Skip to main content
Log in

Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe

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

Abstract

The genotyping of European fruit tree collections has helped to identify synonyms, determine parentage, reveal key specimens in the collections and provide information on the development of modern cultivars from one or several progenitors. However, studies on European plum Prunus domestica L. accessions have been lagging behind, mainly because of the hexaploid chromosome number. In this co-operative study, 104 accessions conserved by 14 partners across Europe were phenotyped for 20 descriptors, and genotyped for 8 SSR loci together with 8 reference cultivars. Based on the descriptors and additional information supplied by the partners, as well as the scientific and horticultural literature, each accession was assigned to one of six pomological groups; (1) egg plums sensu lato (E), (2) prunes of the French d’Agen type (P/A), (3) prunes of the Central-Southeast European Zwetschen type (P/Z), (4) greengages (G), (5) mirabelles (M) and (6) bullaces, damsons and var. pomariorum (D/B). A MANOVA conducted on descriptor data revealed significant differentiation among the pomological groups as well as a geographic impact on the differentiation of local plum accessions in Europe. SSR data showed that two trios and seven pairs of genotypes had very similar allele profiles and possibly are genetically identical in spite of different accession names. An AMOVA indicated sparse genetic differentiation when accessions were grouped according to geographic origin whereas significant differences were obtained among pomological groups. A Bayesian analysis of genetic structure, as well as a discriminant analysis of principal components (DAPC), further revealed levels of similarity among and within the different pomological groups, suggesting that egg plums sensu lato (E) and greengages (G) can be referred to subsp. domestica while damsons and bullaces (D/B) but also Central-Southeast European prunes (P/Z) show more affinity to subsp. insititia. The small and possibly heterogeneous groups with mirabelles (M) and prunes of the d’Agen type (P/A) take an intermediate position suggesting a hybridogenic origin.

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

Access this article

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

Similar content being viewed by others

References

  • Aranzana MJ, Hernández Mora JR, Micheletti D, Micali S, Nazzicari N, Pacheco I, Foschi S, Barreneche T, Quilot-Turion B, Wang L, Ma R, Li X, Iglesias I, Carbó J, Troggio M, Banchi E, Aramini V, Dettori MT, Caprera A, da Silva Linge C, Pascal T, Lambert P, Gao Z, Verde I, Bassi D, Rossini L, Laurens F, Arús P (2017) Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS. Acta Hortic 1172:419–424

    Article  Google Scholar 

  • Athanasiadis I, Nikoloudakis N, Hagidimitriou M, (2013) Genetic Relatedness among cultivars of the greek plum germplasm. Not Botanicae Horti Agrobot Cluj–Napoca 41(2):491

    Article  CAS  Google Scholar 

  • Bourguiba H, Audergon JM, Krichen L, Trifi-Farah N, Mamouni A, Trabelsi S, D’Onofrio C, Asma BM, Santoni S, Khadari B (2012) Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin. BMC Plant Biol 12:49. https://doi.org/10.1186/1471-2229-12-49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Decroocq V, Hagen LS, Favé M-G, Eyquard J-P, Pierronnet A (2004) Microsatellite markers in the hexaploid Prunus domestica species and parentage lineage of three European plum cultivars using nuclear and chloroplast simple-sequence repeats. Mol Breed 13:135–142

    Article  CAS  Google Scholar 

  • Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22(4):1–20

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gharbi O, Wünsch A, Rodrigo J (2014) Characterization of accessions of ‘Reine Claude Verte’ plum using Prunus SRR and phenotypic traits. Sci Hortic 169:57–65

    Article  CAS  Google Scholar 

  • Gower JC (1971) A general coefficient of similarity and some of its properties. Biometrics 23:623–637

    Article  Google Scholar 

  • Grahić A, Grahić J (2017) MADC—Marker Analysis Data Compiler user’s Manual. (www.divisionagro.ba/apps/docs/madc-marker-analysis-data-compiler/user-manual)

  • Halapija Kazija D, Vujević P, Jelačić T, Milinović B, Pejić I, Simon S, Zulj M, Drkenda P, Gaši F, Kurtović M, Nikolić D (2013) Genetic identification of ‘Bistrica’ and its synonyms ‘Pozegača’ and ‘Hauszwetsche’ (Prunus domestica L.) using SSRs. Acta Hortic 976:285–289

