Foundation of China (grant No. 31272128).

Data archiving statement

The authors declare that all the work described in this manuscript followed the standard Tree Genetics and Genomes policy. The sequences will be uploaded soon, and all the sequences in this study will be found in the National Center of Biotechnology Information (NCBI) database.

Author information

Authors and Affiliations

  1. Research Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture, Xinghai South Street 98, Xingcheng, 125100, People’s Republic of China

    Yao-Jun Chang, Yu-Fen Cao, Lu-Ming Tian, Xing-Guang Dong, Ying Zhang, Dan Qi & Xiao-shuang Zhang

  2. National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street 12, Haidian, Beijing, 100081, People’s Republic of China

    Jin-Mei Zhang

Authors
  1. Yao-Jun Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu-Fen Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jin-Mei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lu-Ming Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xing-Guang Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dan Qi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiao-shuang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yu-Fen Cao.

Additional information

Communicated by D. Chagné

Electronic supplementary material

.

Table S1

(DOCX 22 kb)

.

Table S2

(DOCX 19 kb)

.

Table S3

(DOCX 19 kb)

.

Table S4

(DOCX 19 kb)

.

Table S5

(DOCX 20 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chang, YJ., Cao, YF., Zhang, JM. et al. Study on chloroplast DNA diversity of cultivated and wild pears (Pyrus L.) in Northern China. Tree Genetics & Genomes 13, 44 (2017). https://doi.org/10.1007/s11295-017-1126-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-017-1126-z

Keywords

Search

Navigation