Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp

Zhang, Ruixin; Zhu, Xiaoyue; Sun, Zhipeng; Zheng, Xianhu; Shu, Yongjun; Hu, Guo

doi:10.3390/ijms27188315

Open AccessArticle

Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp

by

Ruixin Zhang

^1,2,

Xiaoyue Zhu

^1,2

,

Zhipeng Sun

¹,

Xianhu Zheng

¹,

Yongjun Shu

^2,*

and

Guo Hu

^1,*

¹

Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China

²

Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China

^*

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2026, 27(18), 8315; https://doi.org/10.3390/ijms27188315 (registering DOI)

Submission received: 31 August 2026 / Revised: 13 September 2026 / Accepted: 16 September 2026 / Published: 18 September 2026

(This article belongs to the Section Molecular Genetics and Genomics)

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Abstract

Common carp (Cyprinus carpio) is an important freshwater aquaculture species, yet non-additive genetic effects remain poorly understood for economically important traits. Here, we dissected epistatic interactions affecting standard body length (SL) and fillet fat content (FC) by integrating pathway-level epistasis analysis, genomic selection (GS), and AlphaFold2 (AF2)-based structure prediction. BridGE analysis detected extensive epistatic signals for both traits. Incorporating selected interactions into GS models improved predictive ability within the sampled population, yielding correlations of 0.85 for SL and 0.87 for FC. An epistasis-informed reduction strategy downsized the initial 2.2 million SNPs to 12,902 candidate markers while retaining useful predictive information. AF2-based predictions provided complementary structural support for a subset of candidate driver interactions. Network and enrichment analyses further revealed distinct molecular features associated with SL and FC. Together, these findings suggest that incorporating epistatic information can improve genomic predictive ability of complex traits in common carp, and provide a basis for further evaluation of epistasis-informed selection in independent aquaculture populations.

Keywords: epistasis; genomic prediction; AlphaFold2; SNP reduction; driver interaction pairs

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MDPI and ACS Style

Zhang, R.; Zhu, X.; Sun, Z.; Zheng, X.; Shu, Y.; Hu, G. Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp. Int. J. Mol. Sci. 2026, 27, 8315. https://doi.org/10.3390/ijms27188315

AMA Style

Zhang R, Zhu X, Sun Z, Zheng X, Shu Y, Hu G. Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp. International Journal of Molecular Sciences. 2026; 27(18):8315. https://doi.org/10.3390/ijms27188315

Chicago/Turabian Style

Zhang, Ruixin, Xiaoyue Zhu, Zhipeng Sun, Xianhu Zheng, Yongjun Shu, and Guo Hu. 2026. "Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp" International Journal of Molecular Sciences 27, no. 18: 8315. https://doi.org/10.3390/ijms27188315

APA Style

Zhang, R., Zhu, X., Sun, Z., Zheng, X., Shu, Y., & Hu, G. (2026). Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp. International Journal of Molecular Sciences, 27(18), 8315. https://doi.org/10.3390/ijms27188315

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Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp

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