    Article  Google Scholar 

  • Halapija Kazija D, Jelačić T, Vujević P, Milinović B, Čiček D, Biško A, Pejić I, Šimon S, Žulj Mihaljević M, Pecina M, Nikolić D, Grahić J, Drkenda P, Gaši F (2014) Plum germplasm in Croatia and neighbouring countries assessed by microsatellites and DUS descriptors. Tree Genet Genom 10:761–778

    Article  Google Scholar 

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

    Article  Google Scholar 

  • Hedrick UP (1911) The plums of New York. New York State Deparment of Agriculture 28, Annual Report, vol 3, part III. Lyon Company, Albany

  • Hjeltnes SH, Giovannini D, Blouin M, Benedikova D, Drogoudi P, Höfer M, Lacis G, Ognjanov V, Lateur M, Engels JM, Maggioni L (2017) PRUNDOC—a project to define accessions for the European Collection. Acta Hortic 1175:19–24. https://doi.org/10.17660/ActaHortic.2017.1175.5

    Article  Google Scholar 

  • Horvath A, Balsemin E, Barbot JC, Christmann H, Manzano G, Reynet P, Laigret F, Mariette S (2011) Phenotypic variability and genetic structure in plum (Prunus domestica L.), cherry plum (P. cerasifera Ehrh.) and sloe (P. spinosa L.). Sci Hortic 129:283–293

    Article  CAS  Google Scholar 

  • Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94. https://doi.org/10.1186/1471-2156-11-94

    Article  PubMed  PubMed Central  Google Scholar 

  • Kassambara A, Mundt F (2017) Factoextra: extract and visualize the results of multivariate data analyses. R package version 1.0.5. https://CRAN.R-project.org/package=factoextra

  • Laurens F, Aranzana MJ, Arús P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grapadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E (2018) An integrated approach for increasing breeding efficiency in apple and peach in Europe. Hortic Res 1(5):11. https://doi.org/10.1038/s41438-018-0016-3

    Article  CAS  Google Scholar 

  • Le S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25(1):1–18. https://doi.org/10.18637/jss.v025.i01

    Article  Google Scholar 

  • Ligges U, Mächler M (2003) Scatterplot3d—an R package for visualizing multivariate data. J Stat Softw 8(11):1–20

    Article  Google Scholar 

  • Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K (2018) Cluster: cluster analysis basics and extensions. R package version 2.0.7-1

  • Makovics-Zsohár N, Tóth M, Surányi D, Kovács S, Hegedüs A, Halász J (2017) Simple sequence repeat markers reveal Hungarian plum (Prunus domestica L.) germplasm as a valuable gene resource. HortScience 52:1655–1660

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Mariette S, Tavaud M, Arunyawat U, Capdeville G, Millan M (2010) Salin F (2010) Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. BMC Genet 11:77. https://doi.org/10.1186/1471-2156-11-77

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meirmans P, Van Tienderen P (2004) Genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794

    Article  Google Scholar 

  • Merkouropoulos G, Ganopoulos I, Tsaftaris A, Papadopoulos I, Drogoudi P (2016) Combination of high resolution melting (HRM) analysis and SSR molecular markers speeds up plum genotyping: case study genotyping the Greek plum GeneBank collection. Plant Genet Resour 15:366–375. https://doi.org/10.1017/S1479262116000022

    Article  CAS  Google Scholar 

  • Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Linge CD, Foschi S, Banchi E, Barreneche T, Quilot-Turion B, Lambert P, Pascal T, Iglesias I, Carbó J, Wang L-R, Ma R-J, Li X-W, Gao Z-S, Nazzicari N, Troggio M, Bassi D, Rossini L, Verde I, Laurens F, Arús P, Aranzana MJ (2015) Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. PLoS One. https://doi.org/10.1371/journal.pone.0136803

    Article  PubMed  PubMed Central  Google Scholar 

  • Milošević T, Milošević N (2012) Phenotypic diversity of autochtonous European (Prunus domestica L.) and damson (Prunus insititia L.) plum accessions based on multvariate analysis. Hortic Sci (Prague) 39(1):8–20

