An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers
Machine learning (ML) methods have rapidly developed in various theoretical and practical research areas, including predicting genomic breeding values for large livestock animals. However, few studies have investigated the application of ML in broiler breeding. In this study, seven different ML meth...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124010678 |
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| author | Bogong Liu Huichao Liu Junhao Tu Jian Xiao Jie Yang Xi He Haihan Zhang |
| author_facet | Bogong Liu Huichao Liu Junhao Tu Jian Xiao Jie Yang Xi He Haihan Zhang |
| author_sort | Bogong Liu |
| collection | DOAJ |
| description | Machine learning (ML) methods have rapidly developed in various theoretical and practical research areas, including predicting genomic breeding values for large livestock animals. However, few studies have investigated the application of ML in broiler breeding. In this study, seven different ML methods—support vector regression (SVR), random forest (RF), gradient boosting decision tree (GBDT), extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM), kernel ridge regression (KRR) and multilayer perceptron (MLP) were employed to predict the genomic breeding values of laying traits, growth and carcass traits in a yellow-feathered broiler breeding population. The results indicated that classic methods, such as GBLUP and Bayesian, achieved superior prediction accuracy compared to ML methods in five of the eight traits. For half-eviscerated weight (HEW), ML methods showed an average improvement of 54.4% over GBLUP and Bayesian methods. Among the ML methods, SVR, RF, GBDT, and XGBoost exhibited improvements exceeding 60%, with respective values of 61.3%, 61.0%, 60.4%, and 60.7%; while MLP improved by 54.4% and LightGBM by 53.7%, KRR had the lowest improvement at 29.4%. For eviscerated weight (EW), ML methods still outperformed GBLUP and Bayesian methods. MLP gained the largest improvement at 19.0%, while SVR, RF, GBDT, XGBoost, LightGBM, and KRR improved by 15.0%, 16.5%, 9.5%, 7.0%, 1.6%, and 15.9%, respectively. Compared to default hyperparameters, the average improvement of ML methods with tuned hyperparameters was 34.0%, 32.9%, 27.0%, 19.3%, 26.8%, 13.2%, 18.9%, and 46.3%, respectively. The prediction accuracy of above algorithms could be optimized using genome-wide association study (GWAS) to select subsets of significant SNPs. This work provides valuable insights into genomic prediction, aiding genetic breeding in broilers. |
| format | Article |
| id | doaj-art-235a96ea3fb34fb3b20f0f65fce33e33 |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-235a96ea3fb34fb3b20f0f65fce33e332025-01-22T05:40:13ZengElsevierPoultry Science0032-57912025-01-011041104489An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilersBogong Liu0Huichao Liu1Junhao Tu2Jian Xiao3Jie Yang4Xi He5Haihan Zhang6College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, ChinaCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, ChinaCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, ChinaHunan Xiangjia Husbandry Co., Ltd, Changde, Hunan, ChinaHunan Xiangjia Husbandry Co., Ltd, Changde, Hunan, ChinaCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China; Hunan Engineering Research Center of Poultry Production Safety, Changsha, Hunan, China; Yuelushan Laboratory, Changsha 410128, ChinaCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China; Hunan Engineering Research Center of Poultry Production Safety, Changsha, Hunan, China; Yuelushan Laboratory, Changsha 410128, China; Corresponding author at: College of Animal Science and Technology, Hunan Agricultural University, China.Machine learning (ML) methods have rapidly developed in various theoretical and practical research areas, including predicting genomic breeding values for large livestock animals. However, few studies have investigated the application of ML in broiler breeding. In this study, seven different ML methods—support vector regression (SVR), random forest (RF), gradient boosting decision tree (GBDT), extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM), kernel ridge regression (KRR) and multilayer perceptron (MLP) were employed to predict the genomic breeding values of laying traits, growth and carcass traits in a yellow-feathered broiler breeding population. The results indicated that classic methods, such as GBLUP and Bayesian, achieved superior prediction accuracy compared to ML methods in five of the eight traits. For half-eviscerated weight (HEW), ML methods showed an average improvement of 54.4% over GBLUP and Bayesian methods. Among the ML methods, SVR, RF, GBDT, and XGBoost exhibited improvements exceeding 60%, with respective values of 61.3%, 61.0%, 60.4%, and 60.7%; while MLP improved by 54.4% and LightGBM by 53.7%, KRR had the lowest improvement at 29.4%. For eviscerated weight (EW), ML methods still outperformed GBLUP and Bayesian methods. MLP gained the largest improvement at 19.0%, while SVR, RF, GBDT, XGBoost, LightGBM, and KRR improved by 15.0%, 16.5%, 9.5%, 7.0%, 1.6%, and 15.9%, respectively. Compared to default hyperparameters, the average improvement of ML methods with tuned hyperparameters was 34.0%, 32.9%, 27.0%, 19.3%, 26.8%, 13.2%, 18.9%, and 46.3%, respectively. The prediction accuracy of above algorithms could be optimized using genome-wide association study (GWAS) to select subsets of significant SNPs. This work provides valuable insights into genomic prediction, aiding genetic breeding in broilers.http://www.sciencedirect.com/science/article/pii/S0032579124010678Genomic predictionMachine learningBroilerGenomic selection |
| spellingShingle | Bogong Liu Huichao Liu Junhao Tu Jian Xiao Jie Yang Xi He Haihan Zhang An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers Poultry Science Genomic prediction Machine learning Broiler Genomic selection |
| title | An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers |
| title_full | An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers |
| title_fullStr | An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers |
| title_full_unstemmed | An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers |
| title_short | An investigation of machine learning methods applied to genomic prediction in yellow-feathered broilers |
| title_sort | investigation of machine learning methods applied to genomic prediction in yellow feathered broilers |
| topic | Genomic prediction Machine learning Broiler Genomic selection |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124010678 |
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