Bovinesnp50v2

Blood samples of 2,942 cows and semen samples of 383 bulls (Table 1) were used to extract the DNA by routine procedures. After that, the DNAs were quantified and genotyped using the BovineSNP50 v2 (Illumina, Inc., San Diego CA). The rate of missing genotypes was lower than 10% in all individuals. The SNPs were removed from dataset if it exhibited: 1) a call rate less than 90%; 2) minor allele frequency (MAF) less than 5%; 3) Fisher’s exact test p-value for Hardy-Weinberg Equilibrium (HWE) greater than or equal to 1 × 10⁻⁶; and 4) chromosome and position were unknown.
Of the total 54,609 SNPs, 42,307 on the 30 bovine chromosomes satisfied these selection criteria. The number of SNPs varied among chromosomes, with Bos Taurus autosome 1(BTA1) having the largest number of SNPs (2,711) and BTA 27 and BTA 28 having the fewest number of SNPs (778). The distribution of the minor allele frequency (MAF), heterozygous rate, linkage disequilibrium (LD) changed by marker distance and the average marker distance were shown in Fig 1.

Genotypic data were obtained using two SNP panels: BovineSNP50 v2 and BovineSNP50 v3 (Illumina Inc., USA). These two SNP panels were imputed to BovineSNP50 version 3 using Fimpute version 2.2 [12 ]. After excluding unmapped SNPs and SNPs on sex chromosomes, the available number of SNP markers was 54,931. After performing marker quality control, genotypes at each locus were excluded based on the following criteria: average call rate lower than 0.90; minor allele frequency less than 0.01; markers not in Hardy–Weinberg equilibrium, with a chi-square value (χ²) greater than 95%; and SNPs in extreme linkage disequilibrium (LD, r² >0.99). After editing, 50,765 SNP genotypes were available for analysis. Furthermore, genotyped animals were excluded from analysis based on the following criteria: duplicate animals, twin animals, and animals that failed parentage tests. Duplicate animals and twin animals were removed based on marker call rates. Furthermore, genotype identification that could not be matched to the corresponding animal in the phenotypic data set was removed from a total of 2,032 Holstein dairy cattle. Finally, for ss-GBLUP for all traits, the genotype data set comprised 1,919 animals, whereas for Bayes-B, the number of animals available for MY305, FY305, and PY305 was 963, 943, and 946, respectively.