Fig. 2

Segregating variants after selection for genetic improvement and conservation (impcons). Relationships are computed based on pedigree, 50 K SNP chip (SNP) or whole-genome sequence (WGS), using either the method described by Yang et al. [24] or the similarity-based method. The first histogram is for all variants (MAF ≥ 1 %), the second for common variants (MAF ≥ 5 %) and the last for rare variants (MAF between 1 and 5 %). In each histogram, the first block corresponds to the case without constraint on the number of selected individuals, the second, third and fourth histograms correspond to the cases that constrain the number of selected individuals to 20, 10 and 5, respectively