, Volume 29, Issue 3, pp 775–783 | Cite as

Genetic diversity and population structure analysis of mango (Mangifera indica) cultivars assessed by microsatellite markers

  • Kundapura V. RavishankarEmail author
  • Padmakar Bommisetty
  • Anju Bajpai
  • Navin Srivastava
  • Bellam H. Mani
  • Chinnaiyan Vasugi
  • Shailendra Rajan
  • Makki R. Dinesh
Original Paper


Key message

SSR marker characterization of Indian mango cultivars revealed two distinct groups of populations with geographical affiliation. Six SSR loci with low PI have been identified as universal markers for mango characterization.


In this study, genetic diversity and population structure of mango cultivars were assessed by employing fourteen simple sequence repeat markers, with high polymorphic information content. A set of 387 mango accessions from different regions of India was used. Model-based structure analysis revealed the presence of two subpopulations comprising the cultivars from ‘South-West’ region and ‘North-East’ region. A similar clustering pattern was observed in the dendrogram analysis, with two major groups identified that were further sub-grouped based on their genetic relatedness. Analysis of molecular variance showed a significant variance component among and within mango sub-populations derived from the structure analysis. The proportion of genetic differentiation among individuals within the two populations was found to be significant with a F ST value of 0.248. The extent of genetic diversity was found to be higher in case of ‘South and West’ population than ‘North and East’ population. Six SSR loci with low probability of identity values have been chosen as universal markers for mango characterization. Our results highlight genetic diversity encompassed by mango cultivars and genetic distinctness of ‘South-West’ and ‘North-East’ region cultivars.


Genetic diversity Mangifera indica Population structure AMOVA SSR loci Shannon diversity index 



Analysis of molecular variance


Polymorphic information content


Probability of identity


Simple sequence repeat


Author contribution statement

KVR and AB proposed, initiated and led the project, interpreted scientific information and participated in manuscript preparation. PB, NS, BHM and CV participated in DNA extraction, genotyping and MS preparation. KVR and BP involved in statistical analysis. SR and MRD maintained the mango germplasm and participated in MS preparation.


The authors acknowledge financial support for this work from the Department of Biotechnology (GOI), New Delhi, India. Authors thank anonymous reviewers for their valuable suggestions to improve the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

468_2015_1155_MOESM1_ESM.docx (39 kb)
Supplementary material 1 (DOCX 39 kb)


