Additional file 12: Table S7. Relationships identified for triploids inferred with less than 300 Mendelian Errors (ME) for duos and trios, and less than 1200 tri-hom/di-het with the parent giving a diploid gamete, indicating the preferred name of the triploid offspring (Triploid Offspring) and its MUNQ (MUNQ O), the preferred name of the parent giving a diploid gamete (2n-gamete Parent) and its MUNQ (MUNQ 2n P), the number of ME for the duo triploid-2n-gamete parent (#ME 2n P), the number of tri-hom/di-het SNPs for the duo triploid-2n-gamete parent (# Hom-Het), the preferred name of the parent giving a haploid gamete (n-gamete Parent) and its MUNQ (MUNQ n P), the number of ME for the duo triploid-n-gamete parent (#ME n P), and when available, the number of ME for the trio (# ME trio).

Additional file 12: Table S7. Relationships identified for triploids inferred with less than 300 Mendelian Errors (ME) for duos and trios, and less than 1200 tri-hom/di-het with the parent giving a diploid gamete, indicating the preferred name of the triploid offspring (Triploid Offspring) and its MUNQ (MUNQ O), the preferred name of the parent giving a diploid gamete (2n-gamete Parent) and its MUNQ (MUNQ 2n P), the number of ME for the duo triploid-2n-gamete parent (#ME 2n P), the number of tri-hom/di-het SNPs for the duo triploid-2n-gamete parent (# Hom-Het), the preferred name of the parent giving a haploid gamete (n-gamete Parent) and its MUNQ (MUNQ n P), the number of ME for the duo triploid-n-gamete parent (#ME n P), and when available, the number of ME for the trio (# ME trio).

Additional file 1: Table S1. List of the 1433 unique Malus domestica individuals (MUNQ) involved in the study, with the accession number of the accession used to represent the MUNQ in genotyping (Accession code), the preferred name attributed to the MUNQ (Preferred Name), and its short version (Preferred Name Short), the original reason for genotyping the MUNQ (Origin), their ploidy level (Ploidy), the date of origin, first description, introduction, recording or inclusion in collections of cultivars corresponding to the preferred name (Date), and reference(s) enabling to document the date (Source for date).

Additional file 2: Table S2. List of the 253,095 robust SNPs used in the study, with their chromosome location, and position on chromosome, in bp. SNPs located on chromosome 18 are those located on contigs or scaffold that could not be attributed to a chromosome. SNPs located on chromosome 19 are those for which no clear position could be found (either no BLAST results for the probe, or several equivalent results). Inclusion of a SNP in the 25 K subset is indicated by a “yes” in column “in.25 K.subset”.

Additional file 2: Table S2. List of the 253,095 robust SNPs used in the study, with their chromosome location, and position on chromosome, in bp. SNPs located on chromosome 18 are those located on contigs or scaffold that could not be attributed to a chromosome. SNPs located on chromosome 19 are those for which no clear position could be found (either no BLAST results for the probe, or several equivalent results). Inclusion of a SNP in the 25 K subset is indicated by a “yes” in column “in.25 K.subset”.

Additional file 3: Table S3. Complete parent-offspring trios inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred names of the parents (Preferred Name P1, Preferred Name P2) and their MUNQ (MUNQ P1, MUNQ P2), the number of ME (# ME), presupposed parents (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parents with literature (P1_confirmed and P2_confirmed), consistency of dates, i.e. offspring younger than its inferred parent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent P1 and Date consistent P2). The trios for which presupposed parent(s) were identified are listed in the first 143 lines, while the remaining are below. In each part, the trios are sorted alphabetically according to the preferred name of the offspring. When presupposed parents were identified, parents considered as P1 and P2 were sorted according to literature. For the remaining trios, parents were attributed to P1 and P2 arbitrarily.

Additional file 3: Table S3. Complete parent-offspring trios inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred names of the parents (Preferred Name P1, Preferred Name P2) and their MUNQ (MUNQ P1, MUNQ P2), the number of ME (# ME), presupposed parents (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parents with literature (P1_confirmed and P2_confirmed), consistency of dates, i.e. offspring younger than its inferred parent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent P1 and Date consistent P2). The trios for which presupposed parent(s) were identified are listed in the first 143 lines, while the remaining are below. In each part, the trios are sorted alphabetically according to the preferred name of the offspring. When presupposed parents were identified, parents considered as P1 and P2 were sorted according to literature. For the remaining trios, parents were attributed to P1 and P2 arbitrarily.

Additional file 1: Table S1. List of the 1433 unique Malus domestica individuals (MUNQ) involved in the study, with the accession number of the accession used to represent the MUNQ in genotyping (Accession code), the preferred name attributed to the MUNQ (Preferred Name), and its short version (Preferred Name Short), the original reason for genotyping the MUNQ (Origin), their ploidy level (Ploidy), the date of origin, first description, introduction, recording or inclusion in collections of cultivars corresponding to the preferred name (Date), and reference(s) enabling to document the date (Source for date).

Additional file 5: Table S4. Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred name of the parent (Preferred Name P) and its MUNQ (MUNQ P), the number of ME (# ME), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (one parent confirmed), consistency of dates, i.e. offspring younger than its inferred parent, on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent). The duos for which presupposed parents were identified are listed in the first 25 lines, while the remaining are below. In each part, the duos are sorted alphabetically according to the preferred name of the offspring.

Additional file 5: Table S4. Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred name of the parent (Preferred Name P) and its MUNQ (MUNQ P), the number of ME (# ME), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (one parent confirmed), consistency of dates, i.e. offspring younger than its inferred parent, on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent). The duos for which presupposed parents were identified are listed in the first 25 lines, while the remaining are below. In each part, the duos are sorted alphabetically according to the preferred name of the offspring.