BACKGROUND: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. RESULTS: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. CONCLUSIONS: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

Agroscope Institute for Plant Production Sciences IPS Schloss 1 P O Box 8820 Wädenswil Switzerland

CRA W Centre Wallon de Recherches Agronomiques Plant Breeding and Biodiversity Bâtiment Emile Marchal Rue de Liroux 4 5030 Gembloux Belgium

Department of Agricultural Sciences University of Bologna Viale Giuseppe Fanin 44 40127 Bologna Italy

Department of Plant Breeding Balsgård Fjälkestadsvägen 459 Swedish University of Agricultural Sciences 291 94 Kristianstad Sweden

Department of Plant Breeding Swedish University of Agricultural Sciences Box 101 230 53 Alnarp Sweden

IRHS INRA AGROCAMPUS Ouest Université d'Angers SFR 4207 QUASAV 42 rue Georges Morel 49071 Beaucouzé cedex France

Kyrgyz National Agrarian University 68 Mederova Street 720005 Bishkek Kyrgyzstan

NCRRIH and 5 North Caucasian Regional Research Institute of Horticulture and Viticulture 39 40 letiya Pobedy street Krasnodar 350901 Russian Federation

NIAB EMR East Malling Research East Malling Kent ME19 6BJ United Kingdom

Plateforme Gentyane INRA UMR1095 Genetics Diversity and Ecophysiology of Cereals 63100 Clermont Ferrand France

Public University of Navarre Campus Arrosadia 31006 Pamplona Spain

RBIPH Research and Breeding Institute of Pomology Holovousy Ltd 508 01 Horice Czech Republic

School of Agriculture Policy and Development University of Reading Whiteknights Reading RG6 6AR UK

VNIISPK The All Russian Research Institute of Fruit Crop Breeding 302530 p o Zhilina Orel district Russian Federation

Washington State University Tree Fruit Research and Extension Center 1100 N Western Ave Wenatchee WA 98801 USA

Zobrazit více v PubMed

Food and Agriculture Organization of the United Nations. FAO statistics database on the World Wide Web http://faostat.fao.org/site/567/DesktopDefault.aspx?PageID0567#ancor. Accessed 27 July 2015.

Hokanson SC, Lamboy WF, Szewc-McFadden AK, McFerson JR. Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids. Euphytica. 2001;118:281–94. doi: 10.1023/A:1017591202215. DOI

Janick J, Moore JN. Fruit breeding. Volume I: tree and tropical fruits. New York: Wiley; 1996.

Laurens F, Durel CE, Patocchi A, Peil A, Salvi S, Tartarini S, Velasco R, van de Weg WE. Review on apple genetics and breeding programs and presentation of a new initiative of a news European initiative to increase fruit breeding efficiency. J Fruit Sci. 2010;27:102–7.

Noiton DAM, Alspach PA. Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Soc Hortic Sci. 1996;121:773–82.

Brooks RM, Olmo HP. Register of new fruit and nut varieties list 35. HortScience. 1991;26:951–78.

Brooks RM, Olmo HP. Register of new fruit and nut varieties list 36. HortScience. 1994;29:942–69.

Brooks RM, Olmo HP. Register of fruit and nut varieties. Alexandria: ASHS; 1997.

de Vicente . The evolving role of genebanks in the fast-developing field of molecular genetics. Ed. Issues in genetic resources No XI, August 2004. Rome: International Plant Genetic Resources Institute-IPGRI; 2004.

Jing RC, Vershinin A, Grzebyta J, Shaw P, Smykal P, Marshall D, Ambrose MJ, Ellis THN, Flavell AJ. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol. 2010;10:44. doi: 10.1186/1471-2148-10-44. PubMed DOI PMC

van Treuren R, Kemp H, Ernsting G, Jongejans B, Houtman H, Visser L. Microsatellite genotyping of apple (Malus x domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genet Resour Crop Evol. 2010;57:853–65. doi: 10.1007/s10722-009-9525-0. DOI

Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. Investig Genet. 2014;5:1. doi: 10.1186/2041-2223-5-1. PubMed DOI PMC

Bacilieri R, Lacombe T, Le Cunff L, Di Vecchi-Staraz M, Laucou V, Genna B, Péros JP, This P, Boursiquot JM. Genetic structure in cultivated grapevines is linked to geography and human selection. BMC Plant Biol. 2013;13:25. doi: 10.1186/1471-2229-13-25. PubMed DOI PMC

