Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Indexed in KCI
OPEN ACCESS, PEER REVIEWED
pISSN 1226-5543
eISSN 2586-4297
Research Article

Effect of the number of QTL of carcass weight on the accuracy of genomic estimated breeding values in Hanwoo

Youngjae Choi1, Yeongkuk Kim2, Dooho Lee3, Dong Jae Lee3, Seung Hwan Lee3*

1Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea
2Quantomic Research & Solution, Daejeon 34134, Republic of Korea
3Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea

Correspondence to Seung Hwan Lee, E-mail: slee46@cnu.ac.kr

Volume 7, Number 4, Pages 179-188, December 2023.
Journal of Animal Breeding and Genomics 2023, 7(4), 179-188. https://doi.org/10.12972/jabng.20230019
Received on 21 November, 2023, Revised on 26 December, 2023, Accepted on 26 December, 2023, Published on 31 December, 2023.
Copyright © 2023 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).

ABSTRACT

The objective of this study was to investigate the relationship between the number of QTL (Quantitative Trait Loci) affecting the carcass weight of Hanwoo and the accuracy of GEBV (Genomic Estimated Breeding Values). The study was performed simulation study to generate three populations comprising 100, 500 and 1,000 QTL. Each population consisted of 13,500 individuals which were selected from the 6th to 10th generations of all 10 generations, while keeping litter size constant (N=1) in population parameters. The genetic parameters for these populations were set at 0.45 trait heritability, 0.3 QTL heritability and 48,578 total markers. In order to confirm the number of significant QTL under the threshold of Bonferroni correction, both GWAS (Genome-wide association study) and GWAS based on Random Forest (RF) were performed. In each population, there were 33, 50 and 32 QTL identified by only GWAS, with 100, 500 and 1,000 QTL. Additionally, RF-based GWAS detected 65, 260 and 491. These results showed that the number of significant QTL is not related to the overall number of QTL in the population. Furthermore, machine learning based GWAS is more accurate than solely using GWAS. To estimate the accuracy of GEBV (Genomic Best Linear Unbiased Prediction) in each population, 5-fold cross-validation was employed using SNP effect of the QTL over p-value. In the result of the estimation, GEBV rose with an increase in the number of QTL in the population, and the correlation between TBV (True Breeding Values) followed the same tendency. As a result, this study suggested that the number of QTL related to carcass weight in Hanwoo could exert a significant influence on genetic improvement.
KEYWORDS

Hanwoo, QTL, GWAS, Random Forest, GEBV

ACKNOWLEDGEMENTS

이 논문은 2023년도 정부(과학기술정보통신부)의 재원으로 정보통신기획평가원의 지원을 받아 수행된 연구임(No.RS-202200155857, 인공지능융합혁신인재양성(충남대학교)).

CONFLICT OF INTERESTS

No potential conflict of interest relevant to this article is reported.

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