Genomic breeding value prediction and accuracy assessment for carcass traits in Jeju Black Cattle using Hanwoo...

This study aimed to evaluate the accuracy of genomic prediction for carcass traits, specifically 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.

The dataset comprised genotypes and phenotypes from 19,153 Hanwoo steers, 6,200 Hanwoo cows, 676 JBC steers, and 654 JBC cows, genotyped using Illumina 50K and Affymetrix 160K SNP chips. The entire population was divided into three groups. In Group 1, Hanwoo steers served as the reference population, whereas JBC steers and cows as the testing population (HSJB). Group 2 expanded the reference population by including both Hanwoo steers and cows, with the same JBC testing set (HAJB). In Group 3, JBC were used only as the reference population (JBJB). The single-trait genomic best linear unbiased prediction analysis was performed using ASReml SA-4.2 software.

In HSJB, 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 ranged from 0.12 to 0.54 in cows and from 0.28 to 0.58 in steers. In Group 2, ACCT improved to 0.48-0.55, with ACCR of 0.25 (CWT), 0.37 (EMA), 0.28 (BF), and 0.47 (MS) in the total population. JBC cows had values between 0.27 to 0.31, while steers from 0.26 to 0.51 across various traits. JBJB showed the highest ACCT values of 0.50-0.54, with ACCR values of 0.46 (CWT), 0.65 (EMA), 0.38 (BF), and 0.55 (MS).

The results indicate that the highest accuracies were obtained in Group 3, where JBC used only as a reference population. Therefore, to increase the prediction accuracy of JBC, it is essential to have breed-specific large populations.