Bühlmann A, Gassmann J, Ingenfeld A, Hunziker K, Kellerhals M, Frey JE. Molecular characterization of the Swiss fruit genetic resources. Erwerbs-Obstbau. 2015;57:29–34. doi: 10.1007/s10341-015-0230-1. DOI

McCouch SR, McNally KL, Wang W, Sackville HR. Genomics of gene banks: a case study in rice. Am J Bot. 2012;99:407–23. doi: 10.3732/ajb.1100385. PubMed DOI

Wünsch A, Hormaza JI. Cultivar identification and genetic fingerprinting of temperate fruit tree species using DNA markers. Euphytica. 2002;125:59–67. doi: 10.1023/A:1015723805293. DOI

Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 2004;5:435–45. doi: 10.1038/nrg1348. PubMed DOI

Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ. Current trends in microsatellite genotyping. Mol Ecol Resour. 2011;11:591–611. doi: 10.1111/j.1755-0998.2011.03014.x. PubMed DOI

Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK. Microsatellite markers: an overview of the recent progress in plants. Euphytica. 2011;177:309–34. doi: 10.1007/s10681-010-0286-9. DOI

Sunnucks P. Efficient genetic markers for population biology. Trends Ecol Evol. 2000;15:199–03. doi: 10.1016/S0169-5347(00)01825-5. PubMed DOI

Urrestarazu J, Royo JB, Santesteban LG, Miranda CM. Evaluating the influence of the microsatellite marker set on the genetic structure inferred in Pyrus communis L. PLoS One. 2015;10:e0138417. doi: 10.1371/journal.pone.0138417. PubMed DOI PMC

Garkava-Gustavsson L, Kolodinska Brantestam A, Sehic J, Nybom H. Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis. Hereditas. 2008;145:99–112. doi: 10.1111/j.0018-0661.2008.02042.x. PubMed DOI

Lassois L, Denancé C, Ravon E, Guyader A, Guisnel R, Hibrand-Saint-Oyant L, Poncet C, Lasserre-Zuber P, Feugey L, Durel CE. Genetic diversity, population structure, parentage analysis and construction of core collections in the French apple germplasm based on SSR markers. Plant Mol Biol Rep. 2015

Liang W, Dondini L, De Franceschi P, Paris R, Sansavini S, Tartarini S. Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germplasm. Plant Mol Biol Rep. 2015;33:458–73. doi: 10.1007/s11105-014-0754-9. DOI

Patzak J, Paprštein F, Henychová A, Sedlák J. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus × domestica) genetic resources. Genome. 2012;55:647–65. doi: 10.1139/g2012-054. PubMed DOI

Urrestarazu J, Miranda C, Santesteban LG, Royo JB. Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers. Tree Genet Genomes. 2012;8:1163–80. doi: 10.1007/s11295-012-0502-y. DOI

Sehic J, Garkava-Gustavsson L, Nybom H. More harmonization needed for DNA-based identification of apple germplsm. Acta Hortic. 2013;976:277–83. doi: 10.17660/ActaHortic.2013.976.37. DOI

Laurens F, Aranzana MJ, Arús P, Bassi D, Bonany J, Corelli L, Durel CE, Mes J, Pascal T, Patocchi A, Peil A, Quilot B, Salvi S, Tartarini S, Troggio M, Vecchietti A, Velasco R, van de Weg WE. Review of fruit genetics and breeding programmes and a new European initiative to increase fruit breeding efficiency. Acta Hortic. 2012;929:95–102.

Morin PA, Manaster C, Mesnick SL, Holland R. Normalization and binning of historical and multi-source microsatellite data: overcoming the problems of allele size shift with ALLELOGRAM. Mol Ecol Resour. 2009;9:1451–5. doi: 10.1111/j.1755-0998.2009.02672.x. PubMed DOI

Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol. 2014;4:4399–28. PubMed PMC

Gasi F, Simon S, Pojskic N, Kurtovic M, Pejic I. Genetic assessment of apple germplasm in Bosnia and Herzegovina using microsatellite and morphologic markers. Sci Hortic. 2010;126:164–71. doi: 10.1016/j.scienta.2010.07.002. DOI

Gharghani A, Zamani Z, Talaie A, Oraguzie NC, Fatahi R, Hajnajari H, Wiedow C, Gardiner SE. Genetic identity and relationships of Iranian apple (Malus x domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis. Genet Resour Crop Evol. 2009;56:829–42. doi: 10.1007/s10722-008-9404-0. DOI

Gao Y, Liu F, Wang K, Wang D, Gong X, Liu L, Richards CM, Henk AD, Volk GM. Genetic diversity of Malus cultivars and wild relatives in the Chinese National Repository of Apple Germplasm Resources. Tree Genet Genomes. 2015

Gross BL, Volk GM, Richards CM, Forsline CL, Fazio G, Chao CT. Identification of “duplicate” accessions within the USDA-ARS National Plant Germplasm System Malus Collection. J Am Soc Hortic Sci. 2012;137:333–42.

Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F, Le Cam B, Nerseyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 2012;8:e1002703. doi: 10.1371/journal.pgen.1002703. PubMed DOI PMC

Cornille A, Giraud T, Smulders MJM, Roldán-Ruiz I, Gladieux P. The domestication and evolutionary ecology of apples. Trends Genet. 2014;30:57–65. doi: 10.1016/j.tig.2013.10.002. PubMed DOI

Gross BL, Henk AD, Richards CM, Fazio G, Volk GM. Genetic diversity in Malus x domestica (Rosaceae) through time in response to domestication. Am J Bot. 2014;101:1770–9. doi: 10.3732/ajb.1400297. PubMed DOI

Hartmann HT, Kester DE, Davies FT, Geneve RL. Plant propagation: principles and practices. 7. Upper Saddle River: Prentice Hall; 2002.

Zohary D, Hopf D. Domestication of plants in the Old World: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley. Oxford: Oxford University Press; 2000.

De Franceschi P, Dondini L, Sanzol J. Molecular bases and evolutionary dynamics of self-incompatibility in the Pyrinae (Rosaceae) J Exp Bot. 2012;63:4015–32. doi: 10.1093/jxb/ers108. PubMed DOI

Knutson L, Stoner AK. Biotic diversity and germplasm preservation: global imperative. Boston: Kluwer Academic Publishers; 1989.

McCouch S. Diversifying selection in plant breeding. PLoS Biol. 2004;2:e347. doi: 10.1371/journal.pbio.0020347. PubMed DOI PMC

World Apple and Pear Association . European apple and pear crop forecast. Brussels: World Apple and Pear Association; 2013.

Miller AJ, Gross BL. Forest to field: perennial fruit crop domestication. Am J Bot. 2011;98:1389–1414. doi: 10.3732/ajb.1000522. PubMed DOI

Biswas S, Akey JM. Genomic insights into positive selection. Trends Genet. 2006;22:437–46. doi: 10.1016/j.tig.2006.06.005. PubMed DOI

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

Blanquart F, Gandon S, Nuismer SL. The effects of migration and drift on local adaptation to a heterogeneous environment. J Evol Biol. 2012;25:1351–63. doi: 10.1111/j.1420-9101.2012.02524.x. PubMed DOI

Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol. 2013;13:39. doi: 10.1186/1471-2229-13-39. PubMed DOI PMC

Lia VV, Poggio L, Confalonieri VA. Microsatellite variation in maize landraces from Northwestern Argentina: genetic diversity, population structure and racial affiliations. Theor Appl Genet. 2009;119:1053–67. doi: 10.1007/s00122-009-1108-0. PubMed DOI

Li XW, Meng XQ, Jia HJ, Yu ML, Ma RJ, Wang LR, Cao K, Shen ZJ, Niu L, Tian JB, Chen MJ, Xie M, Arus P, Gao ZS, Aranzana MJ. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genet. 2013;14:84. doi: 10.1186/1471-2156-14-84. PubMed DOI PMC

Jacobs MMJ, Smulders MJM, van den Berg RG, Vosman B. What’s in a name; genetic structure in Solanum section Petota studied using population-genetic tools. BMC Evol Biol. 2011;11:42. doi: 10.1186/1471-2148-11-42. PubMed DOI PMC

Jing R, Ambrose MA, Knox MR, Smykal P, Hybl M, Ramos A, Caminero C, Burstin J, Duc G, van Soest LJM, Swiecicki WK, Pereira MG, Vishnyakova M, Davenport GF, Flavell AJ, Ellis THN. Genetic diversity in European Pisum germplasm collections. Theor Appl Genet. 2012;125:365–80. doi: 10.1007/s00122-012-1839-1. PubMed DOI PMC

Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment. Mol Ecol. 2007;16:1099–2006. doi: 10.1111/j.1365-294X.2007.03089.x. PubMed DOI

