Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population

Hyo Sang Lee; Yeongkuk Kim; Doo Ho Lee; Dongwon Seo; Dong Jae Lee; Chang Hee Do; Phuong Thanh N Dinh; Waruni Ekanayake; Kil Hwan Lee; Duhak Yoon; Seung Hwan Lee; Yang Mo Koo

doi:10.5187/jast.2023.e5

Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population

J Anim Sci Technol. 2023 Jul;65(4):720-734. doi: 10.5187/jast.2023.e5. Epub 2023 Jul 30.

Authors

Affiliations

¹ Genetic Information Division, Korea Animal Improvement Association, Livestock Hall, Seoul 06668, Korea.
² Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.
³ Division of Animal and Dairy Science, Chungnam National University, Daejeon 34148, Korea.
⁴ TNT Research Co., Anyang 14059, Korea.
⁵ Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Korea.
⁶ Department of Animal Science and Biotechnology, Kyungpook National University, Sangju 37224, Korea.

Abstract

In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (M_e) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between M_e and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between M_e and accuracy were -0.74 in CWT, -0.75 in EMA, -0.73 in MS, and -0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the M_e, the higher the accuracy of EBV.

Keywords: Accuracy; Effective number of chromosome segments (Me); Genomic estimated breeding value; Hanwoo cattle; Pedigree estimated breeding value; Pedigree index.