Genome-wide identification of functional enhancers and their potential roles in pig breeding

AnimalGWASAtlas: Annotation and prioritization of GWAS loci and quantitative trait loci for animal complex traits

Genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping methods provide valuable insights and opportunities for identifying functional gene underlying phenotype formation. However, the majority of GWAS risk loci and QTLs located in noncoding regions poses significant challenges in pinpointing the protein-coding genes associated with specific traits. Moreover, growing evidence suggests not all GWAS risk loci and QTLs are functional, emphasizing the critical need for prioritizing causal sites-a task of paramount importance for biologists. The accumulation of publicly available multiomics data provides an unprecedented opportunity to annotate and prioritize GWAS risk loci and QTLs. Therefore, we developed a comprehensive multiomics database encompassing four major agricultural species-pig, sheep, cattle, and chicken. This database integrates publicly accessible datasets, including 140 GWAS studies (covering 471 traits), 2625 QTL datasets (spanning 1235 traits), 86 Hi-C datasets (from eight cells/tissue types), 95 epigenomic datasets (from four cells/tissue types), and 769 transcription factor motifs. The database aims to link GWAS-QTL loci located in the noncoding regions to the target genes they regulate and prioritize functional and causal regulatory elements. Ultimately, it provides a valuable resource and potential validation targets for elucidating the genes and molecular pathways underlying economically important traits in agricultural animals.

Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits

IMPORTANCE

Chromatin accessibility is vital for gene regulation, determining the ability of DNA-binding proteins to access the genomic regions and drive transcriptional activity, reflecting environmental changes. Although human and murine studies have advanced the understanding of chromatin dynamics, domestic animals remain comparatively underexplored despite their importance in agriculture and veterinary medicine. Investigating the accessibility of chromatin in these species is crucial for improving traits such as productivity, disease resistance, and environmental adaptation. This review assessed chromatin accessibility research in domestic animals, highlighting its significance in understanding and improving livestock traits.

OBSERVATIONS

This review outlines chromatin accessibility research in domestic animals, focusing on critical developmental processes, tissue-specific regulation, and economically significant traits. Advances in techniques, such as Assay for Transposase-Accessible Chromatin using sequencing, have enabled detailed mapping of regulatory elements, shedding light on epigenetic regulation of traits, such as muscle development and productivity. Comparative studies have uncovered conserved and species-specific cis-regulatory elements across multiple species. These findings offer insights into regulatory mechanisms that can enhance breeding strategies and animal management. In addition, high-throughput techniques, such as single-cell analysis and deep-learning models, have advanced the study of chromatin accessibility in lesser-studied species.

CONCLUSIONS AND RELEVANCE

Chromatin accessibility is crucial in gene regulation in domestic animals, influencing development, immune response, and productivity. Despite the progress, more comprehensive epigenomic datasets and cross-species analytical tools are needed to harness chromatin accessibility in domestic animal research. Understanding these mechanisms has practical applications in improving livestock traits, advancing breeding programs, and developing disease-resistant animals, highlighting the importance of integrating epigenetic and genomic tools for enhancing animal health and productivity.

Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs

Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico-predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination.

Cis-Regulatory Elements in Mammals

In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our understanding of gene regulatory networks, shedding new light on mammalian development, evolution and disease pathways. In this review, we provide a comprehensive overview of the intrinsic structural attributes, detection methodologies as well as the operational mechanisms of enhancers and promoters, coupled with the relevant novel and innovative investigative techniques used to explore their actions. We further elucidated the state-of-the-art research on the roles of enhancers and promoters in the realms of mammalian development, evolution and disease, and we conclude with forward-looking insights into prospective research avenues.

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

Understanding the mechanisms of gene expression regulation is crucial in animal breeding. Cis-regulatory DNA sequences, such as enhancers, play a key role in regulating gene expression. Identifying enhancers is challenging, despite the use of experimental techniques and computational methods. Enhancer prediction in the pig genome is particularly significant due to the costliness of high-throughput experimental techniques. The study constructed a high-quality database of pig enhancers by integrating information from multiple sources. A deep learning prediction framework called PorcineAI-enhancer was developed for the prediction of pig enhancers. This framework employs convolutional neural networks for feature extraction and classification. PorcineAI-enhancer showed excellent performance in predicting pig enhancers, validated on an independent test dataset. The model demonstrated reliable prediction capability for unknown enhancer sequences and performed remarkably well on tissue-specific enhancer sequences.The study developed a deep learning prediction framework, PorcineAI-enhancer, for predicting pig enhancers. The model demonstrated significant predictive performance and potential for tissue-specific enhancers. This research provides valuable resources for future studies on gene expression regulation in pigs.

Effective Quality Breeding Directions-Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds

The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.