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Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers


In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10−28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014–0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as “King of Pippin” and “Calville Rouge d’Hiver” as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

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The authors thank the Fondation pour la Recherche sur la Biodiversité (FRB), which contributed to the funding of this study (entitled “CorePom” AAP-IN-2009-14), and the French “Pays de la Loire” region for the post-doctoral grant of L. Lassois.

They greatly thank all of the following amateur groups, associations, governmental and non-governmental organizations for their kind contribution of apple leaf material for this study, in addition to their general support and collaboration:

• Association Nationale des Amateurs Bénévoles pour la Sauvegarde des Variétés Fruitières Régionales en voie de Disparition, dite “Les Croqueurs de Pommes®” (especially J. Lefèvre, J. Marchand, J.C. Hénin, H. Fourrey, C. Scribe)

• Association “Les Mordus de la Pomme” (especially J.F. Aubert)

• Association pour la Sauvegarde des Variétés Fruitières du Terroir, dite “I z’on creuqué eun’pomm” (especially E. Verbrugghe)

• Association “Fruits Oubliés Réseau” (especially C. Sunt)

• Confédération des Producteurs de Fruits d’Alsace (especially P. Heitzler, D. Siegel)

• Conseil Général du Tarn - Service Biodiversité Végétale/Conservatoire des Espèces Fruitières et de Vignes Anciennes (CREFAV) (especially I. Calvière)

• Conservatoire Végétal Régional d’Aquitaine (CVRA) (especially E. Leterme)

• Espaces Naturels Régionaux/Centre Régional de Ressources Génétiques du Nord-Pas-de-Calais (CRRG) (especially J.B. Rey, R. Stievenard)

• Jardin du Luxembourg (especially G. Bachelier)

• Parc Naturel Régional du Luberon (especially J.P. Talichet)

• Société Pomologique du Berry (especially F. Moyse, D. Labouret)

• Verger Conservatoire de Pétré (especially S. Guérin)

• Union Pomologique de France (UPF) (especially D. Retournard)

The staffs of the ANAN genotyping platform of the SFR 149 QUASAV (Angers, France), the GENTYANE genotyping platform (INRA, Clermont-Ferrand, France) and the Unité Expérimentale Horticole (INRA, Angers, France) are warmly acknowledged, for their help in producing the genotyping data and for maintaining the apple germplasm collection in experimental plots, respectively.

Thanks are also due to Xavier Perrier, working at the CIRAD, Montpellier, France, for his valuable assistance in data analysis using DARwin software, to Tristan Marshall for his assistance in using CERVUS software, and to Laurana Serres-Giardi for her help with structure and duplicate analyses.

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Correspondence to Charles-Eric Durel.

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List of the 2163 accessions considered in the present study with their accession code (AcceNumber), name (AcceName), the name of the partner who furnished the leaf sample, their usage (mainly Dessert or Cider apple) and cultivar selection date (Old or Modern = before or after 1950), their ploidy level determined according to the occurrences of three alleles per locus (see text), their duplicate code according to the SSR profile (see text), their subgroup assignment inferred by the STRUCTURE analysis with the highest membership probability (qI), their group prior to the STRUCTURE analysis (subpopulation: 1: Modern cultivars, 2: Old Cider cultivars, 3: Old Dessert cultivars), their involvement in statistical analyses, and their selection in the dessert and cider core collections (see text).

In the “Cultivar Usage” column, the asterisk (*) indicates an accession initially classified as Cider (resp. Dessert) that has finally been considered as Dessert (resp. Cider) in the statistical analyses because of more consistent information derived from its duplicate(s). In addition, seven accessions of the Dessert core collection (“CC-dessert-278” in the column “Core Collection”) identified by “Cider!” were initially considered as Dessert cultivars but finally corrected as Cider cultivars thanks to additional information from partners; since the core collection was already vegetatively propagated and genotyped for further association studies, they were maintained in the Dessert core collection for contingency reasons.

In the “Old/Modern” column, the asterisk (*) indicates an accession initially classified as Old (resp. Modern) that has finally been considered as Modern (resp. Old) in the statistical analyses because of more consistent information derived from its duplicate(s).

In the “Subgroup” column, a bold number indicates that the highest subgroup membership probability (qI) is greater than 0.8.

In the “Analyzed/Excluded” column:

– A indicates an accession that has been considered in the statistical analyses.

– E indicates an accession that has been excluded from the statistical analyses (mostly because another duplicated accession has been retained; in that case, the subgroup membership and the qI probability has been imputed according to the analyzed duplicate accession).

– E (SSR) indicates an accession that has been excluded from the statistical analyses because of an exceedingly low number of SSR marker data (<17 SSR).

– E (Ext.) indicates an accession that has been excluded from the statistical analyses because of its extreme situation in a preliminary FCA.

– E (Rs) indicates an accession that has been excluded from the statistical analyses because of its rootstock status identified using the SSR profile (generally MM106 instead of the expected accession). (XLS 476 kb).

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Lassois, L., Denancé, C., Ravon, E. et al. Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers. Plant Mol Biol Rep 34, 827–844 (2016).

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