FIGURE 3.

Genomic prediction accuracies of sample-to-positive (S/P) ratio across different SNP sets. (A,B) Genomic prediction accuracies for the within-breed and between-breed genomic prediction, respectively. SNP_All represents the set of SNPs using all 29,799 SNPs across the genome, while SNP_MHC accounts for only SNPs in the QTL that harbors the major histocompatibility complex (MHC) region. For SNP_Rest, all SNPs across the genome were used excluding those in the MHC region and a 2-Mb window surrounding the QTL in the MHC region to avoid having any SNPs in linkage disequilibrium with this QTL. The error bars in panel (A) represent the standard deviations across the 5-fold used to calculate genomic prediction accuracies.