A. Abbreviations, Amplified fragment Length Polymorphism; BLAST: Basic Local Alignment Search Tool; BIC: Bayesian Information Criterion; CPU: Central Processing Unit; DAPC: Discriminant Analysis of Principal Components

, Deoxyribose Nucleic Acid; FAO: Food and Agriculture Organization of the United Nations; F IS : Inbreeding Coefficient; Fst: Fixation Index, DNA

, GDR: Genome Database for Rosaceae; GnpIS: Genetic and Genomic Information System; GSI: Gametophytic Self-Incompatibility; GUI: Graphical User Interface

, HWE: Hardy Weinberg equilibrium; H o : Observed heterozygosity

, INRA: French National Institute for Agricultural Research; LD: Linkage Disequilibrium; LG: Linkage Group; MAF: Minor Allele Frequency

, Mb: Megabase; MCIA: Mésocentre de Calcul Intensif Aquitain; MCMC: Monte Carlo Markov Chain, NCBI: National Center for Biotechnology Information

, Next Generation Sequencing; PC: Principal Component; PCA: Principal Component Analysis; PCoA: Principal Coordinate Analysis; PGTB: Bordeaux Genome-Transcriptome facility, SNP: Single Nucleotide Polymorphism

, Simple Sequence Repeats; TORQUE: Terascale Open-source Resource and QUEue Manager; TPM: Two-Phase Mutation; UEA: Fruit Tree Experimental Unit

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