Skip to main content
SpringerLink
Log in

Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

The main objective of this research was to add genotyping information to previous phenotyping findings of Pakistani guava for the purposes of selective breeding. Inter-primer binding site (iPBS) and microsatellite (SSR) markers were used to assess the molecular variation and genetic structure of 51 promising Pakistani guava (Psidium guajava L.) genotypes which were then compared with 19 others from different geographical regions across the world. PCR of 6 iPBS primers (dominant markers) produced a total of 97 bands (96.63 % polymorphic) ranging from 100 to 2800 bp and the mean PIC for primers ranged from 0.1687 to 0.3522. The mean unbiased expected heterozygosity (0.183), Shannon’s information index (0.275) and average fixation index (Fst or inbreeding) (0.925) indicated a high level of inbreeding among the accessions tested. Multi-locus DNA fingerprints using 18 SSR loci unambiguously differentiated all accessions and demonstrated an absence of duplicated samples. Diversity analysis revealed a total of 172 alleles (from 124 to 553 bp) ranging from 2 to 17 with a mean value of 9.56 alleles per locus. The mean unbiased expected heterozygosity (0.091), Shannon’s information index (0.130) and mean inbreeding coefficient (0.854) also indicated a high level of inbreeding among the accessions. Ordination and cluster analysis from both iPBS and SSR markers showed that the genetic relationships between all accessions could be separated into geographic origin, specifically Pakistan, Mexico, Hawaii and India. Guava accessions cultivated in Pakistan and wild guava germplasm are highly divergent and possess abundant genetic diversity. The iPBS PCR-based genome fingerprinting technology used in this study is low-cost and provides an effective alternative in differentiating accessions of guava and their related species or genera.

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
Fig. 7

Similar content being viewed by others

References

  • Ahmed B, Mannan MA, Hossain SA (2011) Molecular characterization of guava (Psidium guajava L.) germplasm by RAPD analysis. Int J Nat Sci 1:62–67

    Article  Google Scholar 

  • Aranguren Y, Briceno A, Fermin G (2010) Assessment of the variability of Venezuelan guava landraces by microsatellites. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 147–154

  • Baijnath H, Ramcharun S, Naicker S (1982) Psidium spp., (Myrtaceae); very successful weeds. S Afr J Bot 1:78

    Article  Google Scholar 

  • Baranek M, Meszaros M, Sochorova J, Cechova J, Raddova J (2012) Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovicka. Sci Hortic 143:1–6. doi:10.1016/j.scienta.2012.05.022

    Article  CAS  Google Scholar 

  • Briceno A, Aranguren Y, Fermin G (2010) Assessment of guava-derived SSR markers for the molecular characterization of Myrtaceae from different ecosystems in Venezuela. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 139–146

  • Chen T-W, Ng C-C, Wang C-Y, Shyu Y-T (2007) Molecular identification and analysis of Psidium guajava L. from indigenous tribes of Taiwan. J Food Drug Anal 15:82–88

    CAS  Google Scholar 

  • Coser SM, da Silva Ferreira MF, Ferreira A, Mitre LK, Carvalho CR, Clarindo WR (2012) Assessment of genetic diversity in Psidium guajava L. using different approaches. Sci Hortic 148:223–229. doi:10.1016/j.scienta.2012.09.030

    Article  CAS  Google Scholar 

  • da Costa SR, Santos CAF, Castro JMC (2012) Assessing Psidium guajava × P. guineense hybrids tolerance to Meloidogyne enterolobii. In: Santos CAF, Mitra SK, Griffis Jr JL (eds) Acta Hortic, vol 959, pp 59–66

  • Dayanandan S, Bawa KS, Kesseli R (1997) Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 84:1658–1663. doi:10.2307/2446463

    Article  CAS  PubMed  Google Scholar 

  • Dettori MT, Palombi MA (2000) Identification of Feijoa sellowiana Berg accessions by RAPD markers. Sci Hortic 86:279–290. doi:10.1016/s0304-4238(00)00157-6

    Article  CAS  Google Scholar 

  • FAO (2002) Commodity market: reviews 2001–2002. Food and Agriculture Organization of the United Nations, Rome

    Google Scholar 

  • Felsenstein J (2005) PHYLIP (Phylogeny Inference Package), 3.6 edn. Distributed by the author, Department of Genetics, University of Washington, Seattle, Washington

  • Feria-Romero IA, Astudillo-de la Vega H, Chavez-Soto MA, Rivera-Arce E, Lopez M, Serrano H, Lozoya X (2009) RAPD markers associated with quercetin accumulation in Psidium guajava. Biol Plant 53:125–128. doi:10.1007/s10535-009-0017-z

