ECPGR recommended SSR loci for analyses of European plum (Prunus domestica) collections

Main Article Content

Hilde Nybom
https://orcid.org/0000-0002-4355-8106
Daniela Giovannini
https://orcid.org/0000-0003-0977-390X
Matt Ordidge
https://orcid.org/0000-0003-0115-5218
Stein Harald Hjeltnes
Jasmin Grahić
Fuad Gaši
https://orcid.org/0000-0002-7348-7433

Abstract

A set of nine Simple Sequence Repeat (SSR) loci, approved by the ECPGR Prunus working group, are proposed as a standard set for genotyping European plum accessions. These loci show sufficient reliability in spite of problems caused by hexaploidy. Polymorphism in the loci is high and enables differentiation between unique plum accessions as well as analyses of genetic grouping and overall genetic structure. A set of seven reference accessions are described. A compiled dataset with allelic information for 165 accessions is presented. Genetic structure reveals three different K-values (2, 4 and 9) demonstrating a major dichotomy between Prunus insititia-related accessions and cultivars belonging to Prunus domestica sensu stricto, as well as differentiation among minor subgroups defined by pomological traits and geographical origin.

Article Details

How to Cite
Nybom, H., Giovannini, D., Ordidge, M., Hjeltnes, S. H., Grahić, J. and Gaši, F. (2020) “ECPGR recommended SSR loci for analyses of European plum (Prunus domestica) collections”, Genetic Resources, 1(1), pp. 40-48. doi: 10.46265/genresj.2020.1.40-48.
Section
Short Communications
References

Abdallah, Donia et al. (2019). “Analysis of self-incompatibility and genetic diversity in diploid and hexaploid plum genotypes”. Frontiers in Plant Science 10. URL: https://dx.doi.org/10.3389/fpls.2019.00896.

Adler, D and D Murdoch (2013). rgl: 3D visualization device system (Open GL) (R package version 0.93.945). URL: http://rgl.neoscientists.org.

Akkaya, M S, A A Bhagwat, and P B Cregan (1992). “Length polymorphisms of simple sequence repeat DNA in soybean”. Genetics 132, pp. 1131–1139. URL: https://www.genetics.org/content/132/4/1131.

Cipriani, G. et al. (1999). “AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus”. Theoretical and Applied Genetics 99(1-2), pp. 65–72. URL: https://dx.doi.org/10.1007/s001220051209.

Clark, Lindsay V. and Marie Jasieniuk (2011). “POLYSAT: an R package for polyploid microsatellite analysis”. Molecular Ecology Resources 11(3), pp. 562–566. URL: https://dx.doi.org/10.1111/j.1755-0998.2011.02985.x.

Clarke, J. B. and K. R. Tobutt (2009). “A standard set of accessions, microsatellites and genotypes for harmonising the fingerprinting of cherry collections of the ECPGR”. Acta Horticulturae 814(814), pp. 615–618. URL: https://dx.doi.org/10.17660/actahortic.2009.814.104.

Decroocq, V. et al. (2003). “Development and transferability of apricot and grape EST microsatellite markers across taxa”. Theoretical and Applied Genetics 106(5), pp. 912–922. URL: https://dx.doi.org/10.1007/s00122-002-1158-z.

Dirlewanger, E. et al. (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.)” Theoretical and Applied Genetics 105(1), pp. 127–138. URL: https://dx.doi.org/10.1007/s00122-002-0867-7.

Earl, D A and B M Von Holdt (2011). “Structure harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method”. Conservation Genetics Resources 4, pp. 359–361. URL: https://doi.org/10.1007/s12686-011-9548-7.

Evanno, G., S. Regnaut, and J. Goudet (2005). “Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study”. Molecular Ecology 14(8), pp. 2611–2620. URL: https://dx.doi.org/10.1111/j.1365-294x.2005.02553.x.

Evans, K. M., F. Fernández-Fernández, and C. Govan (2009). “Harmonizing fingerprinting protocols to allow comparisons between germplasm collections - Pyrus”. Acta Horticulturae 814(814), pp. 103–106. URL: https://dx.doi.org/10.17660/actahortic.2009.814.10.

