Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers

  • 649 Accesses

  • 20 Citations

Abstract

Genetic diversity and phylogenetic relationships among 48 pear accessions belonging to six species were determined using 23 morphological traits and 20 simple sequence repeat (SSR) primers. To assess the genetic diversity, data on morphological (both quantitative and qualitative) traits were recorded during 2010–2012 using standard pear descriptors. It was observed that the traits ratio of fruit length to diameter, persistency of calyx on mature fruits and fruit surface and pulp texture were important in detecting variation across pear species. At molecular level, 20 SSR primers amplified 190 polymorphic alleles with an average of 9.5 alleles per primer. Size of amplified alleles ranged from 85 to 450 bp. Mean polymorphic information content (PIC) was 0.80 showing high level of SSR polymorphism. Bayesian model-based STRUCTURE analysis assigned genotypes into five clusters and also showed the extent of admixture within individuals. Genotypes belonging to Pyrus pyrifolia were clustered into two different clusters indicating broad genetic base for this species while Pyrus communis genotypes appeared to have conserved genetic makeup. Dendrogram-based on Jaccard’s similarity coefficient and neighbor-joining tree showed two major groups of Asiatic (P. pyrifolia, Pyrus pashia, Pyrus serotina and Pyrus jacquemontiana) and European (P. communis) pears. However, accessions belonging to P. pyrifolia were further divided into subgroups. Cluster analysis based on morphological traits was in agreement with the dendrogram and structure clusters obtained with SSR data. The Mantel matrix correspondence test was used to further compare the molecular and morphological similarity matrices and positive correlation coefficient (r = 0.164; P = 0.001) was observed. Results of this study present important information about genetic structure of Indian pear accessions which can contribute significantly to future breeding and improvement programmes in this species.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  1. Akcay ME, Burak M, Kazan K, Yuksel C, Mutaf F, Bakir M, Ayanoglu H, ErgÜl A (2014) Genetic analysis of Anatolian pear germplasm by simple sequence repeats (SSRs). Ann Appl Biol 164:441–452

  2. Asanidze Z, Akhalkatsia M, Gvritishvili M (2011) Comparative morphometric study and relationships between the Caucasian species of wild pear (Pyrus spp.) and local cultivars in Georgia. Flora-Morphol Distrib Funct Ecol Plants 206:974–986

  3. Bailey LH (1953) Standard cyclopedia of horticulture. The Mac Milan Co., New York

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

  5. 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

  6. Baraket G, Chatti K, Saddoud O, Abdelkarim AB, Mars M, Trifi M, Hannachi AS (2011) Comparative assessment of SSR and AFLP markers for evaluation of genetic diversity and conservation of Fig, Ficus carica L., genetic resources in Tunisia. Plant Mol Biol Rep 29:171–184

  7. Belaj A, Munoz-Diez C, Baldoni L, Proceddu A, Barranco D, Satovic Z (2007) Genetic diversity and population structure of wild olives from the north-western Mediterranean assessed by SSR markers. Ann Bot 20:1–10

  8. Bhat ZA, Dhillon WS, Singh K (2013) Genetic diversity studies on some pear genotypes using simple sequence repeats (SSRs) derived from apple and pear. Indian J Hort 70:1–6

  9. Botstein D, White KL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

  10. Cao Y, Luming T, Yuan G, Fengzhi L (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

  11. Dolatowski J, Nowosielski J, Podyma W, Szymanska M, Zych M (2004) Molecular studies on the variability of Polish semi-wild pears (Pyrus) using AFLP. J Fruit Orna Plant Res 12:331–37

  12. Dhillon BS, Rana JC (2004) Temperate fruits genetic resources management in India—issues and strategies. Acta Hort 662:139–146

  13. Dhillon BS, Dhillon WS (2008) Evaluation of hard pears germplasm for fruit bearing and quality attributes. Indian J Hort 65:389–392

  14. Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15

  15. Earl DA, von Holdt BM (2011) Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361

  16. Erfani J, Ebadi A, Abdollahi H, Fatahi R (2012) Genetic diversity of some pear cultivars and genotypes using simple sequence repeat (SSR) markers. Plant Mol Biol Rep 30:1065–1072

  17. 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

  18. FAOSTAT (2012) Food and Agricultural Organization of United Nations, http://faostat.fao.org/site/567/default.aspx

  19. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

  20. Fowler C, Mooney P (1990) The threatened gene-food, politics and the loss of genetic diversity. University of Arizona Press, Tucson, p 104

