Skip to main content
SpringerLink
Log in

Sweet Cherry Cultivar Identification by High-Resolution-Melting (HRM) Analysis Using Gene-Based SNP Markers

  • Brief Communication
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

Single nucleotide polymorphisms (SNPs) provide an important tool for cultivar identification in studies of genetic diversity, but until now, the time-consuming and costly nature of DNA sequencing has limited the identification of new markers. Herein, we describe the application of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analysis, for the characterization of polymerase chain reaction products and the identification of nine gene-based SNPs for distinguishing the main Greek sweet cherry cultivars. The expected heterozygosity value of nine SNPs averaged at 0.518. The combined power of discrimination for the SNP markers was 0.999969. The ability of HRM to accurately discern nucleotide changes in a DNA sequence makes it a cost- and time-effective alternative to traditional sequencing for the detection of gene-based SNPs.

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

References

  • Bonasera J, Kim J, Beer S (2006) PR genes of apple: identification and expression in response to elicitors and inoculation with Erwinia amylovora. BMC Plant Biol 6:23

    Article  PubMed  Google Scholar 

  • Cabrera A, Rosyara U, De Franceschi P, Sebolt A, Sooriyapathirana S, Dirlewanger E, Quero-Garcia J, Schuster M, Iezzoni A, van der Knaap E (2011) Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map. Tree Genet Genomes 8:237–247

    Article  Google Scholar 

  • Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353–358

    Article  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Fernandez I, Marti A, Athanson B, Koepke T, Font I, Forcada C, Dhingra A, Oraguzie N (2012) Genetic diversity and relatedness of sweet cherry (Prunus avium L.) cultivars based on single nucleotide polymorphic (SNP) markers. Front Plant Sci 3:116

    Google Scholar 

  • Frenette Charron J-B, Ouellet F, Pelletier M, Danyluk J, Chauve C, Sarhan F (2005) Identification, expression, and evolutionary analyses of plant lipocalins. Plant Physiol 139:2017–2028

    Article  Google Scholar 

  • Ganopoulos I, Argiriou A, Tsaftaris A (2011a) Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products. Food Control 22:532–541

    Article  CAS  Google Scholar 

  • Ganopoulos IV, Kazantzis K, Chatzicharisis I, Karayiannis I, Tsaftaris AS (2011b) Genetic diversity, structure and fruit trait associations in Greek sweet cherry cultivars using microsatellite based (SSR/ISSR) and morpho-physiological markers. Euphytica 181:237–251

    Article  Google Scholar 

  • Guo W-J, David Ho T-H (2008) An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. Plant Physiol 147:1710–1722

    Article  PubMed  CAS  Google Scholar 

  • Hampl V, Pavlicek A, Flegr J (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol 51:731–735

    Article  PubMed  CAS  Google Scholar 

  • Han Y, Khu D-M, Monteros M (2012) High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.). Mol Breed 29:489–501

    Article  PubMed  Google Scholar 

  • Hedrick UP (1915) The cherries of New York. J B Lyon, Albany

    Google Scholar 

  • Hurley JD, Engle LJ, Davis JT, Welsh AM, Landers JE (2004) A simple, bead-based approach for multi-SNP molecular haplotyping. Nucleic Acids Res 32:e186

    Article  Google Scholar 

  • Koepke T, Schaeffer S, Krishnan V, Jiwan D, Harper A, Whiting M, Oraguzie N, Dhingra A (2012) Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3′UTR sequencing. BMC Genom 13:18

    Article  CAS  Google Scholar 

  • Koukourojiannis V (1996) Οι τάσεις στην παραγωγή και εμπορία των κερασιών. Γεωργία-Κτηνοτροφία (Greek) 2:24–31

    Google Scholar 

  • Kwok P-Y (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genom Hum Genet 2:235–258

    Article  CAS  Google Scholar 

  • Kwok PY, Chen X (2003) Detection of single nucleotide polymorphisms. Curr Issues Mol Biol 5:43–60

    PubMed  CAS  Google Scholar 

  • Lehmensiek A, Sutherland M, McNamara R (2008) The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley. Theor Appl Genet 117:721–728

    Article  PubMed  CAS  Google Scholar 

  • Mackay JF, Wright CD, Bonfiglioli RG (2008) A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Meth 4:8

    Article  Google Scholar 

  • Marshall RE (1954) Cherries and cherry products. Economic crops, vol 5. Inter-science, New York

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, Waterman MR, Gotoh O, Coon MJ, Estabrook RW, Gunsalus IC, Nebert DW (1996) P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenet 6:1–42

    Article  CAS  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

    Article  Google Scholar 

  • Stanys V, Baniulis D, Morkunaite-Haimi S, Siksnianiene JB, Frercks B, Gelvonauskiene D, Stepulaitiene I, Staniene G, Siksnianas T (2012) Characterising the genetic diversity of Lithuanian sweet cherry (Prunus avium L.) cultivars using SSR markers. Sci Hortic 142:136–142

    Article  Google Scholar 

  • 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 28:2731–2739

    Article  PubMed  CAS  Google Scholar 

  • Webster AD (1996) The taxonomic classification of sweet and sour cherries and a brief history of their cultivation. In: Webster AD, Looney NE (eds) Cherries. Cab International, Wallingford, pp 3–25

    Google Scholar 

  • Wilhelm J, Pingoud A (2003) Real-time polymerase chain reaction. ChemBioChem 4:1120–1128

    Article  PubMed  CAS  Google Scholar 

  • Wu SB, Wirthensohn MG, Hunt P, Gibson JP, Sedgley M (2008) High resolution melting analysis of almond SNPs derived from ESTs. Theor Appl Genet 118:1–14

    Article  PubMed  CAS  Google Scholar 

  • Wunsch A, Hormaza JI (2002) Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences. Heredity 89:56–63

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research has been co-financed by the European Union (European Social Fund-ESF) and Hellenic national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Heracletus-II. Continuous support for the Institute of Agrobiotechnology/CERTH from the General Secretariat of Research and Technology of Greece is also acknowledged.

Author information

Authors and Affiliations

  1. Department of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54 124, Greece

    Ioannis Ganopoulos, Aphrodite Tsaballa, Aliki Xanthopoulou & Athanasios Tsaftaris

  2. Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, Thessaloniki, 57001, Greece

    Ioannis Ganopoulos, Aphrodite Tsaballa, Aliki Xanthopoulou, Panagiotis Madesis & Athanasios Tsaftaris

Authors
  1. Ioannis Ganopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aphrodite Tsaballa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Aliki Xanthopoulou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Panagiotis Madesis
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Athanasios Tsaftaris
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Athanasios Tsaftaris.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 162 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ganopoulos, I., Tsaballa, A., Xanthopoulou, A. et al. Sweet Cherry Cultivar Identification by High-Resolution-Melting (HRM) Analysis Using Gene-Based SNP Markers. Plant Mol Biol Rep 31, 763–768 (2013). https://doi.org/10.1007/s11105-012-0538-z

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-012-0538-z

Keywords

Search

Navigation