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Short communication: Genomic prediction based on unbiased estimation of the genomic relationship matrix in pigs

文献类型： 外文期刊

作者： Li, M. Y. 1 ; Shi, L. Y. 2 ; Machugh, D. E. 3 ; Wang, X. Q. 1 ; Tian, J. J. 1 ; Wang, L. G. 1 ; Deng, Y. J. 4 ; Wang, L. X. 1 ; Zhao, F. P. 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Anim Sci, State Key Lab Anim Biotech Breeding, Beijing 100193, Peoples R China

2.Wuhan Polytech Univ, Sch Anim Sci & Nutr Engn, Wuhan 430023, Peoples R China

3.Univ Coll Dublin, UCD Sch Agr & Food Sci, Anim Genom Lab, Dublin D04 V1W8, Ireland

4.Anim Husb & Aquat Affairs Ctr Xiangxi Autonomous P, Jishou 416000, Hunan, Peoples R China

关键词： Genomic best linear unbiased prediction; Genomic selection; Kinship matrix; Large White pigs; Simulation study

期刊名称：ANIMAL （ 影响因子：4.2； 五年影响因子：4.2 ）

ISSN： 1751-7311

年卷期： 2025 年 19 卷 2 期

页码：

收录情况： SCI

摘要： The traditional genomic relationship matrix (GRM) has shown to be a biased estimation of true kinship, which can affect subsequent genetic analyses. In this study, we employed an unbiased kinship ( UKin ) estimation method within the genomic best linear unbiased prediction framework to evaluate its prediction performance on both a simulated dataset and a Large White pig dataset. The simulated dataset encompasses six traits, 900 quantitative trait loci, and 36 000 single nucleotide polymorphisms (SNPs). Two scenarios (small effect genes; major genes and small effect genes) and three heritabilities (0.1, 0.3 and 0.5) were considered. The Large White pig dataset includes two traits, 3 290 animals and 35 172 SNPs. The prediction performance of the Ukin method was compared with several other GRM construction methods, including VanRaden1 and 2 methods, Goudet method, and the runs of homozygosity (ROH) method. In the simulated dataset, VanRaden2 method and the UKin+VanRaden1 method achieved relatively higher prediction accuracies, averaging 0.561 and 0.558 for the six traits, respectively. Apart from the ROH method, all methods demonstrated similar levels of unbiasedness, around 1.10. In the Large White pig dataset, the accuracy of two traits hovered around 0.780, and the unbiasedness around 0.99, again with the ROH method as an exception. This study underscores the potential of the unbiased kinship estimation method in animal breeding. (c) 2024 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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