  21. Franceschi PD, Pierantoni L, Dondini L, Grandi M, Sansavini S, Sanzol J (2011) Evaluation of candidate F-box genes for the pollen S of gametophytic self-incompatibility in the Pyrinae (Rosaceae) on the basis of their phylogenomic context. Tree Genet Genomes 7:663–683

  22. Harada T, Kurahashi W, Yanai M, Wakasa Y, Satoh T (2005) Involvement of cell proliferation and cell enlargement in increasing the fruit size of Malus species. Sci Hortic 105:447–456

  23. Hedrick UP, Howe GH, Taylor OM, Francis EH, Tukey HB (1921) The pears of New York. 29th Annual Report, New York Department of Agriculture. JB Lyon Co. Printers, Albany, New York

  24. Hemmat M, Weeden NF, Brown SK (2003) Mapping and evaluation of Malus x domestica microsatellites in apple and pear. J Am Soc Hort Sci 128:515–520

  25. Iezzoni AF (2008) Cherries. In: Hancock JF (ed) Temperate fruit crop breeding. Springer, Berlin, pp 151–175

  26. Iezzoni AF, Pritts MP (1991) Applications of principal components analysis to horticultural research. Hort Sci 26:334–338

  27. 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 Evol 45:533–539

  28. Iketani H, Katayama H, Uematsu C, Mase N, Sato Y, Yamamoto T (2012) Genetic structure of East Asian cultivated pears (Pyrus spp.) and their reclassification in accordance with the nomenclature of cultivated plants. Plant Syst Evol 298:1689–1700

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

  30. Kim CS, Lee CH, Park KW, Kang SJ, Shin IS, Lee GP (2005) Phylogenetic relationships among Pyrus pyrifolia and P. communis detected by randomly amplified polymorphic DNA (RAPD) and conserved rDNA sequences. Sci Hortic 106:491–501

  31. Kumar A, Bist LD, Avasthe RK (2010) Germplasm evaluation of low-chill pears (Pyrus spp.) for vegetative, reproductive and fruit quality parameters in Tarai Area of Uttarakhand. Indian J Plant Genet Resour 23:13–17

  32. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg E, Gessler C (2002) Development and characterisation of 140 new microsatellites in Apple (Malus X domestica Borkh.). Mol Breed 10:217–241

  33. Lombard P, Westwood MN (1987) Pear rootstocks. In: Rom RC, Carlson RF (eds) Rootstocks for fruit trees. Wiley, New York, pp 145–183

  34. Santiago-Pereira L, Ferreira AR, dos Santosa AMR-C, Saub F, Díaz-Hernándeza MB (2012) Morphological variation in local pears from north-western Spain. Sci Hortic 138:176–182

  35. Mahajan RK, Gangopadhyay KK, Gunjeet K, Dobhal YK, Srivastava U, Gupta PN, Pareek SK (2002) Minimal descriptors of Agri-horticultural crops. Part ll J. Fruit Crops- National Bureau of Plant Genetic Resources, New Delhi, pp 223–228

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

  37. Mondini L, Noorani A, Pagnotta MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1:19–35

  38. Nishitani C, Terakami S, Sawamura Y, Takada N, Yamamoto T (2009) Development of novel EST-SSR markers derived from Japanese pear (Pyrus pyrifolia). Breed Sci 59:391–400

  39. Nybom H, Weising K (2010) DNA-based identification of clonally propagated cultivars. In: J. JANICK (ed.) Plant Breeding Reviews. 34:221–295

  40. Oliveira CM, Mota M, Monte-Corvo L, Goulao L, Silva DL (1999) Molecular typing of Pyrus based on RAPD markers. Sci Hortic 79:163–174

  41. Paganová V (2003) Taxonomic reliability of leaf and fruit morphological characteristics of the Pyrus L. taxa in Slovakia. Hort Sci (Prague) 30:98–107

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

  43. Perrier X, Jacquemoud-Collet JP (2006) DARwin software http://darwin.cirad.fr/darwin

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

  45. Rakonjac V, Fotiric Aksic M, Nikolic D, Milatovic D, Colic S (2010) Morphological characterization of ‘Oblacinska’ sour cherry by multivariate analysis. Sci Hortic 125:679–684

  46. Rana JC, Pradheep K, Verma VD (2007) Naturally occurring wild relatives of temperate fruits in western Himalayan region of India: an analysis. Biodivers Conserv 16:3963–3991

  47. Rana JC, Dutta M, Rathi RS (2012) Plant genetic resources of the Indian Himalayan region—an overview. Indian J Genet 72:115–129

