Table 3.

Proportion of overlap between minor allele frequency spectra calculated using all individuals and using core animals for each core definition and size

Core size	Core definition
	MPA	Rnd	Ped	Fam	Unrel	LPM	LPF	QR
Eigen50	0.85	0.84	0.85	0.84	0.81	0.80	0.79	0.73
Eigen80	0.93	0.94	0.92	0.92	0.87	0.85	0.85	0.78
Eigen90	0.94	0.95	0.95	0.94	0.90	0.86	0.86	0.79
Eigen95	0.93	0.96	0.96	0.96	0.91	0.86	0.86	0.79
Eigen99	0.93	0.98	0.98	0.96	0.92	0.87	0.87	0.80
Eigen > 99	0.93	0.98	0.98	0.97	0.93	0.89	0.88	0.81

Eigen50, Eigen80, Eigen90, Eigen95, Eigen99 and Eigen > 99 denote core sizes equal to the largest number of eigenvalues explaining 50% (n = 160), 80% (n = 700), 90% (n = 1363), 95% (n = 2344), 99% (n = 7320) and > 99% (n = 10,000) of the genomic relationship matrix, respectively

MPA: popular animals with more than15 progeny, both parents known and with own performance record; Rnd: a random subset of animals is sampled from all genotyped animals; Ped: animals were evenly selected from the pedigree sorted in genealogical order; Fam: from each full sib family, one progeny was allowed to be in the core group; Unrel: animals with $\le$ 0.27 genomic relationship were assigned to the core group; LPM: males with both parents known, without progeny, and without own performance records were used as core; LPF: females with both parents known, without progeny and own performance records were used as core; QR: animals selected based on a QR decomposition of the gene content matrix