Combination of Simple Sequence Repeat, S-Locus Polymorphism and Phenotypic Data for Identification of Tunisian Plum Species (Prunus spp.)

  • Ghada BaraketEmail author
  • Donia Abdallah
  • Sana Ben Mustapha
  • Hend Ben Tamarzizt
  • Amel Salhi-Hannachi
Original Article


Plums (Prunus spp.) are among the first fruit tree species that attracted human interest. Artificial crosses between wild and domesticated species of plums are still paving the way for creation of new phenotypic variability. In Tunisia, despite a considerable varietal richness of plum as well as a high economic value, the plum sector is experiencing a significant regression. The main reason of this regression is the absence of a national program of plum conservation. Hence, this work was aimed to phenotypically and genetically characterize 23 Tunisian plum accessions to preserve this patrimony. Closely related Prunus species from the same subgenus may be differing at two characteristics: ploidy level and phenotypic traits. In this study, single sequence repeat (SSR) markers allowed distinguishing between eighteen diploid accessions and five polyploid accessions, but SSR data alone precluded unambiguous ploidy estimation due to homozygosity. In contrast, S-allele markers were useful to identify the ploidy level between polyploid species, but they did not distinguish species with the same ploidy level. Seven out of 12 phenotypic traits were shown to be discriminant traits for plum species identification. Molecular and phenotypic traits were significantly correlated and revealed a powerful tool to draw taxonomic and genotypic keys. The results obtained in this work are of great importance for local Tunisian plum germplasm management.


Plums Prunus L. Phenotypic analysis S-Locus SSR markers 



Desoxyribonucleic acid


Gametophytic self-incompatibility system


Polymerase chain reaction


S-Haplotype-specific F-box




Union internationale de la Protection des Obtentions Variétales



This research was financed by the Tunisian ‘Ministère de l’Enseignement supérieur et de la Recherche Scientifique’. We would like to gratefully thank Tunisian farmers for kindly providing plant material and for their help during phenotypic measurements in the fields. We wish to thank the anonymous reviewers and the editors for their critical comments which allowed us to improve the original manuscript.

Author Contributions

GB performed the experiments and statistical analyses, developed the genetic analyses and wrote the manuscript. DA provided some plant material discussed and corrected the content. SBM provided some plant material and discussed the content. HBT gave additional information regarding plum and corrected the content. ASH offered experimental instructions, supervised and provided editorial advice.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10528_2019_9922_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 15 kb)