Excoffier, L, P E Smouse, and J M Quattro (1992). “Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data”. Genetics 131, pp. 479–491. URL: https://www.genetics.org/content/131/2/479.long.

Gaši, F. et al. (2020). “Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe”. Genetic Resources and Crop Evolution 67(5), pp. 1137–1161. URL: https://dx.doi.org/10.1007/s10722-020-00901-y.

Gharbi, O., A. Wünsch, and J. Rodrigo (2014). “Characterization of accessions of ‘Reine Claude Verte’ plum using Prunus SRR and phenotypic traits”. Scientia Horticulturae 169, pp. 57–65. URL: https://dx.doi.org/10.1016/j.scienta.2014.02.018.

Halapija-Kazija, D., T. Jelaˇci´c, et al. (2014). “Plum germplasm in Croatia and neighboring countries assessed by microsatellites and DUS descriptors”. Tree Genetics & Genomes 10(3), pp. 761–778. URL: https://dx.doi.org/10.1007/s11295-014-0721-5.

Halapija-Kazija, D., P. Vujevi´c, et al. (2013). “Genetic identification of ’Bistrica’ and its synonyms ’Pozegaca’ and ’Hauszwetsche’ (Prunus domestica L.) using SSRs”. Acta Horticulturae 976(976), pp. 285–289. URL: https://dx.doi.org/10.17660/actahortic.2013.976.38.

Hardy, Olivier J. and Xavier Vekemans (2002). “SPAGeDI: a versatile computer program to analyse spatial genetic structure at the individual or population levels”. Molecular Ecology Notes 2(4), pp. 618–620. URL: https://dx.doi.org/10.1046/j.1471-8286.2002.00305.x.

Horvath, Aniko et al. (2011). “Phenotypic variability and genetic structure in plum (Prunus domestica L.), cherry plum (P. cerasifera Ehrh.) and sloe (P. spinosa L.)” Scientia Horticulturae 129(2), pp. 283–293. URL: https://dx.doi.org/10.1016/j.scienta.2011.03.049.

Makovics-Zsohár, Noémi et al. (2017). “Simple sequence repeat markers reveal Hungarian plum (Prunus domestica L.) germplasm as a valuable gene resource”. HortScience 52(12), pp. 1655–1660. URL: https://dx.doi.org/10.21273/hortsci12406-17.

Manco, Rosanna et al. (2019). “Molecular and phenotypic diversity of traditional European plum (Prunus domestica L.) germplasm of Southern Italy”. Sustainability 11(15), pp. 4112–4112. URL: https://dx.doi.org/10.3390/su11154112.

Meirmans, Patrick G. and Peter H. Van Tienderen (2004). “Genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms”. Molecular Ecology Notes 4(4), pp. 792–794. URL: https://dx.doi.org/10.1111/j.1471-8286.2004.00770.x.

Meland, M. et al. (2020). “Identifying pollen donors and success rate of individual pollinizers in European plum (Prunus domestica L.) using microsatellite markers”. Agronomy 10(2), pp. 264–264. URL: https://dx.doi.org/10.3390/agronomy10020264.

Merkouropoulos, Georgios et al. (2017). “Combination of high resolution melting (HRM) analysis and SSR molecular markers speeds up plum genotyping: case study genotyping the Greek plum GeneBank collection”. Plant Genetic Resources 15(4), pp. 366–375. URL: https://dx.doi.org/10.1017/s1479262116000022.

Mnejja, M. et al. (2004). “Simple-sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl.) are highly polymorphic and transferable to peach and almond”. Molecular Ecology Notes 4(2), pp. 163–166. URL: https://dx.doi.org/10.1111/j.1471-8286.2004.00603.x.

Muller, Ludo A. H. and John H. McCusker (2009). “Microsatellite analysis of genetic diversity among clinical and nonclinical Saccharomyces cerevisiae isolates suggests heterozygote advantage in clinical environments”. Molecular Ecology 18(13), pp. 2779–2786. URL: https://dx.doi.org/10.1111/j.1365-294x.2009.04234.x.

