Annotation and assessment of functional variants in livestock through epigenomic data

Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding. However, the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods. In this study, we gather 1030 raw epigenomic datasets from 10 farm animal species and systematically annotate 7 types of key regulatory regions, creating a comprehensive functional annotation map of animal genomic variants. Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits, underscoring the utility of these annotations in functional variant discovery. Using our functional annotations, we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories, with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs. Incorporating these variants into genomic prediction models can improve estimated breeding value (EBV) accuracy, demonstrating their practical utility in breeding programs. To facilitate the use of our results, we develop the Integrated Functional Mutation (IFmut: http://www.ifmutants.com:8212) platform, enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently. Our study provides a robust framework for functional genomic annotations in farm animals, enhancing variant function assessment and breeding precision.