  1. Abdallah D, Baraket G, Ben Tamarzizt H, Ben Mustapha S, Salhi-Hannachi A (2016) Identification, evolutionary patterns and intragenic recombination of the gametophytic self incompatibility pollen gene (SFB) in Tunisian Prunus species (Rosaceae). Plant Mol Biol Rep 34:339–352CrossRefGoogle Scholar
  2. Arús P, Messeguer R, Viruel F, Tobutt K, Dirlewanger E, Santi F, Quarta R, Ritter E (1994) The European Prunus mapping Project 1994b. In: Schmidt H, Kellerhals M (eds) Progress in temperate furit breeding. Kluwer Academic Publishers, Amsterdam, pp 305–308CrossRefGoogle Scholar
  3. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331Google Scholar
  4. Browicz K, Zohary D (1996) The genus Amygdalus L. (Rosaceae): species relationships, distribution and evolution under domestication. Genet Resour Crop Evol 43:229–247CrossRefGoogle Scholar
  5. Carrière EA (1872) Amygdalopsis lindleyi. Rev Hortic 1872:33–34Google Scholar
  6. Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus. Theor Appl Genet 99:65–72CrossRefGoogle Scholar
  7. Darlington CD, Ammal Janaki EK (1945) Chromosome atlas of flowering plants. Allen Unwin LTD, LondonGoogle Scholar
  8. Das B, Ahmed N, Singh P (2011) Prunus diversity—early and present development: a review. Int J Biodivers Conserv 14:721–734Google Scholar
  9. Dirlewanger E, Cosson P, Tavaud M, Aranzana MJ, Poizat C, Zanetto A, Arùs P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105:127–138CrossRefGoogle Scholar
  10. Doyle JJ, Doyle JL (1987) Isolation of DNA from fresh plant tissue. Focus 12:13–15Google Scholar
  11. El Dabbagh N (2016) Analyse de la diversité de processus de développement racinaire chez les Prunus. Aptitude au bouturage et réponses à la contrainte hydrique. Science agricoles. Université d‘Avignon, FranceGoogle Scholar
  12. Eldridge L, Ballard R, Baird WV, Abbot A, Morgens P, Callahan A, Scorza R, Monet R (1992) Application of RFLP analysis to genetic linkage mapping in peaches. Sci Hortic 27:160–163Google Scholar
  13. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50CrossRefGoogle Scholar
  14. FAOstat (2016) Food and agriculture organization of the United Nations. 798 FAO Statistics DivisionGoogle Scholar
  15. Fernández-Cruz J, Fernández-López J, Miranda-Fontaíña ME, Díaz Vazquez R, Toval G (2014) Molecular characterization of Spanish Prunus avium plus trees. For Syst 23:120–128Google Scholar
  16. Galli ZS, Halàsz G, Kiss E, Heszky L, Dobrànszki J (2005) Molecular identification of commercial apple cultivars with microsatellite markers. Sci Hortic 40:1974–1977Google Scholar
  17. García-Verdugo D, Calleja JA, Vargas P, Silva L, Moreira O, Pulido F (2013) Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa? Mol Ecol 22:1546–1557CrossRefGoogle Scholar
  18. Gu CZ, Bartholomew B (2003) Prunus Linnaeus. Flora China 9:401–403Google Scholar
  19. Halász J, Makovics-Zsoha N, Szöke F, Ercilis S, Hegedüs A (2017) Simple sequence repeat and S-locus genotyping to explore genetic variability in polyploid Prunus spinosa and P. insititia. Biochem Genet 55:22–33CrossRefGoogle Scholar
  20. Hammer O, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Google Scholar
  21. Janick J (2005) The origins of fruits, fruit growing, and fruit breeding. Plant breeding reviews. Wiley, New York, pp 255–321Google Scholar
  22. Janick J, Moore JN (1975) Advances in fruit breeding. Purdue University Press, West LafayetteGoogle Scholar
  23. Kao TH, Tsukamoto T (2004) The molecular and genetic bases of SRNase-based self-incompatibility. Plant Cell 16:72–83CrossRefGoogle Scholar
  24. Khadivi-Khub A, Anjam K (2014) Morphological characterization of Prunus scoparia using multivariate analysis. Plant Syst Evol 300:1361–1372CrossRefGoogle Scholar
  25. Kota-Dombrovska I, Lācis G (2013) Evaluation of selfincompatibility locus diversity of domestic plum (Prunus domestica L.) using DNA-based S-genotyping. Proc Latv Acad Sci Sect B 67(2):109–115Google Scholar
  26. Lee S, Wen J (2001) A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of ribosomal DNA. Am J Bot 88:150–160CrossRefGoogle Scholar
  27. Li Y, Smith T, Liu CJ, Awasthi N, Yang J, Wang YF, Li CS (2011) Endocarps of Prunus (Rosaceae: Prunoideae) from the early Eocene of Wutu, Shandong Province, China. Taxon 60:555–564CrossRefGoogle Scholar
  28. Linnaeus C (1753) Species plantarum. Salvius, StockholmGoogle Scholar