Nei, M (1978). “Estimation of average heterozygosity and genetic distance from a small number of individuals”. Genetics 89, pp. 583–590. URL: https://www.genetics.org/content/89/3/583.

Nybom, Hilde and Kurt Weising (2010). “DNA-based identification of clonally propagated cultivars”. In: Plant Breeding Reviews. Ed. by Jules Janick et al. Vol. 34. USA: Wiley, pp. 221–295. DOI: 10.1002/9780470880579.ch6. URL: https://doi.org/10.1002/9780470880579.ch6.

Öz, M. H. et al. (2013). “Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers”. Genetics and Molecular Research 12(4), pp. 5310–5320. URL: https://dx.doi.org/10.4238/2013.november.7.6.

Pop, Rodica et al. (2018). “Genetic diversity and population structure of plum accessions from a Romanian germplasm collection assessed by simple sequence repeat (SSR) markers”. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 46(1), pp. 90–96. URL: https://dx.doi.org/10.15835/nbha46110884.

Pritchard, J K, M Stephens, and P Donnelly (2000). “Inference of population structure using multilocus genotype data”. Genetics 155, pp. 945–959. URL: https://www.genetics.org/content/155/2/945.

R Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: http://www.R-project.org/.

Reales, Antonio et al. (2010). “Phylogenetics of Eurasian plums, Prunus L. section Prunus (Rosaceae), according to coding and non-coding chloroplast DNA sequences”. Tree Genetics & Genomes 6(1), pp. 37–45. URL: https://dx.doi.org/10.1007/s11295-009-0226-9.

Sehic, J., L. Garkava-Gustavsson, and Hilde Nybom (2013). “More harmonization needed for DNA-based identification of apple germplasm”. Acta Horticulturae 976(976), pp. 277–283. URL: https://dx.doi.org/10.17660/actahortic.2013.976.37.

Sehic, J., F. Gaši, et al. (2019). “Genetic diversity of Prunus domestica selected from ten countries across Europe”. Acta Horticulturae 1260(1260), pp. 159–162. URL: https://dx.doi.org/10.17660/actahortic.2019.1260.25.

Sehic, J., H. Nybom, et al. (2015). “Genetic diversity and structure of Nordic plum germplasm preserved ex situ and on-farm”. Scientia Horticulturae 190, pp. 195–202. URL: https://dx.doi.org/10.1016/j.scienta.2015.03.034.

Urrestarazu, Jorge, Caroline Denancé, et al. (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 Biology 16(1). DOI: 10.1186/s12870-016-0818-0. URL: https://dx.doi.org/10.1186/s12870-016-0818-0.

Urrestarazu, Jorge, Pilar Errea, et al. (2018). “Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying”. PLOS ONE 13(4), e0195591–e0195591. URL: https://dx.doi.org/10.1371/journal.pone.0195591.

Weir, B S and C C Cockerham (1984). “Estimating F-statistics for the analysis of population structure”. Evolution 38, pp. 1358–1370. DOI: 10.2307/2408641.

Xuan, H. et al. (2011). “Microsatellite markers (SSR) as a tool to assist in identification of European plum (Prunus domestica L.)” Acta Horticulturae 918(918), pp. 689–692. URL: https://dx.doi.org/10.17660/actahortic.2011.918.88.

Author Biographies

Hilde Nybom, Swedish University of Agricultural Sciences, Kristianstad, Sweden

Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, SE-29194 Kristianstad, Sweden

Daniela Giovannini, CREA-Research Centre for Olive, Fruit and Citrus Crops, Forlì, Italy

via la Canapona 1 bis, 47121 Forlì, Italy

Matt Ordidge, University of Reading, Great Britain

School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, Great Britain

Stein Harald Hjeltnes, Njøs Fruit and Berry Centre, Leikanger, Norway

Njøsavegen 5, N-6863 Leikanger, Norway

Jasmin Grahić, University of Sarajevo, Sarajevo, Bosnia and Herzegovina

Faculty of Agriculture and Food Sciences

Fuad Gaši, University of Sarajevo, Sarajevo, Bosnia and Herzegovina

Faculty of Agriculture and Food Sciences