    Article  CAS  Google Scholar 

  • Gailite A, Rungis D (2012) An initial investigation of the taxonomic status of Saussurea esthonica Baer ex Rupr. utilising DNA markers and sequencing. Plant Syst Evol 298:913–919. doi:10.1007/s00606-012-0600-1

    Article  Google Scholar 

  • Guo D-L, Guo M-X, Hou X-G, Zhang G-H (2014) Molecular diversity analysis of grape varieties based on iPBS markers. Biochem Syst Ecol 52:27–32. doi:10.1016/j.bse.2013.10.008

    Article  CAS  Google Scholar 

  • Hayes WB (1970) Fruit growing in India, 3rd edn. Kitabistan, Allahabad, p 72

    Google Scholar 

  • Hernandez-Delgado S, Padilla-Ramirez JS, Nava-Cedillo A, Mayek-Perez N (2007) Morphological and genetic diversity of Mexican guava germplasm. Plant Genet Resour Charact Util 5:131–141. doi:10.1017/s1479262107827055

    Article  Google Scholar 

  • Jaiswal U, Jaiswal VS (2005) Psidium guajava guava. In: Litz RE (ed) Biotechnology of fruit and nut crops. Biotechnology in agricultural series, vol 29. CAB Publishers, Cambridge, pp 394–401

    Google Scholar 

  • Kalendar R, Antonius K, Smykal P, Schulman A (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121:1419–1430. doi:10.1007/s00122-010-1398-2

    Article  CAS  PubMed  Google Scholar 

  • Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520–530. doi:10.1038/hdy.2010.93

    Article  CAS  PubMed  Google Scholar 

  • Landrum LR (1990) Accara—a new genus of Myrtaceae, Myrtinae from Brazil. Syst Bot 15:221–225. doi:10.2307/2419176

    Article  Google Scholar 

  • Lepitre V et al (2010) The microsatellite (SSR)/AFLP reference linkage map of guava. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 183–192

  • Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398

    Article  Google Scholar 

  • Mehmood A, Jaskani MJ, Khan IA, Ahmad S, Ahmad R, Luo S, Ahmad NM (2014) Genetic diversity of Pakistani guava (Psidium guajava L.) germplasm and its implications for conservation and breeding. Sci Hortic 172:221–232. doi:10.1016/j.scienta.2014.04.005

    Article  Google Scholar 

  • Mehmood A, Jaskani MJ, Saeed A, Rashid A (2013) Evaluation of genetic diversity in open pollinated guava by iPBS primers. Pak J Agric Sci 50:591–597

    Google Scholar 

  • Menzel CM (1985) Guava: an exotic fruit with potential in Queensland. Qld Agric J 111:93–98

    Google Scholar 

  • Nei M, Li WH (1979) Mathematical-model for studying genetic-variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273. doi:10.1073/pnas.76.10.5269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Odong TL, van Heerwaarden J, Jansen J, van Hintum TJL, van Eeuwijk FA (2011) Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data? Theor Appl Genet 123:195–205. doi:10.1007/s00122-011-1576-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Padilla-Ramirez JS, Gonzalez-Gaona E (2010) Collection and characterization of Mexican guava (Psidium guajava L.) germplasm. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 49–54

  • Pakistan Statistical Yearbook (2010) Government of Pakistan, Islamabad

  • Pathak RK, Ojha CM (1993) Genetic resources of guava. Advances in horticulture: fruit crops, vol 1. Malhotra Publishing House, New Delhi

    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. doi:10.1111/j.1471-8286.2005.01155.x

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. doi:10.1093/bioinformatics/bts460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pommer CV (2012) Guava world-wide breeding: major techniques and cultivars and future challenges. In: Santos CAF, Mitra SK, Griffis Jr JL (eds) Acta Hortic, vol 959, pp 81–88

  • Pommer CV, Murkami KRN (2009) Breeding guava (Psidium guajava L.). In: Jain SM, Pommer CV (eds) Breeding plantation tree crop: tropical species. Springer, Berlin, pp 83–120

    Chapter  Google Scholar 

  • Prakash DP, Narayanaswamy P, Sondur SN (2002) Analysis of molecular diversity in guava using RAPD markers. J Hortic Sci Biotechnol 77:287–293

    Article  CAS  Google Scholar 

  • Risterucci AM, Duval MF, Rohde W, Billotte N (2005) Isolation and characterization of microsatellite loci from Psidium guajava L. Mol Ecol Notes 5:745–748. doi:10.1111/j.1471-8286.2005.01050.x

    Article  CAS  Google Scholar 

  • Ritter E (2012) Guava biotechnologies, genomic achievements and future needs. In: Santos CAF, Mitra SK, Griffis Jr JL (eds) Acta Hortic, vol 959, pp 131–140

