Genomic Breeding Value Prediction and Accuracy Assessment for Carcass Traits in Jeju Black Cattle Using Hanwoo Reference Populations

ObjectiveThis study aimed to assess genomic prediction accuracy for carcass traits, including carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) in Jeju Black Cattle (JBC) using a single-trait animal model and to compare the results with those obtained using Korean Hanwoo reference populations. MethodsThe dataset comprised genotypes and phenotypes from 19,153 Hanwoo steers, 6,200 Hanwoo cows, 676 JBC steers, and 654 JBC cows, genotyped with Illumina 50K and Affymetrix 160K SNP chips.The entire population were divided into three groups.In Group 1, Hanwoo steers were used as the reference population and JBC steers and cows as the testing population (HSJB).Group 2 extended the reference population by including both Hanwoo steers and cows, with the same JBC testing set (HAJB).In Group 3, only JBC were used as the reference population (JBJB).The single-trait GBLUP analysis was performed using ASReml SA-4.2 software. ResultsIn Group 1HSJB, theoretical accuracies (ACCT) ranged from 0.47 to 0.53, while realized accuracies (ACCR) for the total population were 0.23 (CWT), 0.22 (EMA), 0.28 (BF), and 0.53 (MS).For JBC, ACCR realized accuracies ranged from 0.12 to 0.54 in cows and from 0.28 to 0.58 in steers.In Group 2, ACCTtheoretical accuracies improved to 0.48-0.55,with ACCRrealized accuracies of 0.25 (CWT), 0.37 (EMA), 0.28 (BF), and 0.47 (MS) in the total population.JBC cows ranged from 0.27 to 0.31 and steers from 0.26 to 0.51 across traits.Group 3JBJB showed the highest ACCTaccuracy with theoretical values of 0.50-0.54and : : 12 pt :