Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp
- 1Key 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
- 2Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
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.
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BibTeX
@article{zhang2026integrating,
title = {{Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp}},
author = {Ruixin Zhang and Xiaoyue Zhu and Zhipeng Sun and Xianhu Zheng and Yongjun Shu and Guo Hu},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27188315},
url = {https://www.mdpi.com/1422-0067/27/18/8315},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp
AU - Ruixin Zhang
AU - Xiaoyue Zhu
AU - Zhipeng Sun
AU - Xianhu Zheng
AU - Yongjun Shu
AU - Guo Hu
PY - 2026
DA - 2026/09/18
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27188315
UR - https://www.mdpi.com/1422-0067/27/18/8315
AB - 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.
SN - 1422-0067
ER -