  • Rodriguez-Medina NN, Valdes-Infante J, Gonzalez G, Fuentes V, Canizares J (2010) Genetic resources of guava (Psidium guajava) in Cuba: germplasm characterization and breeding. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 341–348

  • Rodríguez N, Valdés-Infante J, Becker D, Velázquez B, Coto O, Ritter E, Rohde W (2004) Morphological, agronomic and molecular characterization of Cuban accessions of guava (Psidium guajava L.). J Genet Breed 58:79–90

    Google Scholar 

  • Rodriguez N et al (2007) Characterization of guava accessions by SSR markers, extension of the molecular linkage map, and mapping of QTLs for vegetative and reproductive characters. In: Singh G, Kishun R, Chandra R (eds) Proceedings of the 1st international Guava symposium. Acta Hortic, vol 735, pp 201–215

  • Sanchez-Teyer LF, Barraza-Morales A, Keb L, Barredo F, Quiroz-Moreno A, O’Connor-Sanchez A, Padilla-Ramirez JS (2010) Assessment of genetic diversity of Mexican guava germplasm using DNA molecular markers. In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 133–138

  • Sitther V, Zhang D, Harris DL, Yadav AK, Zee FT, Meinhardt LW, Dhekney SA (2014) Genetic characterization of guava (Psidium guajava L.) germplasm in the United States using microsatellite markers. Genet Resour Crop Evol 61:829–839. doi:10.1007/s10722-014-0078-5

    Article  CAS  Google Scholar 

  • Smykal P, Bacova-Kerteszova N, Kalendar R, Corander J, Schulman AH, Pavelek M (2011) Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 122:1385–1397. doi:10.1007/s00122-011-1539-2

    Article  CAS  PubMed  Google Scholar 

  • Valdés-Infante D et al (2003) Molecular characterization of Cuban accessions of guava (Psidium guajava L.), establishment of a first molecular linkage map and mapping of QTLs for vegetative characters. J Genet Breed 57:349–358

    Google Scholar 

  • Valdes-Infante J et al (2010) Comparison of the polymorphism level, discriminating capacity and informativeness of morpho-agronomic traits and molecular markers in guava (Psidium guajava L.). In: Rohde W, Fermin G (eds) Acta Hortic, vol 849, pp 121–132

  • Van Wyk AE (1980) A note on the seed morphology of the genus Eugenia Myrtaceae in Southern Africa. S Afr J Bot 46:115–120

    Google Scholar 

  • Van Wyk AE, Botha R (1984) The genus Eugenia (Myrtaceae) in Southern-Africa—ontogeny and taxonomic value of the seed. S Afr J Bot 3:63–80

    Article  Google Scholar 

  • Watson L, Dallwitz MJ (2007) The families of flowering plants: descriptions, illustrations, identification, and information retrieval. DELTA—DEscription Language for TAxonomy. http://delta-intkey.com. Accessed June 28, 2015

  • Wright S (1965) The interpretation of population structure by F-statistics with special regards to systems of mating. Evolution 19:395–420

    Article  Google Scholar 

  • Wuensch A (2009) Cross-transferable polymorphic SSR loci in Prunus species. Sci Hortic 120:348–352. doi:10.1016/j.scienta.2008.11.012

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This project is part of Ph.D. research funded by the Higher Education Commission (HEC) of Pakistan. We thank Professor Emeritus R.A. McIntosh for assistance in the preparation of the manuscript. The authors would also like to thank the Editor and reviewers for their most helpful comments and suggestions. We would like also to thank Dr. Urmil Bansal for her help with LI-COR DNA analyzer. Our thanks are also due to Dr. Xiaochun Zhao, Dr. Hanif Miah, Dr. Akram Khan, Mr. Muhammad B. Gill and Mr. Keshab Kandel for providing some of the plant samples. We greatly appreciate the help of Dr. Abdul Karim in the DNA extractions of the Pakistani guava accessions. Our thanks are also due to Dr. Faisal Saeed Awan (CABB) who provided useful materials for this research.

Author information

Authors and Affiliations

  1. Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia

    A. Mehmood, S. Luo, N. M. Ahmad, C. Dong, T. Mahmood & P. Sharp

  2. Institute of Horticultural Science, University of Agriculture Faisalabad, Faisalabad, Pakistan

    A. Mehmood & M. J. Jaskani

  3. Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, 57000, Pakistan

    A. Mehmood

  4. Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan

    Y. Sajjad

Authors
  1. A. Mehmood
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. N. M. Ahmad
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. T. Mahmood
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Y. Sajjad
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. J. Jaskani
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. P. Sharp
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. M. Ahmad.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mehmood, A., Luo, S., Ahmad, N.M. et al. Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers. Genet Resour Crop Evol 63, 1345–1361 (2016). https://doi.org/10.1007/s10722-015-0322-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-015-0322-7

Keywords

Search

Navigation