Assessment of genomic breeding values and their accuracies for carcass traits in Jeju Black cattle using whole‐genome SNP chip panels

Abstract

The objective of the present study was to evaluate the breeding value and accuracy of genomic estimated breeding values (GEBVs) of carcass traits in Jeju Black cattle (JBC) using Hanwoo steers and JBC as a reference population using the single‐trait animal model. Our research included genotype and phenotype information on 19,154 Hanwoo steers with 1097 JBC acting as the reference population. Likewise, the test population consisted of 418 genotyped JBC individuals with no phenotypic records for those carcass traits. For estimating the accuracy of GEBV, we divided the entire population into three groups. Hanwoo and JBC make up the first group; Hanwoo and JBC, who has both the genotype and phenotypic records, are referred to as the reference (training) population, and JBC, who lacks phenotypic information is referred to as the test (validation) population. The second group consists of the JBC (without phenotype) as the test population and Hanwoo as a reference population with phenotype and genotypic data. The only JBCs in the third group are those who have genotypic and phenotypic data on them as a reference population but no phenotypic data on them as a test population. The single‐trait animal model was used in all three groups for statistical purposes. The reference populations estimated heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) as 0.30, 0.26, 0.26, and 0.34 for the Hanwoo steer and 0.42, 0.27, 0.26, and 0.48 for JBC. The average accuracy for carcass traits in Group 1 was 0.80 for the Hanwoo and JBC reference population compared with 0.73 for the JBC test population. Although the average accuracy for carcass traits in Group 2 was 0.80, it was 0.80 for the Hanwoo reference population and only 0.56 for the JBC test population. The average accuracy for the JBC reference and test populations was 0.68 and 0.50, respectively, when they were included in the accuracy comparison without the Hanwoo reference population. Groups 1 and 2 used Hanwoo as reference population, which led to a better average accuracy; however, Group 3 only used the JBC reference and test population, which led to a lower average accuracy. This might be due to the fact that Group 3 used a smaller reference size than the group that came before it and that the genetic makeup of the Hanwoo and JBC breeds differed. The GEBV accuracy for MS was higher than that of other traits across all three analysis groups, followed by CWT, EMA, and BF, which may be partially explained by the MS traits' higher heritability. This study suggests that in order to achieve more accuracy, a large reference population particular to a breed should be established. Therefore, to increase the accuracy of GEBV prediction and the genetic benefit from genomic selection in JBC, individual reference breeds, and large populations are required.

Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle

“…Our study reported h 2 (GBLUP, Bayes B) for the Hanwoo population as follows: CWT (0.42, 0.47), EMA (0.36, 0.37), BF (0.36, 0.36), and MS (0.47, 0.42). These estimates significantly differ from the h 2 estimates obtained in recent studies by Haque et al [29], who reported h 2 for CWT, EMA, BF, and MS using the GBLUP method as 0.30, 0.26, 0.26, and 0.34, respectively. Mehrban et al [30] also estimated h 2 for these four traits using Bayes C and Bayes L methods and obtained almost similar values.…”

“…Additionally, the backfat thickness was estimated to be 14.09 (14.53 for steers), and the eye muscle area was 94.16 (96.70 for steers) in our study, both of which showed higher estimates compared to the values reported by Kwon. In another recent report by Haque et al [29], the authors examined genomic selection methods for the same four carcass traits in Jeju Black cattle, using Hanwoo steers as a reference population at approximately 24 to 35 months of age. The recorded average values for CWT, EMA, BF, and MS were 445.00 kg, 96.70 cm 2 , 14.20 mm, and 5.99, respectively, which aligns closely with our steers data records.…”

Evaluation of accuracies of genomic predictions for body conformation traits in Korean Holstein

“…Notably, the genomic BLUP models and Bayesian variable selection or variable shrinkage models have gained widespread recognition and utilization. The idea of enhancing body conformation traits of Korean Holsteins by GS led to the estimation of GEBVs and their accuracy using GBLUP model, which presupposes a homogenous variance across SNPs and an equal contribution from each SNP to the overall variance [ 37 ]. Approximately a decade ago, Misztal et al [ 38 ] introduced a novel approach known as the single-step genomic BLUP method (ssGBLUP).…”

“…The widespread application of GBLUP within livestock species is primarily due to the polygenic nature observed in most traits [ 39 ]. Additionally, the GBLUP method is favored for its simplicity, lower computational requirements, and higher accuracy in contrast to the conventional pedigree-based BLUP (PBLUP) approach [ 37 ]. Other species have transitioned away from GBLUP to single-step methods, especially in dairy cattle, largely due to the cost and technical complexities associated with the latter.…”

Quality Properties and Flavor-Related Components of Beef Longissimus Lumborum Muscle from Four Korean Native Cattle Breeds

“…Hanwoo beef is known worldwide as a highly-marbled, tender and palatable meat type ( Cho et al, 2017 ; Chung et al, 2018 ). In contrast to the Hanwoo, the other three remaining breeds are only reared in several locals with a limited population size (hundreds to thousands of heads per breed; Alam et al, 2021 ; Haque et al, 2023 ; Park et al., 2020 ). Recently, beef producers have paid more attention to these cattle breeds ( Song et al, 2018 ).…”