    Google Scholar 

  • Muller LAH, McCusker JH (2009) Microsatellite analysis of genetic diversity among clinical and nonclinical Saccharomyces cerevisiae isolates suggests heterozygote advantage in clinical environments. Mol Ecol 18:2779–2786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muranty H, Denancé C, Feugey L, Crépin J-L, Barbier Y, Tartarini S, Ordidge M, Troggio M, Lateur M, Nybom H, Paprstein F, Laurens F, Durel CE (2020) Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC Plant Biol 20:2. https://doi.org/10.1186/s12870-019-2171-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nybom H, Garkava-Gustavsson L (2009) Gene banks: for breeding, research or public entertainment. Acta Hortic 814:71–75

    Article  Google Scholar 

  • Ohta T, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22:201–204

    Article  CAS  PubMed  Google Scholar 

  • Ordidge M, Kirdwichai P, Baksh MF, Venison EP, Gibbings JG, Dunwell JM (2018) Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships. PLoS One. https://doi.org/10.1371/journal.pone.0202405

    Article  PubMed  PubMed Central  Google Scholar 

  • Pagès J (2014) Multiple factor analysis by example using R. Chapman & Hall/CRC The R Series, London, p 272

    Book  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Reales A, Sargent DJ, Tobutt KR, Rivera D (2010) Phylogenetics of Eurasian plums. Prunus L. section Prunus (Rosaceae), according to coding and non-coding chloroplast DNA sequences. Tree Genet Genom 6:37–45

    Article  Google Scholar 

  • Rohlf FJ (2000) NTSYS-Pc: numerical taxonomy and multivariate analysis system (version 2.1). Exeter Software, Setauket

    Google Scholar 

  • R Core Team (2018) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/

  • Sehic J, Nybom H, Hjeltnes SH, Gaši F (2015) Genetic diversity and structure of Nordic plum germplasm preserved ex situ and on-farm. Sci Horticult 160:195–202

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M, Fernandez-Fernandez F, Evans KM, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Miranda C, Gassmann J, Kellerhalls M, Suprun I, Pikunova AV, Krasova NG, Torutaeva E, Dondini L, Tartarini S, Laurens F, Durel CE (2016) Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level. BMC Plant Biol 16(1):130. https://doi.org/10.1186/s12870-016-0818-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton J-M, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE (2017) Genome-wide association mapping of flowering and ripening periods in apple. Front Plant Sci. https://doi.org/10.3389/fpls.2017.01923

    Article  PubMed  PubMed Central  Google Scholar 

  • Urrestarazu J, Errea P, Miranda C, Santesteban LG, Pina A (2018) Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying. PLoS One 13(4):e0195591

    Article  PubMed  PubMed Central  Google Scholar 

  • Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sánchez GJ, Doebley J (2008) Population structure and genetic diversity of New World maize races assessed by DNA microsatellites. Am J Bot 95:1240–1253

    Article  PubMed  Google Scholar 

  • Woldring H (2000) On the origin of plums: a study of sloe, damson, cherry plum, domestic plums and their intermediates. Palaeohistoria 40:535–562

    Google Scholar 

  • Xuan H, Ding Y, Spann D, Möller O, Büchele M, Neumüller M (2011) Microsatellite markers (SSR) as a tool to assist in identification of European plum (Prunus domestica L.). Acta Hort 918:689–692

    Article  Google Scholar 

  • Zhebentyayeva T, Shankar V, Scorza R, Callahan A, Ravelonandro C, Castro S, DeJong T, Saski CA, Dardick C (2019) Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping. Hortic Res 6:12. https://doi.org/10.1038/s41438-018-0090-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Financial support was obtained through the ECPGR Activity Grant Scheme (Phase IX) First Call (PRUNDOC Project) and Fifth Call (Prunus Alignment Project). Valuable information on the plant material was supplied by Zsusanna Békefi, Hedi Kaldmäe, Erika Zetochová.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to F. Gaši.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 49 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gaši, F., Sehic, J., Grahic, J. et al. Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe. Genet Resour Crop Evol 67, 1137–1161 (2020). https://doi.org/10.1007/s10722-020-00901-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-020-00901-y

Keywords

Navigation