Fig. 5

Prediction accuracy and bias of SNP sets for real traits in GBLUP and BayesR models in the validation population. a and b Results of the GBLUP model. c and d results of the BayesR model. CC_50k commercial chip 50K, CC_80k commercial chip 80K, GBS genotyping-by-sequencing, LCS low-coverage sequencing, LCS_LD1 low-coverage sequencing set after removing completely linked disequilibrium SNPs, LDP linkage disequilibrium pruning and parameter (r²) optimized in the training population, SLDP selective linkage disequilibrium pruning and parameters (P-value and r²) optimized in the training population. The accuracy was defined as the Pearson correlation between GEBV and phenotypes