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Until now, the studies of diversity and genetic structure conducted in European apple have been based on the analyses of material from limited geographic areas (mostly nation-scale) [11, 14, 22–26].By contrast, the extent and structure of the apple genetic diversity conserved at a European level have remained largely unknown.

The gradual replacement of the traditional and locally well-adapted cultivars by a few wide-spread modern varieties has led to a dramatic loss of genetic diversity in the orchards and may also hamper future plant breeding.

Data allowed identifying some obvious labeling errors, e.g., X2698 ‘Court Pendu Plat’ which was shown to be the rootstock ‘MM106’, or CRAW-0362 ‘Transparente de Croncels’ which was found likely to actually be ‘Filippa’ (Additional file 1).

Following these observations, the apple germplasm dataset was reduced to 2,031 unique genotypes (i.e., exhibiting distinct SSR profiles).

The cumulative probability of identity (P, thus highlighting the low risk of erroneous attribution of accessions to duplicate groups.

Redundancies were found both within and between collections, leading to the confirmation of numerous previously documented synonyms (e.g., ‘Papirovka’ and ‘White Transparent’, ‘London Pippin’ and ‘Calville du Roi’, or ‘Président van Dievoet’ and ‘Cabarette’) and allowing the putative identification of numerous unknown synonyms or mutant groups (e.g., ‘Gloria Mundi’ = ‘Mela Zamboni’ = ‘Audiena de Oroz’ = ‘Belle Louronnaise’, ‘Court-Pendu Plat/Doux/Gris’ = ‘Krátkostopka královská’, ‘Reinette de Champagne’ = ‘Maestro Sagarra’ or ‘Reinette Simirenko’ = ‘Renetta Walder’ = ‘Burdinche’).

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