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Additional file 1: Figure S1. Location of body measurement parts in Hanwoo cattle.

Additional file 3: Figure S2. Manhattan plots of genome-wide association analyses for four carcass traits. This figure provides the log10 p-values of the SNPs analyzed in the genome-wide association analyses for backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS) traits. The horizontal lines represent the 5% significance level with a p value threshold of 1.46 × 10−6 for backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS) traits.

Additional file 2: Table S1. Mean square error (SE) of genomic prediction for four carcass traits in Hanwoo beef cattle. This table provides the mean square errors of GBLUP, BayesL and BayesC genomic prediction for backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS) traits.

Additional file 1: Figure S1. Estimates of effective population size ( $$N_{e}$$ N e ) in the past generations. Thresholds of 0.1 and 0.2 were considered for minor allelic frequency (MAF). The figure describes the changes of N e over generations for two different minor allelic frequencies (0.1 and 0.2).

Additional file 4: Table S2. Genomic variance ( $$\sigma_{g}^{2}$$ σ g 2 ), marker variance explained ( $$\sigma_{g}^{2} /\sigma_{a}^{2}$$ σ g 2 / σ a 2 ) and genomic heritability ( $$h_{g}^{2}$$ h g 2 ) obtained when using fully corrected phenotypes and high-density SNPs with the GBLUP method. Description: This table provides the results for the genomic variance ( $$\sigma_{g}^{2}$$ σ g 2 ), marker variance explained ( $$\sigma_{g}^{2} /\sigma_{a}^{2}$$ σ g 2 / σ a 2 ) and genomic heritability ( $$h_{g}^{2}$$ h g 2 ) obtained when a high-density chip (777 k) was used to analyze backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS) traits under the GBLUP method.