Comparison on genomic prediction using pedigree BLUP and single step GBLUP through the Hanwoo (Korean cattle) full-sib family

Kim, Eun Ho; Kang, Ho-Chan; Myung, Cheol-Hyun; Kim, Ji-Yeong; Sun, Du-Won; Lee, Doo-Ho; Lee, Seung-Hwan; Lim, Hyun-Tae

doi:.0.0.0

Article

https://doi.org/10.5713/ab.22.0327 [Accepted] Published online May 2, 2023.

Comparison on genomic prediction using pedigree BLUP and single step GBLUP through the Hanwoo (Korean cattle) full-sib family

Eun Ho Kim¹

, Ho-Chan Kang^2,*

, Hyun-Tae Lim^1,2

¹Department of Animal Science, Gyeongsang National University, Jinju, 52828, Korea
²Department of Animal Science and Biotechnology, Gyeongsang National University, Jinju, 52828, Korea
³Gyeongnam Animal Science & Technology, Gyeongsang National University, Jinju, 52828, Korea
⁴Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, 34134, Korea

Correspondence: Ho-Chan Kang,Email: s_htim@gnu.ac.kr

Received: 26 August 2022 • Revised: 3 January 2023 • Accepted: 16 March 2023

Abstract

Objective
When evaluating individuals with the same parent and no phenotype by pedigree BLUP, it is difficult to explain carcass grade difference and select individuals because they have the same value in pedigree BLUP (PBLUP). However, single step GBLUP (ssGBLUP), which can estimate the breeding value suitable for the individual by adding genotype, is more accurate than the existing method.
Methods
The breeding value and accuracy were estimated with pedigree BLUP and ssGBLUP using pedigree and genotype of 408 Hanwoo cattle from 16 families with the same parent among siblings produced by fertilized egg transplantation. A total of 14,225 Hanwoo cattle with pedigree, genotype and phenotype were used as the reference population. PBLUP obtained estimated breeding value (EBV) using the pedigree of the test and reference populations, and ssGBLUP obtained genomic EBV (GEBV) after constructing and H-matrix by integrating the pedigree and genotype of the test and reference populations.
Results
For all traits, the accuracy of GEBV using ssGBLUP is 0.18 ~ 0.20 higher than the accuracy of EBV obtained with PBLUP. Comparison of EBV and GEBV of individuals without phenotype, since the value of EBV is estimated based on expected values of alleles passed down from common ancestors. it does not take Mendelian sampling into consideration, so the EBV of all individuals within the same family is estimated to be the same value. However, GEBV makes estimating true kinship coefficient based on different genotypes of individuals possible, so GEBV that corresponds to each individual is estimated rather than a uniform GEBV for each individual.
Conclusion
Since Hanwoo cows bred through embryo transfer have a high possibility of having the same parent, if ssGBLUP after adding genotype is used, estimating true kinship coefficient corresponding to each individual becomes possible, allowing for more accurate estimation of breeding value.

Keywords: Acuuracy; Full-sib; Genomic Selection; Genotype; Hanwoo