Genomic selection in pig breeding: comparative analysis of machine learning algorithms

作者：Ruijun Su, Jingbo Lv, Yahui Xue, Sheng Jiang, Lei Zhou, Li Jiang, Junyan Tan, Zhencai Shen, Ping Zhong, Jianfeng Liu · 发表于：Genetics Selection Evolution · 年份：2025 · DOI：10.1186/s12711-025-00957-3 · 被引用次数：17 · 研究领域：Genetic and phenotypic traits in livestock、Genetic Mapping and Diversity in Plants and Animals、Animal Behavior and Welfare Studies

BACKGROUND: The effectiveness of genomic prediction (GP) significantly influences breeding progress, and employing SNP markers to predict phenotypic values is a pivotal aspect of pig breeding. Machine learning (ML) methods are usually used to predict phenotypic values since their advantages in processing high dimensional data. While, the existing researches have not indicated which ML methods are suitable for most pig genomic prediction. Therefore, it is necessary to select appropriate methods from a large number of ML methods as long as genomic prediction is performed. This paper compared the performance of popular ML methods in predicting pig phenotypes and then found out suitable methods for most traits. RESULTS: In this paper, five commonly used datasets from other literatures were utilized to compare the performance of different ML methods. The experimental results demonstrate that Stacking performs best on the PIC dataset where the trait information is hidden, and the performs of kernel ridge regression with rbf kernel (KRR-rbf) closely follows. Support vector regression (SVR) performs best in predicting reproductive traits, followed by genomic best linear unbiased prediction (GBLUP). GBLUP achieves the best performance on growth traits, with SVR as the second best. CONCLUSIONS: GBLUP achieves good performance for GP problems. Similarly, the Stacking, SVR, and KRR-RBF methods also achieve high prediction accuracy. Moreover, LR statistical analysis shows that Stacking, S...