Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle
ABSTRACT: Cattle body size measurements constitute the conformation traits that facilitate their production, fertility, and longevity status. Prioritizing functional variants and causal genes of conformation traits is essential for understanding their genetic basis. In this study, we conducted singl...
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Elsevier
2025-08-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030225003649 |
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| author | Jun Teng Chongwei Duan Xinyi Zhang Zhujun Chen Chao Ning Rongling Li Yundong Gao Hongding Gao Huiming Liu Jianbin Li Xiao Wang Qin Zhang |
| author_facet | Jun Teng Chongwei Duan Xinyi Zhang Zhujun Chen Chao Ning Rongling Li Yundong Gao Hongding Gao Huiming Liu Jianbin Li Xiao Wang Qin Zhang |
| author_sort | Jun Teng |
| collection | DOAJ |
| description | ABSTRACT: Cattle body size measurements constitute the conformation traits that facilitate their production, fertility, and longevity status. Prioritizing functional variants and causal genes of conformation traits is essential for understanding their genetic basis. In this study, we conducted single-trait and multitrait GWAS for 20 body conformation traits using imputed sequence data in 7,674 Chinese Holstein individuals and identified 27 QTL regions. Leveraging these QTL regions, we performed multitrait Bayesian fine-mapping to identify 30 independent credible sets of putative causal variants. Incorporating GWAS and cis-acting expression QTL data, Mendelian randomization was used to infer 153 putative causal gene-trait relationships. The previously reported genes, such as CCND2, TMTC2, and NRG3, were confirmed in our study. Of note, several novel candidate causal genes were also identified, such as C1R, RIMS1, SERPINB8, NETO2, TTYH3, TTC3, ANAPC4, and PSMD13. Our results provide new insights into the regulatory mechanisms of body conformation traits in cattle. |
| format | Article |
| id | doaj-art-98a3813865ba4e3582d79f9b8903044d |
| institution | Kabale University |
| issn | 0022-0302 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj-art-98a3813865ba4e3582d79f9b8903044d2025-08-20T03:55:48ZengElsevierJournal of Dairy Science0022-03022025-08-0110888637864710.3168/jds.2025-26361Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattleJun Teng0Chongwei Duan1Xinyi Zhang2Zhujun Chen3Chao Ning4Rongling Li5Yundong Gao6Hongding Gao7Huiming Liu8Jianbin Li9Xiao Wang10Qin Zhang11Shandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, ChinaInstitute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, ChinaInstitute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, ChinaNatural Resources Institute Finland (Luke), Jokioinen 31600, FinlandCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, DenmarkInstitute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, ChinaInstitute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; Corresponding authorsShandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China; Corresponding authorsABSTRACT: Cattle body size measurements constitute the conformation traits that facilitate their production, fertility, and longevity status. Prioritizing functional variants and causal genes of conformation traits is essential for understanding their genetic basis. In this study, we conducted single-trait and multitrait GWAS for 20 body conformation traits using imputed sequence data in 7,674 Chinese Holstein individuals and identified 27 QTL regions. Leveraging these QTL regions, we performed multitrait Bayesian fine-mapping to identify 30 independent credible sets of putative causal variants. Incorporating GWAS and cis-acting expression QTL data, Mendelian randomization was used to infer 153 putative causal gene-trait relationships. The previously reported genes, such as CCND2, TMTC2, and NRG3, were confirmed in our study. Of note, several novel candidate causal genes were also identified, such as C1R, RIMS1, SERPINB8, NETO2, TTYH3, TTC3, ANAPC4, and PSMD13. Our results provide new insights into the regulatory mechanisms of body conformation traits in cattle.http://www.sciencedirect.com/science/article/pii/S0022030225003649GWASBayesian fine-mappingMendelian randomizationbody conformation traitscattle |
| spellingShingle | Jun Teng Chongwei Duan Xinyi Zhang Zhujun Chen Chao Ning Rongling Li Yundong Gao Hongding Gao Huiming Liu Jianbin Li Xiao Wang Qin Zhang Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle Journal of Dairy Science GWAS Bayesian fine-mapping Mendelian randomization body conformation traits cattle |
| title | Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| title_full | Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| title_fullStr | Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| title_full_unstemmed | Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| title_short | Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| title_sort | bayesian fine mapping and mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle |
| topic | GWAS Bayesian fine-mapping Mendelian randomization body conformation traits cattle |
| url | http://www.sciencedirect.com/science/article/pii/S0022030225003649 |
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