Salvi S, Micheletti D, Magnago P, Fontanari M, Viola R, Pindo M, Velasco R. One-step reconstruction of multi-generation pedigree networks in apple (Malus × domestica Borkh.) and the parentage of Golden Delicious. Mol Breed. 2014;34:511–24. doi: 10.1007/s11032-014-0054-y. DOI

Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, et al. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh) PloS ONE. 2014;9:e110377. doi: 10.1371/journal.pone.0110377. PubMed DOI PMC

Bianco L, Cestaro A, Linsmith G, Muranty H, Denancé C, Théron A, Poncet C, Micheletti D, Kersshbamer E, Di Pierro EA, Larger S, Pindo M, van de Weg WE, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M. Development and validation of the Axiom®Apple480K SNP genotyping array. Plant J. 2016;86:62–74. PubMed

Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, et al. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PloS ONE. 2012;7:e31745. doi: 10.1371/journal.pone.0031745. PubMed DOI PMC

Morgan J, Richards A, Dowle E. The new book of Apples: the definitive guide to apples, including over 2000 varieties. London: Ebury Press; 2002.

Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus x domestica Borkh. core subset collection. Theor Appl Genet. 1998;97:671–83. doi: 10.1007/s001220050943. DOI

Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, van de Weg E, Gessler C. Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.) Mol Breed. 2002;10:217–41. doi: 10.1023/A:1020525906332. DOI

Silfverberg-Dilworth E, Matasci CL, van de Weg WE, van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A. Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes. 2006;2:202–24. doi: 10.1007/s11295-006-0045-1. DOI

Vinatzer BA, Patocchi A, Tartarini S, Gianfranceschi L, Sansavini S, Gessler C. Isolation of two microsatellite markers from BAC clones of the Vf scab resistance region and molecular characterization of scab-resistant accessions in Malus germplasm. Plant Breed. 2004;123:321–6. doi: 10.1111/j.1439-0523.2004.00973.x. DOI

Evans KM, Fernández F, Govan C. Harmonising fingerprinting protocols to allow comparisons between germplasm collections - Pyrus. Acta Hortic. 2009;814:103–6. doi: 10.17660/ActaHortic.2009.814.10. DOI

Fernández-Fernández F. Fingerprinting the National apple and pear collections. Final report of DEFRA research project GC0140. 2010. pp. 1–18.

Hardy OJ, Vekemans X. SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes. 2002;2:618–20. doi: 10.1046/j.1471-8286.2002.00305.x. DOI

Waits LP, Luikart G, Taberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol. 2001;10:249–56. doi: 10.1046/j.1365-294X.2001.01185.x. PubMed DOI

Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59. PubMed PMC

Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14:2611–20. doi: 10.1111/j.1365-294X.2005.02553.x. PubMed DOI

Earl DA, von Holdt BM. Structure harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Cons Genet Resour. 2012;4:359–61. doi: 10.1007/s12686-011-9548-7. DOI

Breton C, Pinatel C, Médail F, Bonhomme F, Bervillé A. Comparison between classical and Bayesian methods to investigate the history of olive cultivars using SSR-polymorphisms. Plant Sci. 2008;175:524–32. doi: 10.1016/j.plantsci.2008.05.025. DOI

Miranda C, Urrestarazu J, Santesteban LG, Royo JB, Urbina V. Genetic diversity and structure in a collection of ancient Spanish pear cultivars assessed by microsatellite markers. J Am Soc Hortic Sci. 2010;135:428–37.

Marra FP, Caruso T, Costa F, Di Vaio C, Mafrica R, Marchese A. Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers. Tree Genet Genomes. 2013;9:961–73. doi: 10.1007/s11295-013-0609-9. DOI

Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007;23:801–6. doi: 10.1093/bioinformatics/btm233. PubMed DOI

Rosenberg NA. Distruct: a program for the graphical display of population structure. Mol Ecol Notes. 2004;4:137–8. doi: 10.1046/j.1471-8286.2003.00566.x. DOI

Perrier X, Jacquemoud-Collet JP. DARwin Software. 2006.

Meirmans PG, van Tienderen PH. Genotype and Genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes. 2004;4:792–4. doi: 10.1111/j.1471-8286.2004.00770.x. DOI

Goudet J. FSTAT 2.9.3.2. 2002.

Lacombe T, Boursiquot JM, Laucou V, Di Vecchi-Staraz M, Péros JP. This P. Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.) Theor Appl Genet. 2013;126:401–14. doi: 10.1007/s00122-012-1988-2. PubMed DOI

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin

Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple