Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

Evaluation of heritability partitioning approaches in livestock populations

BACKGROUND

Heritability partitioning approaches estimate the contribution of different functional classes, such as coding or regulatory variants, to the genetic variance. This information allows a better understanding of the genetic architecture of complex traits, including complex diseases, but can also help improve the accuracy of genomic selection in livestock species. However, methods have mainly been tested on human genomic data, whereas livestock populations have specific characteristics, such as high levels of relatedness, small effective population size or long-range levels of linkage disequilibrium.

RESULTS

Here, we used data from 14,762 cows, imputed at the whole-genome sequence level for 11,537,240 variants, to simulate traits in a typical livestock population and evaluate the accuracy of two state-of-the-art heritability partitioning methods, GREML and a Bayesian mixture model. In simulations where a single functional class had increased contribution to heritability, we observed that the estimators were unbiased but had low precision. When causal variants were enriched in variants with low (< 0.05) or high (> 0.20) minor allele frequency or low (below 1st quartile) or high (above 3rd quartile) linkage disequilibrium scores, it was necessary to partition the genetic variance into multiple classes defined on the basis of allele frequencies or LD scores to obtain unbiased results. When multiple functional classes had variable contributions to heritability, estimators showed higher levels of variation and confounding between certain categories was observed. In addition, estimators from small categories were particularly imprecise. However, the estimates and their ranking were still informative about the contribution of the classes. We also demonstrated that using methods that estimate the contribution of a single category at a time, a commonly used approach, results in an overestimation. Finally, we applied the methods to phenotypes for muscular development and height and estimated that, on average, variants in open chromatin regions had a higher contribution to the genetic variance (> 45%), while variants in coding regions had the strongest individual effects (> 25-fold enrichment on average). Conversely, variants in intergenic or intronic regions showed lower levels of enrichment (0.2 and 0.6-fold on average, respectively).

CONCLUSIONS

Heritability partitioning approaches should be used cautiously in livestock populations, in particular for small categories. Two-component approaches that fit only one functional category at a time lead to biased estimators and should not be used.

Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends

The importance of boar reproductive traits, including semen quality, in the sustainability of pig production system is increasingly being acknowledged by academic and industrial sectors. Research is needed to understand the biology and genetic components underlying these traits so that they can be incorporated into selection schemes and managerial decisions. This article reviews our current understanding of genome biology and technologies for genome, transcriptome and epigenome analysis which now facilitate the identification of causal variants affecting phenotypes more than ever before. Genetic and transcriptomic analysis of candidate genes, Genome-Wide Association Studies, expression microarrays, RNA-Seq of coding and noncoding genes and epigenomic evaluations have been conducted to profile the molecular makeups of pig sperm. These studies have provided insightful information for a several semen-related parameters. Nonetheless, this research is still incipient. The spermatozoon harbors a reduced transcriptome and highly modified epigenome, and it is assumed to be transcriptionally silent for nuclear gene expression. For this reason, the extent to which the sperm's RNA and epigenome recapitulate sperm biology and function is unclear. Hence, we anticipate that single-cell level analyses of the testicle and other male reproductive organs, which can reveal active transcription and epigenomic profiles in cells influencing sperm quality, will gain popularity and markedly advance our understanding of sperm-related traits. Future research will delve deeper into sperm fertility, boar resilience to environmental changes or harsh conditions, especially in the context of global warming, and also in transgenerational inheritance and how the environment influences the sperm transcriptome and epigenome.

Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development

BACKGROUND

Given their physiological similarities to humans, pigs are increasingly used as model organisms in human-oriented biomedical studies. Additionally, their value to animal agriculture across the globe has led to the development of numerous studies to investigate how to improve livestock welfare and production efficiency. As such, pigs are uniquely poised as compelling models that can yield findings with potential implications in both human and animal contexts. Despite this, many gaps remain in our knowledge about the foundational mechanisms that govern gene expression in swine across different developmental stages, particularly in early development. To address some of these gaps, we profiled the histone marks H3K4me3, H3K27ac, and H3K27me3 and the SWI/SNF central ATPase BRG1 in two porcine cell lines representing discrete early developmental time points and used the resulting information to construct predicted chromatin state maps for these cells. We combined this approach with analysis of publicly available RNA-seq data to examine the relationship between epigenetic status and gene expression in these cell types.

RESULTS

In porcine fetal fibroblast (PFF) and trophectoderm cells (PTr2), we saw expected patterns of enrichment for each of the profiled epigenetic features relative to specific genomic regions. H3K4me3 was primarily enriched at and around global gene promoters, H3K27ac was enriched in promoter and intergenic regions, H3K27me3 had broad stretches of enrichment across the genome and narrower enrichment patterns in and around the promoter regions of some genes, and BRG1 primarily had detectable enrichment at and around promoter regions and in intergenic stretches, with many instances of H3K27ac co-enrichment. We used this information to perform genome-wide chromatin state predictions for 10 different states using ChromHMM. Using the predicted chromatin state maps, we identified a subset of genomic regions marked by broad H3K4me3 enrichment, and annotation of these regions revealed that they were highly associated with essential developmental processes and consisted largely of expressed genes. We then compared the identities of the genes marked by these regions to genes identified as cell-type-specific using transcriptome data and saw that a subset of broad H3K4me3-marked genes was also specifically expressed in either PFF or PTr2 cells.

CONCLUSIONS

These findings enhance our understanding of the epigenetic landscape present in early swine development and provide insight into how variabilities in chromatin state are linked to cell identity. Furthermore, this data captures foundational epigenetic details in two valuable porcine cell lines and contributes to the growing body of knowledge surrounding the epigenetic landscape in this species.

Effects of foetal size, sex and developmental stage on adaptive transcriptional responses of skeletal muscle to intrauterine growth restriction in pigs

Intrauterine growth restriction (IUGR) occurs both in humans and domestic species. It has a particularly high incidence in pigs, and is a leading cause of neonatal morbidity and mortality as well as impaired postnatal growth. A key feature of IUGR is impaired muscle development, resulting in decreased meat quality. Understanding the developmental origins of IUGR, particularly at the molecular level, is important for developing effective strategies to mitigate its economic impact on the pig industry and animal welfare. The aim of this study was to characterise transcriptional profiles in the muscle of growth restricted pig foetuses at different gestational days (GD; gestational length ~ 115 days), focusing on selected genes (related to development, tissue injury and metabolism) that were previously identified as dysregulated in muscle of GD90 fetuses. Muscle samples were collected from the lightest foetus (L) and the sex-matched foetus with weight closest to the litter average (AW) from each of 22 Landrace x Large White litters corresponding to GD45 (n = 6), GD60 (n = 8) or GD90 (n = 8), followed by analyses, using RT-PCR and protein immunohistochemistry, of selected gene targets. Expression of the developmental genes, MYOD, RET and ACTN3 were markedly lower, whereas MSTN expression was higher, in the muscle of L relative to AW littermates beginning on GD45. Levels of all tissue injury-associated transcripts analysed (F5, PLG, KNG1, SELL, CCL16) were increased in L muscle on GD60 and, most prominently, on GD90. Among genes involved in metabolic regulation, KLB was expressed at higher levels in L than AW littermates beginning on GD60, whereas both IGFBP1 and AHSG were higher in L littermates on GD90 but only in males. Furthermore, the expression of genes specifically involved in lipid, hexose sugar or iron metabolism increased or, in the case of UCP3, decreased in L littermates on GD60 (UCP3, APOB, ALDOB) or GD90 (PNPLA3, TF), albeit in the case of ALDOB this only involved females. In conclusion, marked dysregulation of genes with critical roles in development in L foetuses can be observed from GD45, whereas for a majority of transcripts associated with tissue injury and metabolism differences between L and AW foetuses were apparent by GD60 or only at GD90, thus identifying different developmental windows for different types of adaptive responses to IUGR in the muscle of porcine foetuses.

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs

BACKGROUND

Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking.

RESULTS

Here, employing the pig as a model, we conducted a comprehensive study using H3K27ac histone ChIP-seq and RNA-seq data to construct eRNA expression profiles from multiple tissues of two distinct pig breeds, namely Enshi Black (ES) and Duroc. In addition to revealing the regulatory landscape of eRNAs at the tissue level, we developed an innovative network construction and refinement method by integrating RNA-seq, ChIP-seq, genome-wide association study (GWAS) signals and enhancer-modulating effects of single nucleotide polymorphisms (SNPs) measured by self-transcribing active regulatory region sequencing (STARR-seq) experiments. Using this approach, we unraveled eGRN that significantly influence the growth and development of muscle and fat tissues, and identified several novel genes that affect adipocyte differentiation in a cell line model.

CONCLUSIONS

Our work not only provides novel insights into the genetic basis of economic pig traits, but also offers a generalizable approach to elucidate the eRNA-mediated transcriptional regulation underlying a wide spectrum of complex traits for diverse organisms.

Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver

Surgical castration can effectively avoid boar taint and improve pork quality by removing the synthesis of androstenone in the testis, thereby reducing its deposition in adipose tissue. The expression of genes involved in testis-derived hormone metabolism was altered following surgical castration, but the upstream regulatory factors and underlying mechanism remain unclear. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics in liver tissue of castrated and intact full-sibling Yorkshire pigs. First, we identified 897 differentially expressed genes and 6864 differential accessible regions (DARs) using RNA- and ATAC-seq. By integrating the RNA- and ATAC-seq results, 227 genes were identified, and a significant positive correlation was revealed between differential gene expression and the ATAC-seq signal. We constructed a transcription factor regulatory network after motif analysis of DARs and identified a candidate transcription factor (TF) SP1 that targeted the HSD3B1 gene, which was responsible for the metabolism of androstenone. Subsequently, we annotated DARs by incorporating H3K27ac ChIP-seq data, marking 2234 typical enhancers and 245 super enhancers involved in the regulation of all testis-derived hormones. Among these, four typical enhancers associated with HSD3B1 were identified. Furthermore, an in-depth investigation was conducted on the androstenone-related enhancers, and an androstenone-related mutation was identified in a newfound candidatetypical enhancer (andEN) with dual-luciferase assays. These findings provide further insights into how enhancers function as links between phenotypic and non-coding area variations. The discovery of upstream TF and enhancers of HSD3B1 contributes to understanding the regulatory networks of androstenone metabolism and provides an important foundation for improving pork quality.

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org.

Livestock species as emerging models for genomic imprinting

Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.

Genome-wide association with footrot in hair and wool sheep

Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.

Recent advances in the genomic resources for sheep

Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.

Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle

Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.

The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene

Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.

Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits

Assessment of genomic conservation between humans and pigs at the functional level can improve the potential of pigs as a human biomedical model. To address this, we developed a deep learning-based approach to learn the genomic conservation at the functional level (DeepGCF) between species by integrating 386 and 374 functional profiles from humans and pigs, respectively. DeepGCF demonstrated better prediction performance compared with the previous method. In addition, the resulting DeepGCF score captures the functional conservation between humans and pigs by examining chromatin states, sequence ontologies, and regulatory variants. We identified a core set of genomic regions as functionally conserved that plays key roles in gene regulation and is enriched for the heritability of complex traits and diseases in humans. Our results highlight the importance of cross-species functional comparison in illustrating the genetic and evolutionary basis of complex phenotypes.

The localization of centromere protein A is conserved among tissues

Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development.

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.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.

Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies

Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.

Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle

Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.

The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species

The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.

Harnessing male germline epigenomics for the genetic improvement in cattle

Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.

Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression and identifies putative alternative splicing variation mediating complex trait variation in pigs

BACKGROUND

Alternative splicing is an important step in gene expression, generating multiple isoforms for the same genes and greatly expanding the diversity of proteomes. Genetic variation in alternative splicing contributes to phenotypic diversity in natural populations. However, the genetic basis of variation in alternative splicing in livestock including pigs remains poorly understood.

RESULTS

In this study, using a Duroc x Pietrain F2 pig population, we performed genome-wide analysis of alternative splicing estimated from stranded RNA-Seq data in skeletal muscle. We characterized the genetic architecture of alternative splicing and compared its basic features with those of overall gene expression. We detected a large number of novel alternative splicing events that were not previously annotated. We found heritability of quantitative alternative splicing scores (percent spliced in or PSI) to be lower than that of overall gene expression. In addition, heritabilities showed little correlation between alternative splicing and overall gene expression. We mapped expression QTLs (eQTLs) and splice QTLs (sQTLs) and found them to be largely non-overlapping. Finally, we integrated sQTL mapping with phenotype QTL (pQTL mapping to identify potential mediator of pQTL effect by alternative splicing.

CONCLUSIONS

Our results suggest that regulatory variation exists at multiple levels and that their genetic controls are distinct, offering opportunities for genetic improvement.

Review: Genetic mutations affecting bull fertility

Cattle are a well-suited "model organism" to study the genetic underpinnings of variation in male reproductive performance. The adoption of artificial insemination and genomic prediction in many cattle breeds provide access to microarray-derived genotypes and repeated measurements for semen quality and insemination success in several thousand bulls. Similar-sized mapping cohorts with phenotypes for male fertility are not available for most other species precluding powerful association testing. The repeated measurements of the artificial insemination bulls' semen quality enable the differentiation between transient and biologically relevant trait fluctuations, and thus, are an ideal source of phenotypes for variance components estimation and genome-wide association testing. Genome-wide case-control association testing involving bulls with either aberrant sperm quality or low insemination success revealed several causal recessive loss-of-function alleles underpinning monogenic reproductive disorders. These variants are routinely monitored with customised genotyping arrays in the male selection candidates to avoid the use of subfertile or infertile bulls for artificial insemination and natural service. Genome-wide association studies with quantitative measurements of semen quality and insemination success revealed quantitative trait loci for male fertility, but the underlying causal variants remain largely unknown. Moreover, these loci explain only a small part of the heritability of male fertility. Integrating genome-wide association studies with gene expression and other omics data from male reproductive tissues is required for the fine-mapping of candidate causal variants underlying variation in male reproductive performance in cattle.

Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation

The placenta is a temporary organ that is essential for the survival of the fetus, with a lifelong effect on the health of both the offspring and the dam. The functions of the placenta are controlled by its dynamic gene expression during gestation. In this study, we aimed to investigate the equine placental DNA methylome as one of the fundamental mechanisms that controls the gene expression dynamic. Chorioallantois samples from four (4M), six (6M), and ten (10M) months of gestation were used to map the methylation pattern of the placenta. Globally, methylation levels increased toward the end of gestation. We identified 921 differentially methylated regions (DMRs) between 4M and 6M, 1225 DMRs between 4M and 10M, and 1026 DMRs between 6M and 10M. A total of 817 genes carried DMRs comparing 4M and 6M, 978 comparing 4M and 10M, and 804 comparing 6M and 10M. We compared the transcriptomes between the samples and found 1381 differentially expressed genes (DEGs) when comparing 4M and 6M, 1428 DEGs between 4M and 10M, and 741 DEGs between 6M and 10M. Finally, we overlapped the DEGs and genes carrying DMRs (DMRs-DEGs). Genes exhibiting (a) higher expression, low methylation and (b) low expression, high methylation at different time points were identified. The majority of these DMRs-DEGs were located in introns (48.4%), promoters (25.8%), and exons (17.7%) and were involved in changes in the extracellular matrix; regulation of epithelial cell migration; vascularization; and regulation of minerals, glucose, and metabolites, among other factors. Overall, this is the first report highlighting the dynamics in the equine placenta methylome during normal pregnancy. The findings presented serve as a foundation for future studies on the impact of abnormal methylation on the outcomes of equine pregnancies.

Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.

Pig fetal skeletal muscle development is associated with genome-wide DNA hypomethylation and corresponding alterations in transcript and microRNA expression

Fetal myogenesis represents a critical period of porcine skeletal muscle development and requires coordinated expression of thousands of genes. Epigenetic mechanisms, including DNA methylation, drive transcriptional regulation during development; however, these processes are understudied in developing porcine tissues. We performed bisulfite sequencing to assess DNA methylation in pig longissimus dorsi muscle at 41- and 70-days gestation (dg), as well as RNA- and small RNA-sequencing to identify coordinated changes in methylation and expression between myogenic stages. We identified 45 739 differentially methylated regions (DMRs) between stages, and the majority (N = 34 232) were hypomethylated at 70 versus 41 dg. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression. Differential miRNA methylation was significantly negatively correlated with abundance, and dynamic expression of assayed miRNAs persisted postnatally. Motif analysis revealed significant enrichment of myogenic regulatory factor motifs among hypomethylated regions, suggesting that DNA hypomethylation may function to increase accessibility of muscle-specific transcription factors. We show that developmental DMRs are enriched for GWAS SNPs for muscle- and meat-related traits, demonstrating the potential for epigenetic processes to influence phenotypic diversity. Our results enhance understanding of DNA methylation dynamics of porcine myogenesis and reveal putative cis-regulatory elements governed by epigenetic processes.

Transcriptome annotation of 17 porcine tissues using nanopore sequencing technology

The annotation of animal genomes plays an important role in elucidating molecular mechanisms behind the genetic control of economically important traits. Here, we employed long-read sequencing technology, Oxford Nanopore Technology, to annotate the pig transcriptome across 17 tissues from two Yorkshire littermate pigs. More than 9.8 million reads were obtained from a single flow cell, and 69 781 unique transcripts at 50 108 loci were identified. Of these transcripts, 16 255 were found to be novel isoforms, and 22 344 were found at loci that were novel and unannotated in the Ensembl (release 102) and NCBI (release 106) annotations. Novel transcripts were mostly expressed in cerebellum, followed by lung, liver, spleen, and hypothalamus. By comparing the unannotated transcripts to existing databases, there were 21 285 (95.3%) transcripts matched to the NT database (v5) and 13 676 (61.2%) matched to the NR database (v5). Moreover, there were 4324 (19.4%) transcripts matched to the SwissProt database (v5), corresponding to 11 356 proteins. Tissue-specific gene expression analyses showed that 9749 transcripts were highly tissue-specific, and cerebellum contained the most tissue-specific transcripts. As the same samples were used for the annotation of cis-regulatory elements in the pig genome, the transcriptome annotation generated by this study provides an additional and complementary annotation resource for the Functional Annotation of Animal Genomes effort to comprehensively annotate the pig genome.

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants

Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (< 50 bp), it has been challenging to accurately identify and genotype SV at the population scale using short-read sequencing. Long-read sequencing technologies are becoming competitively priced and can address several of the disadvantages of short-read sequencing for the discovery and genotyping of SV. In livestock species, analysis of SV at the population scale still faces challenges due to the lack of resources, high costs, technological barriers, and computational limitations. In this review, we summarize recent progress in the characterization of SV in the major livestock species, the obstacles that still need to be overcome, as well as the future directions in this growing field. It seems timely that research communities pool resources to build global population-scale long-read sequencing consortiums for the major livestock species for which the application of genomic tools has become cost-effective.

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues

BACKGROUND

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.

RESULTS

More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.

CONCLUSIONS

The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.

Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants

The RNA-Seq data provides new opportunities for the detection of transcriptome variants' single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.

Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

BACKGROUND

Causal variants for complex traits, such as eQTL are often found in non-coding regions of the genome, where they are hypothesised to influence phenotypes by regulating gene expression. Many regulatory regions are marked by histone modifications, which can be assayed by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Sequence reads from ChIP-seq form peaks at putative regulatory regions, which may reflect the amount of regulatory activity at this region. Therefore, eQTL which are also associated with differences in histone modifications are excellent candidate causal variants.

RESULTS

We assayed the histone modifications H3K4Me3, H3K4Me1 and H3K27ac and mRNA in the mammary gland of up to 400 animals. We identified QTL for peak height (histone QTL), exon expression (eeQTL), allele specific expression (aseQTL) and allele specific binding (asbQTL). By intersecting these results, we identify variants which may influence gene expression by altering regulatory regions of the genome, and may be causal variants for other traits. Lastly, we find that these variants are found in putative transcription factor binding sites, identifying a mechanism for the effect of many eQTL.

CONCLUSIONS

We find that allele specific and traditional QTL analysis often identify the same genetic variants and provide evidence that many eQTL are regulatory variants which alter activity at regulatory regions of the bovine genome. Our work provides methodological and biological updates on how regulatory mechanisms interplay at multi-omics levels.

Progress and opportunities through use of genomics in animal production

The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.

The impact of Piscirickettsia salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon

Salmon rickettsial septicaemia (SRS), caused by the bacteria Piscirickettsia salmonis (P. salmonis), is responsible for significant mortality in farmed Atlantic salmon in Chile. Currently there are no effective treatments or preventive measures for this disease, although genetic selection or genome engineering to increase salmon resistance to SRS are promising strategies. The accuracy and efficiency of these strategies are usually influenced by the available biological background knowledge of the disease. The aim of this study was to investigate DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The head kidney and liver methylomes of 66 juvenile salmon were profiled using reduced representation bisulphite sequencing (RRBS), and compared between P. salmonis infected animals (3 and 9 days post infection) and uninfected controls, and between SRS resistant and susceptible fish. Methylation was correlated with matching RNA-Seq data from the same animals, revealing that methylation in the first exon leads to an important repression of gene expression. Head kidney methylation showed a clear response to the infection, associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases and could inform the incorporation of epigenetic markers into genomic selection for disease resistant and the design of diagnostic epigenetic markers to better manage fish health in salmon aquaculture.

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Background

A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.

Results

Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle.

Conclusions

Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00767-3.

Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing

To identify and annotate transcript isoforms in the chicken genome, we generated Nanopore long-read sequencing data from 68 samples that encompassed 19 diverse tissues collected from experimental adult male and female White Leghorn chickens. More than 23.8 million reads with mean read length of 790 bases and average quality of 18.2 were generated. The annotation and subsequent filtering resulted in the identification of 55,382 transcripts at 40,547 loci with mean length of 1,700 bases. We predicted 30,967 coding transcripts at 19,461 loci, and 16,495 lncRNA transcripts at 15,512 loci. Compared to existing reference annotations, we found ∼52% of annotated transcripts could be partially or fully matched while ∼47% were novel. Seventy percent of novel transcripts were potentially transcribed from lncRNA loci. Based on our annotation, we quantified transcript expression across tissues and found two brain tissues (i.e., cerebellum and cortex) expressed the highest number of transcripts and loci. Furthermore, ∼22% of the transcripts displayed tissue specificity with the reproductive tissues (i.e., testis and ovary) exhibiting the most tissue-specific transcripts. Despite our wide sampling, ∼20% of Ensembl reference loci were not detected. This suggests that deeper sequencing and additional samples that include different breeds, cell types, developmental stages, and physiological conditions, are needed to fully annotate the chicken genome. The application of Nanopore sequencing in this study demonstrates the usefulness of long-read data in discovering additional novel loci (e.g., lncRNA loci) and resolving complex transcripts (e.g., the longest transcript for the TTN locus).

Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits

Background

Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope.

Results

We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21⁺ and CD21⁻ B cells, four T cell fractions (CD4⁺, CD8⁺, CD8⁺CD4⁺, and SWC6γδ⁺), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1).

Conclusion

Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08773-5.

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).

A review of investigated risk factors for developing equine recurrent uveitis

Equine recurrent uveitis (ERU) is an ocular inflammatory disease that can be difficult to manage clinically. As such, it is the leading cause of bilateral blindness for horses. ERU is suspected to have a complex autoimmune etiology with both environmental and genetic risk factors contributing to onset and disease progression in some or all cases. Work in recent years has aimed at unraveling the primary triggers, such as infectious agents and inherited breed-specific risk factors, for disease onset, persistence, and progression. This review has aimed at encompassing those factors that have been associated, implicated, or substantiated as contributors to ERU, as well as identifying areas for which additional knowledge is needed to better understand risk for disease onset and progression. A greater understanding of the risk factors for ERU will enable earlier detection and better prognosis through prevention and new therapeutics.

Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition

Background

Although bovine milk is regarded as healthy and nutritious, its high content of saturated fatty acids (FA) may be harmful to cardiovascular health. Palmitic acid (C16:0) is the predominant saturated FA in milk with adverse health effects that could be countered by substituting it with higher levels of unsaturated FA, such as oleic acid (C18:1cis-9). In this work, we performed genome-wide association analyses for milk fatty acids predicted from FTIR spectroscopy data using 1811 Norwegian Red cattle genotyped and imputed to a high-density 777k single nucleotide polymorphism (SNP)-array. In a follow-up analysis, we used imputed whole-genome sequence data to detect genetic variants that are involved in FTIR-predicted levels of C16:0 and C18:1cis-9 and explore the transcript profile and protein level of candidate genes.

Results

Genome-wise significant associations were detected for C16:0 on Bos taurus (BTA) autosomes 11, 16 and 27, and for C18:1cis-9 on BTA5, 13 and 19. Closer examination of a significant locus on BTA11 identified the PAEP gene, which encodes the milk protein β-lactoglobulin, as a particularly attractive positional candidate gene. At this locus, we discovered a tightly linked cluster of genetic variants in coding and regulatory sequences that have opposing effects on the levels of C16:0 and C18:1cis-9. The favourable haplotype, linked to reduced levels of C16:0 and increased levels of C18:1cis-9 was also associated with a marked reduction in PAEP expression and β-lactoglobulin protein levels. β-lactoglobulin is the most abundant whey protein in milk and lower levels are associated with important dairy production parameters such as improved cheese yield.

Conclusions

The genetic variants detected in this study may be used in breeding to produce milk with an improved FA health-profile and enhanced cheese-making properties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00731-9.

A high-density genome-wide association with absolute blood monocyte count in domestic sheep identifies novel loci

Monocytes are a core component of the immune system that arise from bone marrow and differentiate into cells responsible for phagocytosis and antigen presentation. Their derivatives are often responsible for the initiation of the adaptive immune response. Monocytes and macrophages are central in both controlling and propagating infectious diseases such as infection by Coxiella burnetii and small ruminant lentivirus in sheep. Genotypes from 513 Rambouillet, Polypay, and Columbia sheep (Ovis aries) were generated using the Ovine SNP50 BeadChip. Of these sheep, 222 animals were subsequently genotyped with the Ovine Infinium^® HD SNP BeadChip to increase SNP coverage. Data from the 222 HD genotyped sheep were combined with the data from an additional 258 unique sheep to form a 480-sheep reference panel; this panel was used to impute the low-density genotypes to the HD genotyping density. Then, a genome-wide association analysis was conducted to identify loci associated with absolute monocyte counts from blood. The analysis used a single-locus mixed linear model implementing EMMAX with age and ten principal components as fixed effects. Two genome-wide significant peaks (p < 5x10^-7) were identified on chromosomes 9 and 1, and ten genome-wide suggestive peaks (p < 1x10^-5) were identified on chromosomes 1, 2, 3, 4, 9, 10, 15, and 16. The identified loci were within or near genes including KCNK9, involved into cytokine production, LY6D, a member of a superfamily of genes, some of which subset monocyte lineages, and HMGN1, which encodes a chromatin regulator associated with myeloid cell differentiation. Further investigation of these loci is being conducted to understand their contributions to monocyte counts. Investigating the genetic basis of monocyte lineages and numbers may in turn provide information about pathogens of veterinary importance and elucidate fundamental immunology.

Genome-wide association studies for egg quality traits in White Leghorn layers using low-pass sequencing and SNP chip data

Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

Background

A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle.

Results

Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits.

Conclusions

We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01269-4.

Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning

We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.

Function of m6A and its regulation of domesticated animals' complex traits

N6-methyladenosine (m6A) is the most functionally important epigenetic modification in RNA. The m6A modification widely exists in mRNA and noncoding RNA, influences the mRNA processing, and regulates the secondary structure and maturation of noncoding RNA. Studies showed the important regulatory roles of m6A modification in animal's complex traits, such as development, immunity, and reproduction-related traits. As an important intermediate stage from animal genome to phenotype, the function of m6A in the complex trait formation of domestic animals cannot be neglected. This review discusses recent research advances on m6A modification in well-studied organisms, such as human and model organisms, and introduces m6A detection technologies, small-molecule inhibitors of m6A-related enzymes, interaction between m6A and other biological progresses, and the regulation mechanisms of m6A in domesticated animals' complex traits.

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.

Darwinian genomics and diversity in the tree of life

Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (<1%) have a representative genome sequence in GenBank, and only a fraction of these have ancillary information on genome structure, genetic variation, gene expression, epigenetic modifications, and population diversity. This imbalance reflects a perception that human studies are paramount in disease research. Yet understanding how genomes work, and how genetic variation shapes phenotypes, requires a broad view that embraces the vast diversity of life. We have the technology to collect massive and exquisitely detailed datasets about the world, but expertise is siloed into distinct fields. A new approach, integrating comparative genomics with cell and evolutionary biology, ecology, archaeology, anthropology, and conservation biology, is essential for understanding and protecting ourselves and our world. Here, we describe potential for scientific discovery when comparative genomics works in close collaboration with a broad range of fields as well as the technical, scientific, and social constraints that must be addressed.

Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq

Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.

Dermatophilosis (lumpy wool) in sheep: a review of pathogenesis, aetiology, resistance and vaccines

Lumpy wool (dermatophilosis) develops following prolonged wetting of sheep when bacterial proliferation in wool and on skin induce an exudative dermatitis, causing a superficial skin lesion and damage to wool follicles and fibres. The incidence of dermatophilosis is strongly dependent on wet and warm weather and, hence, infection is sporadic. While older animals are less at risk than are lambs, it is unclear whether this reflects naturally acquired immune resistance or the maturation of skin and wool fibres. Dermatophilosis directly causes wool production losses and it also is a risk factor for blowfly strike, which has a substantial economic impact and increasing challenges associated with current control procedures. This review assessed research on the bacterial causes of lumpy wool, the characteristics of the resulting immune defence reactions in sheep, current control strategies, and limitations of previous attempts to control lumpy wool by sheep vaccination.

A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues

Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55-182 SEs (5-17% in total) and 99-309 BDs (8-16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.