  48. Rana JC, Singh A, Sharma Y, Pradheep K, Mendiratta N (2010) Dynamics of plant bioresources in Western Himalayan Region of India—watershed based case study. Curr Sci 98(2):192–203

  49. Rohlf FJ (1998) NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.0. Applied Biostatistics Inc, Setauket, 37 pp

  50. Said AA, Ahmed O, Fatima G, Marie HS, Cherkaoui EM (2013) Phenotypic biodiversity of an endemic wild pear, Pyrus mamorensis Trab., in North-western Morocco using morphological descriptors. Genet Resour Crop Evol 60:927–938

  51. 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

  52. Sharma M, Rana JC (2010) Pear breeding and improvement. In: Sharma RM, Pandey SN, Pandey V (eds) The pear: production, post-harvest management and protection. IDBC Publishers, Lucknow, pp 47–79

  53. Silva GJ, Souza TM, Barbieri RL, Oliveira ACD (2014) Origin, domestication, and dispersing of pear (Pyrus spp.). Adv Agr. doi:10.1155/2014/541097

  54. Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach (Prunus persica L. Batsch). Theor Appl Genet 101:421–428

  55. Tian L, Gao Y, Cao Y, Liu F, Yang J (2012) Identification of Chinese white pear cultivars using SSR markers. Genet Resour Crop Evol 59:317–326

  56. Trivedi AK, Krishna H, Verma SK, Tyagi RK, Arya RR (2012) Genetic diversity of pear (Pyrus spp.) in Uttarakhand Himalayas. Indian J Plant Genet Resour 26:32–37

  57. Verma VD, Pradheep K, Yadav SK, Rana JC (2009) Evaluation of indigenous and exotic peach germplasm under upper hill conditions. Indian J Hort 66:415–419

  58. Verma VD, Pradheep K, Yaday SK, Rana JC, Chander R (2006) Evaluation of Pears (Pyrus spp.) germplasm under temperate region of Himachal Pradesh. Indian J Plant Genet Resour 19:96–99

  59. Volk GM, Richards CM, Henk AD, Reilley A (2006) Diversity of wild Pyrus communis based on Microsatellite analyses. J Amer Soc Hort Sci 131(3):408–417

  60. Voltas J, Peman J, Fuste F (2007) Phenotypic diversity and delimitation between wild and cultivated forms of the genus Pyrus in North-eastern Spain based on morphometric analyses. Genet Resour Crop Evol 54:1473–1487

  61. Watkins R (1986) Apples (genus Malus), pears (genus Pyrus), and plums, apricots, almonds, peaches cherries (genus Prunus). In: Hora B (ed) The Oxford encyclopaedia of tree of the world, Oxford University Press, p 197–201

  62. Westwood MN, Bjornstad HO (1971) Some fruit characteristics of interspecific hybrids and extent of self-sterility in Pyrus. Bull Torrey Bot Club 98:22–24

  63. Westwood MN, Blaney LT (1963) Non-climatic factors affecting the shape of apple fruits. Nature 200:802–803

  64. Wolko L, Antkowiak W, Lenartowicz E, Bocianowski J (2010) Genetic diversity of European pear cultivars (Pyrus communis L.) and wild pear (Pyrus pyraster (L.) Burgsd.) inferred from microsatellite markers analysis. Genet Resour Crop Evol 57:801–806

  65. Wünsch A, Hormaza JI (2007) Characterisation of variability and genetic similarity of European pear using microsatellite loci developed in apple. Sci Hortic 173:37–43

  66. 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

  67. 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

  68. Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, Kotobuki K, Hayashi T, Matsuta N (2002c) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106:9–18

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

  70. Yeh FC, Boyle TJB (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belgian J Bot 129:157–163

Download references

Acknowledgments

The authors acknowledge the anonymous reviewers for their critical comments and suggestions.

Data archiving statement

The information on accessions used and the phenotypic data files are being submitted to Genomic Database to Rosaceae (GDR) at www.rosaceae.org.

Author information

Correspondence to Jai C. Rana or Tilak R. Sharma.

Additional information

Communicated by D. Chagné

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rana, J.C., Chahota, R.K., Sharma, V. et al. Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers. Tree Genetics & Genomes 11, 821 (2015). https://doi.org/10.1007/s11295-014-0821-2

Download citation

Keywords

  • Pear
  • Pyrus
  • Simple sequence repeat (SSR)
  • Genetic diversity
  • Genetic structure
  • Phylogenetic relationship