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

IRHS INRA AGROCAMPUS Ouest Université d'Angers SFR 4207 QUASAV 42 rue Georges Morel 49071 Beaucouzé cedex France Department of Agricultural Sciences University of Bologna Viale Giuseppe Fanin 44 40127 Bologna Italy Public University of Navarre Campus Arrosadia 31006 Pamplona Spain

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

References provided by Crossref.org