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Mendelian randomization and colocalization reveal potential causal effects of average daily gain on carcass composition and reproductive traits in pigs
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Wondossen Ayalew1, Guangzhen Li1, Yuqiang Liu1, Jinyan Teng1, Xiaodian Cai1, Qing Lin1, Yahui Gao1, Jiaqi Li1, Zhe Zhang1, *
Journal of Animal Science and Biotechnology | 2026, 17(4) : 1895 - 1907
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Journal of Animal Science and Biotechnology | 2026, 17(4): 1895-1907
• ANIMAL GENETICS AND BREEDING •
Mendelian randomization and colocalization reveal potential causal effects of average daily gain on carcass composition and reproductive traits in pigs
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Wondossen Ayalew1, Guangzhen Li1, Yuqiang Liu1, Jinyan Teng1, Xiaodian Cai1, Qing Lin1, Yahui Gao1, Jiaqi Li1, Zhe Zhang1, *
Affiliations
  • 1State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Published: 2026-08-15 doi: 10.1186/s40104-026-01363-5
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Background

Selective breeding has substantially improved productive and reproductive traits in pigs. Yet, these traits are biologically interconnected, and selection for one often affects others in unintended ways. While genomewide association studies (GWAS) have uncovered many loci linked to these traits, they provide limited insight into causal mechanisms. Mendelian randomization (MR) provides a robust framework for inferring causality and identifying shared genetic determinants. Here, we integrated MR, colocalization, and functional genomics to investigate the biological links between growth, carcass composition, and reproduction in pigs.

Results

Using average daily gain (ADG) as the exposure, MR revealed potentially significant causal effects (P < 0.05) of ADG on carcass composition traits, including backfat thickness (BFT: ) and loin muscle depth (LMDEP: ), suggesting a potential causal contribution of increased ADG to both fat deposition and muscle development. Additionally, ADG showed a negative causal association with age at first farrowing (AFF: ), indicating that faster growth promotes earlier sexual maturity and reproductive onset. In addition to the statistical evidence, gene annotation of instrumental variants (IVs) identified overlapping candidate genes, which may help explain the causal associations observed across the four exposure-outcome analyses. Among these, MC4R and CDH20 were supported by colocalization analysis, indicating shared genetic signals potentially linking growth, carcass composition, and reproductive traits. Integrative analysis supported the tissue-specific roles of these genes in regulating growth, carcass composition, and reproduction.

Conclusions

Our findings suggest a shared genetic architecture and provide potential evidence of a causal influence of ADG on carcass composition and reproductive traits in pigs. This integrative framework supports the development of multi-trait breeding strategies that enhance productivity while managing inherent trade-offs in regulating complex traits.

Causal inference  /  Functional genomics  /  Meta-GWAS  /  Pleiotropy  /  Swine
Wondossen Ayalew, Guangzhen Li, Yuqiang Liu, Jinyan Teng, Xiaodian Cai, Qing Lin, Yahui Gao, Jiaqi Li, Zhe Zhang. Mendelian randomization and colocalization reveal potential causal effects of average daily gain on carcass composition and reproductive traits in pigs[J]. Journal of Animal Science and Biotechnology, 2026 , 17 (4) : 1895 -1907 . DOI: 10.1186/s40104-026-01363-5
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Funding
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  • Agricultural Science and Technology Major Project(2022)
  • National Natural Science Foundation of China(32402714)
  • Science and Technology Project of Guangzhou(2024B03J1305)
Appendix
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Year 2026 volume 17 Issue 4
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48
10
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Article Info
doi: 10.1186/s40104-026-01363-5
  • Receive Date：2025-10-21
  • Online Date：2026-08-13
  • Published：2026-08-15
Article Data
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History
  • Received：2025-10-21
  • Accepted：2026-01-21
Funding
Agricultural Science and Technology Major Project(2022)
National Natural Science Foundation of China(32402714)
Science and Technology Project of Guangzhou(2024B03J1305)
Affiliations
    1State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China

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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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