A comprehensive study on size and definition of the core group in the proven and young algorithm for single-step GBLUP

Table 3 Proportion of overlap between minor allele frequency spectra calculated using all individuals and using core animals for each core definition and size

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

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