Table 1 Description of scenarios used in the study
From: Utility of whole-genome sequence data for across-breed genomic prediction
Scenario | Description |
|---|---|
Scenarios with unselected markers | |
Full_seq | All available markers in WGS data that met the quality check criteria were included |
HD | SNPs on the commercial BovineHD SNP chip |
50k | SNPs on the commercial 50k chip |
Scenarios with selected marker + unselected markers | |
HD_Top | Top_markers added to HD |
50k_Top | Top_markers added to 50k |
Scenarios with only selected markers | |
Pval5 | All markers that had a − log10(p) value higher than 5 from the meta-GWAS analysis |
Pval7 | All markers that had a − log10(p) value higher than 7 form the meta-GWAS analysis |
COJO3 | Markers selected using the following COJO model parameters thresholds: conditional and joint p value threshold (p) = 5e–3, collinearity between selected markers = 0.9, window size = 10 Mb |
COJO8 | Markers selected using the following COJO model parameters thresholds: conditional and joint p-value threshold (p) = 5e–8, collinearity between selected markers = 0.9, window size = 10 Mb |
Top_markers | The most significant markers identified in each defined QTL region from the meta-GWAS analysi; only those that passed QC are included here |