  29. Liu WS, Liu DC, Feng CJ, Zhang AM, Li SH (2005) Genetic diversity and phylogenetic relationships in plum germplasm resources revealed by RAPD markers. J Hortic Sci Biotechnol 81:242–250CrossRefGoogle Scholar
  30. Mestre L, Reig G, Betrán J, Moreno MA (2017) Influence of plum rootstocks on agronomic performance, leaf mineral nutrition and fruit quality of ‘Catherina’ peach cultivar in heavy-calcareous soil conditions. Span J Agric Res 15:e0901CrossRefGoogle Scholar
  31. Mnejja M, Garcia J, Howad W, Badenes ML, Arùs P (2004) Simple-sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl.) are highly polymorphic and transferable to peach and almond. Mol Ecol Notes 4:163–166CrossRefGoogle Scholar
  32. Mnejja M, Garcias J, Howad W, Arùs P (2005) Development and transportability across Prunus species of 42 polymorphic almond microsatellites. Mol Eco Notes 5:531–535CrossRefGoogle Scholar
  33. Mowrey BD, Werner DJ (1990) Phylogenetic relationships among species of Prunus as inferred by isoenzyme markers. Theor Appl Genet 80:129–133CrossRefGoogle Scholar
  34. Nabli M (2011) La flore de la Tunisie, Mise à jour 2011Google Scholar
  35. OCDE (2002) Consensus document on the biology of Prunus spp. (stone fruits), Environment Directorate. Org. Eco. Co-op. and Dev. Paris, pp 1–42Google Scholar
  36. Rehder A (1940) Manual of cultivated trees and shrubs hardy in North America. Exclusive of the subtropical and warmer temperate regions, 2nd edn. MacMillan, New YorkGoogle Scholar
  37. Reig G, Jiménez S, Mestre L, Font iForcada C, Betrán JA, Moreno MA (2018) Horticultural, leaf mineral and fruit quality traits of two ‘Greengage’ plum cultivars budded on plum based rootstocks in Mediterranean conditions. Sci Hortic 232:84–91CrossRefGoogle Scholar
  38. Salazar JA, Ruiz D, Campoy JA, Sanchez-Perez R, Crisosto CH, Martinez-Garcia PJ, Blenda A, Jung S, Main D, Martinez-Gomez P, Rubio M (2014) Quantitative trait loci (QTL) and mandelian trait loci (MTL) analysis in Prunus: a breeding perspective and beyond. Plant Mol Biol Rep 32:1–18CrossRefGoogle Scholar
  39. Sonneveld T, Tobutt KR, Vaughan SP, Robbins TP (2005) Loss of pollen-S function in two self-compatible selections of Prunus avium is associated with deletion/mutation of an S-haplotype-specific F-box gene. Plant Cell 17:37–51CrossRefGoogle Scholar
  40. 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 101:421–428CrossRefGoogle Scholar
  41. 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 28:2731–2739CrossRefGoogle Scholar
  42. Tao R, Yamane H, Sugiura A, Murayama H, Sassa H, Mori H (1999) Molecular typing of S-alleles through identification, characterization and cDNA cloning for S-RNases in sweet cherry. J Am Soc Hortic Sci 124:224–233CrossRefGoogle Scholar
  43. UPOV (2014) Union Internationale pour la Protection des Obtentions Végétales. Code UPOV: PRUNU_SAL. Genève.
  44. Vaughan SP, Russell K, Sargent DJ, Tobutt KR (2006) Isolation of S-locus F-box alleles in Prunus avium and their application in a novel method to determine self-incompatibility genotype. Theor Appl Genet 112:856–866CrossRefGoogle Scholar
  45. Wünsch A, Carrera M, Hormaza JI (2006) Molecular characterization of local Spanish peach [Prunus persica (L.) Batsch] germplasm. Genet Resour Crop Evol 53:925–932CrossRefGoogle Scholar
  46. Yamane H, Tao R, Sugiura A, Hauck HR, Iezzoni AF (2001) Identification and characterization of S-RNases in tetraploid sour cherry (Prunus cerasus). J Am Soc Hortic Sci 126:661–667CrossRefGoogle Scholar
  47. Zeinalabedini M, Majourhat K, Khayam-Nekoui M, Grigorian V, Torchi M, Dicenta F, Martinez-Gomez P (2008) Comparison of the use of morphological, protein and DNA markers in the genetic characterization of Iranian wild Prunus species. Sci Hortic 16:80–88CrossRefGoogle Scholar
  48. Zhang SY (1992) Systematic wood anatomy of the Rosaceae. Blumea 37:81–158Google Scholar
  49. Zhengy W, Raven P, Deyuan H (2003) Flora of China, vol 9. Science Press, BeijingGoogle Scholar
  50. Zohary D, Hopf M, Weiss E (2013) Domestication of plants in the Old World: the origin and spread of domesticated plants in Southwest Asia, Europe, and the Mediterranean Basin, 4th edn. OUP, OxfordGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ghada Baraket
    • 1
    Email author
  • Donia Abdallah
    • 1
  • Sana Ben Mustapha
    • 1
  • Hend Ben Tamarzizt
    • 1
  • Amel Salhi-Hannachi
    • 1
  1. 1.Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia

Personalised recommendations