  1. Adato A, Sharon D, Lavi U, Hillel J, Gazit S (1995) Application of DNA fingerprints for identification and genetic analyses of mango (Mangifera indica) genotypes. J Am Soc Hortic Sci 120:259–264Google Scholar
  2. Banks MA, Eichert W, Olsen JB (2003) Which genetic loci have greater population assignment power? Bioinformatics 19:1436–1438CrossRefPubMedGoogle Scholar
  3. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331PubMedCentralPubMedGoogle Scholar
  4. De Candolle AP (1884) Origin of cultivated plants. Hafner, LondonCrossRefGoogle Scholar
  5. Deepa S, Singh AK, Manish Srivastav, Singh NK (2010) Assessment of genetic diversity in mango using inter-simple sequence repeat markers. Indian J Hortic 65:1–8Google Scholar
  6. Degani C, El-Batsri R, Gazit S (1990) Enzyme polymorphisms in mango. J Am Soc Hortic Sci 115:844–847Google Scholar
  7. Dillon NL, Baly ISE, Wright CL, Hucks L, Ines DJ, Dietzgen RG (2013) Genetic diversity of the Australian national mango genebank. Sci Hort 150:213–226CrossRefGoogle Scholar
  8. Duval MF, Bunel J, Sitbon C, Risterucci AM (2005) Development of microsatellite markers for mango (Mangifera indica L.). Mol Ecol Notes 5:824–826CrossRefGoogle Scholar
  9. Earl, Dent A, vonHoldt, Bridgett M (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. doi: 10.1007/s12686-011-9548-7 CrossRefGoogle Scholar
  10. Eiadthong W, Yonemori K, Sugiura A, Utsunomiya N, Subhadrabandhu S (1999) Identification of mango cultivars of Thailand and evaluation of their genetic variation using the amplified fragments by simple sequence repeat-(SSR-) anchored primers. Sci Hortic 82:57–66CrossRefGoogle Scholar
  11. Eiadthong W, Yonemori K, Kanzaki S, Sugiura A (2000) Amplified fragment length polymorphism analysis for studying genetic relationship among Mangifera species in Thailand. J Am Soc Hortic Sci 125:160–164Google Scholar
  12. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  13. Excoffier L, Laval G, Schneider S (2006) An integrated software package for population genetics data analysis. Arlequin v3.1.
  14. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis in bread wheat. Euphytica 113:63–185CrossRefGoogle Scholar
  15. Hartl DL, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer Associates, SunderlandGoogle Scholar
  16. Hemanth Kumar NV, Narayanswamy P, Theertha Prasad D, Mukunda GK, Sondur SN (2001) Estimation of genetic diversity of commercial mango cultivars using RAPD markers. J Hortic Sci Biotech 76:529–533Google Scholar
  17. Hirano R, Htun-Oo T, Watanabe KN (2010) Myanmar mango landraces reveal genetic uniqueness over common cultivars from Florida, India, and Southeast Asia. Genome 53:321–330CrossRefPubMedGoogle Scholar
  18. Honsho C, Nishiyama K, Eiadthong W, Yonemori K (2005) Isolation and characterization of new microsatellite markers in mango (Mangifera indica). Mol Ecol Notes 5:152–154CrossRefGoogle Scholar
  19. IPGRI (2006) Descriptors for mango (Mangifera indica L). International Plant Genetic Resources Institute, RomeGoogle Scholar
  20. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1006–1099CrossRefGoogle Scholar
  21. Karihaloo JL, Dwivedi YK, Archak S, Gaikwad AB (2003) Analysis of genetic diversity of Indian mango cultivars using RAPD markers. J Hortic Sci Biotech 78:285–289Google Scholar
  22. Kashkush K, Jinggui F, Tomer E, Hillel J, Lavi U (2001) Cultivar identification and genetic map of mango (Mangifera indica). Euphytica 122:129–136CrossRefGoogle Scholar
  23. Levin DA, Kerster HW (1974) Gene flow in seeds plants. Evol Biol 7:139–220Google Scholar
  24. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398CrossRefGoogle Scholar
  25. Lopez-Valenzuela JA, Martinez O, Paredes-Lopez O (1997) Geographic differentiation and embryo type identification in Mangifera indica L. cultivars using RAPD markers. HortScience 32:1105–1108Google Scholar
  26. Malathi S, Lakshminarayan RV, Begum H, Purushotham RB, Neetasri C, Nagaraju J, Anwar SY, Siddiq EA (2013) Population structure and genetic analysis of different utility types of mango (Mangiferaindica L.) germplasm of Andhra Pradesh state of India using microsatellite markers. Plant Syst Evol. doi: 10.1007/s00606-013-0790-1 Google Scholar
  27. Mukherjee SK (1951) Origin of mango. Indian J Genet Plant Breed 11:49–56Google Scholar
  28. Muraya MM, de Santie Villiers, Parzies HK, Mutegi E, Sagnard F, Kanyenji BM, Kiambi D, Geiger HH (2011) Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya. Theor Appl Genet. doi: 10.1007/s00122-011-1608-6 Google Scholar
  29. Mustaffa MM (1993) Studies on genetic diversity in some mango and papaya genotypes using isozyme analysis. PhD Thesis, University of Agricultural Sciences, Bangalore, KarnatakaGoogle Scholar
  30. Naik KC, Gangolly SR (1950) Classification and nomenclature of South Indian mangoes. The Madras Department of Agriculture Printing Press, Madras, India, p 311Google Scholar
  31. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323CrossRefPubMedCentralPubMedGoogle Scholar
  32. Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian Polar bears. Mol Ecol 4:347–354CrossRefPubMedGoogle Scholar
  33. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier, pp 43–76Google Scholar
  34. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  35. Rajwant KK, Manoj KR, Sanjay K, Singh Rohtas, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334CrossRefGoogle Scholar
  36. Ravishankar KV, Anand L, Dinesh MR (2000) Assessment of genetic relatedness among mango cultivars of India using RAPD markers. J Hortic Sci Biotech 75:198–201Google Scholar
  37. Ravishankar KV, Mani BH, Anand L, Dinesh MR (2011) Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification. Am J Bot 98:e96–e99CrossRefPubMedGoogle Scholar
  38. Romero-Severson J, Smith JSC, Ziegle J, Hauser JL, Hookstra G (2001) Pedigree analysis and haplotype sharing within diverse groups of Zea mays L. inbreds. Theor Appl Genet 103:567–574CrossRefGoogle Scholar
  39. Sagar SP, Sirsha M, Ashok PG, Keshav HP, Bhimarao PP, Narayan DJ, Vidya SG (2007) Genetic diversity analysis of mango cultivars using inter simple sequence repeat markers. Curr Sci 93:1135–1141Google Scholar
  40. Schnell RJ, Ronning CM, Knight RJ (1995) Identification of cultivars and validation of genetic relationships in Mangifera indica L. using RAPD markers. Theor Appl Genet 90:269–274CrossRefPubMedGoogle Scholar
  41. Schnell RJ, Brown JS, Olano CT, Meerow AW, Campbell RJ, Kuhn DN (2006) Mango genetic diversity analysis and pedigree inferences for Florida cultivars using microsatellite markers. J Am Soc Hortic Sci 13:214–224Google Scholar
  42. Singh S, Bhat KV (2008) Molecular Characterization and analysis of geographical differentiation of Indian Mango (Mangifera indica L) germplasm. Acta Hort (ISHS) 839:599–606Google Scholar
  43. Varshney RK, Graner Andreas, Sorells ME (2005) Genic microsatellite markers in plants: features and application. Trends Biotechnol 23:48–55CrossRefPubMedGoogle Scholar
  44. Viruel MA, Escribano P, Barbieri M, Ferri M, Hormaza JI (2005) Fingerprinting, embryo type and geographic differentiation in mango (Mangifera indica L., Anacardiaceae) with microsatellites. Mol Breed 15:383–393CrossRefGoogle Scholar
  45. Wagner HW, Sefc KM (1999) IDENTITY 1.0. Centre for Applied genetics. University of Agricultural Sciences, Vienna, AustriaGoogle Scholar
  46. Yadav IS, Singh HP (1985) Evaluation of different ecological groups of mango cultivars for flowering and fruiting under subtropics. Prog Hort 17:165–175Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Kundapura V. Ravishankar
    • 1
    Email author
  • Padmakar Bommisetty
    • 1
  • Anju Bajpai
    • 2
  • Navin Srivastava
    • 2
  • Bellam H. Mani
    • 1
  • Chinnaiyan Vasugi
    • 1
  • Shailendra Rajan
    • 2
  • Makki R. Dinesh
    • 1
  1. 1.ICAR-Indian Institute of Horticultural ResearchBengaluruIndia
  2. 2.ICAR-Central Institute for Subtropical HorticultureLucknowIndia

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