MOESM2 of Whole-genome sequence data uncover loss of genetic diversity due to selection

Additional file 2. Pedigree subsets. Impact of using different pedigree subsets that are defined based on depth and completeness on genetic diversity conservation

MOESM1 of Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein–Friesian breeding program from 1986 to 2015

Additional file 1: Fig. S1. Number of SNPs per bin of 50 kb per Bos taurus autosome (BTA)

MOESM2 of Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein–Friesian breeding program from 1986 to 2015

Additional file 2: Table S1. Number of QTL extracted from AnimalQTLdb per trait and trait category

MOESM3 of Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein–Friesian breeding program from 1986 to 2015

Additional file 3: Fig. S2. Moving correlation (of 51 markers) between changes in allele frequency in the 1996–2000 and 2001–2005 periods

MOESM1 of Assigning breed origin to alleles in crossbred animals

Additional file 1. Table S1: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a BC crossbred animal for the chromosome 1. Results are averages (SD) across the 10 replicates. Table S2: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a BC crossbred animal for the chromosome 2. Results are averages (SD) across the 10 replicates. Table S3: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a A(BC) crossbred animal for chromosome 1. Results are averages (SD) across the 10 replicates. Table S4: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a A(BC) crossbred animal for chromosome 2. Results are averages (SD) across the 10 replicates. Table S5: Percentages of BC and A(BC) animals having at least 80 % of assigned alleles, and Spearman rank correlations between the order of the phasing analyses obtained from the forward selection and a predefined order of the same phasing analyses for the A(BC) animals, with a relaxation factor equal to 10 %. Results are averages (SD) across the 10 replicates. Table S6: Percentages of assigned alleles of the chromosomes SSC2 and SSC18 for an EF or a D(EF) animal, and percentages of EF and D(EF) animals having at least 80 % of assigned alleles, with a relaxation factor equal to 10 %. Table S7: Average (SD) percentages of assigned alleles of the chromosomes SSC2 and SSC18 for an EF or a D(EF) animal. Table S8: Percentages of alleles correctly assigned a breed origin (%correct) and incorrectly assigned (%incorrect), for the chromosome 2 with 9 phasing analyses with, or without, the additional rules. Results are averages (SD) across the 10 replicates