Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Bomin Kim1,†, Waruni Ekanayake1,†, Jeongwoen Shin2, Yoonsik Kim1, Dooho Lee1, Yeongkuk Kim3, Seung Hwan Lee1*
1Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University
2TNT Research Co, Jeonju, 54810, South Korea
3Quantomic research & solution, Daejeon, 34134, South Korea
Correspondence to Seung Hwan Lee, E-mail: slee46@cnu.ac.kr
†These authors contributed equally to this work.
Volume 7, Number 4, Pages 157-166, December 2023.
Journal of Animal Breeding and Genomics 2023, 7(4), 157-166. https://doi.org/10.12972/jabng.20230017
Received on 06 December, 2023, Revised on 20 December, 2023, Accepted on 20 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).
Improvement of quantitative traits in livestock is an essential goal of animal breeding. For the achievement of this goal, an accurate breeding value estimation is needed. The genetic relationship between reference and test groups is a key factor in determining the accuracy of genomic estimated breeding value (GEBV) thus, the structure of the reference population is crucial for efficient genomic selection. By the number of sharing parents, the population structure can be divided into half-sibling and full-sibling families. Also, the population structure of Hanwoo cattle primarily consists of half-sibling families because of the production system. Therefore, comparing half-sibling and full-sibling families is challenging in the Hanwoo cattle population, yet an important issue in the direction of breeding strategy in Korea. The objective of this study was to compare the accuracy of GEBV between different family structures and investigate efficient family size in the reference population using simulated data. 6 different populations were simulated using QMSim software, and the individuals in the last generations were separated into reference and test groups. The GEBV was calculated using BLUPF90 software. Practical accuracy was between 0.36-0.52 in half-sibling families and 0.55-0.77 in full-sibling families. The increase rate of accuracy was highest at the sibling size of 20, with practical accuracy of 0.52 in half-sibling families and 0.77 in full-sibling families. As a result, the most efficient population structure for genomic prediction was a sibling size of 20 in a full-sibling family.
Genomic estimated breeding value, Genomic selection, Hanwoo, Population structure, Reference population
This research was financially supported by the Ministry of Small and Medium-sized Enterprises (SMEs) and Startups (MSS), Korea, under the “Regional Specialized Industry Development Program+(R&D, S3370836)” supervised by the Korea Technology and Information Promotion Agency for SMEs (TIPA).
Bomin belongs to the Artificial Intelligence Convergence Research Center as a Master’s student at Chungnam National University. Their research support was supported by the Institute of Information & communications Technology Planning & evaluation (IITP) grant funded by the Korean government (MSIT) (No.RS-2022-00155857, Artificial Intelligence Convergence Research Center (Chungnam National University)).
No potential conflict of interest relevant to this article is reported.
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