Unraveling the Genetic Basis of Feed Efficiency in Cattle through Integrated DNA Methylation and CattleGTEx Analysis.

Feed costs can amount to 75 percent of the total overhead cost of raising cows for milk production. Meanwhile, the livestock industry is considered a significant contributor to global climate change due to the production of greenhouse gas emissions, such as methane. Indeed, the genetic basis of feed efficiency (FE) is of great interest to the animal research community.

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

Background: Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows.

Results: GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE).

Utilisation of antimicrobials used to treat bacterial pneumonia in principal referral hospitals during the COVID-19 pandemic, Australia, 2020.

Background: Concerns have been raised internationally, regarding possible increased antimicrobial use during the COVID-19 pandemic and the potential impact on antimicrobial resistance. This analysis aimed to investigate hospital usage rates of broad-spectrum antibacterial agents used to treat community-acquired pneumonia (CAP) and/or hospital-acquired pneumonia (HAP) in Australian principal referral hospitals during 2020. Secondly, usage rates in Victoria were compared with equivalent national rates.

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.

Transcriptional Reprogramming in Rumen Epithelium during the Developmental Transition of Pre-Ruminant to the Ruminant in Cattle.

We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways.

Comparative analysis of Australian hospital antimicrobial utilization, using the WHO AWaRe classification system and the adapted Australian Priority Antimicrobial List (PAL).

Background: In 2020 the Australian Priority Antibacterial List (PAL) was developed to support national surveillance of antibacterial usage.

Objectives: To compare the WHO AwaRe classification system with the Australian PAL to analyse antibacterial utilization in Australian acute care hospitals.

Methods: Monthly antibacterial usage rates (defined daily dose per 1000 occupied bed days) were calculated using pharmacy dispensing records together with patient occupancy data for all acute care hospitals contributing to the National Antimicrobial Utilisation Surveillance Program for 2015-19.

Single-cell transcriptomic analyses of dairy cattle ruminal epithelial cells during weaning.

Using the 10× Genomics Chromium Controller, we obtained scRNA-seq data of 5064 and 1372 individual cells from two Holstein calf ruminal epithelial tissues before and after weaning, respectively. We detected six distinct cell clusters, designated their cell types, and reported their marker genes. We then examined these clusters' underlining cell types and relationships by performing cell cycle, pseudotime trajectory, regulatory network, weighted gene co-expression network and gene ontology analyses.

Effects of Incorporating Dry Matter Intake and Residual Feed Intake into a Selection Index for Dairy Cattle Using Deterministic Modeling.

The inclusion of feed efficiency in the breeding goal for dairy cattle has been discussed for many years. The effects of incorporating feed efficiency into a selection index were assessed by indirect selection (dry matter intake) and direct selection (residual feed intake) using deterministic modeling. Both traits were investigated in three ways: (1) restricting the trait genetic gain to zero, (2) applying negative selection pressure, and (3) applying positive selection pressure.

Olfactory navigation in the real world: Simple local search strategies for turbulent environments.

Olfaction informs animal navigation for foraging, social interaction, and threat evasion. However, turbulent flow on the spatial scales of most animal navigation leads to intermittent odor information and presents a challenge to simple gradient-ascent navigation. Here we present two strategies for iterative gradient estimation and navigation via olfactory cues in 2D space: tropotaxis, spatial concentration comparison (i.

How Ambient Environment Influences Olfactory Orientation in Search and Rescue Dogs.

Under natural conditions, an animal orienting to an air-borne odor plume must contend with the shifting influence of meteorological variables, such as air temperature, humidity, and wind speed, on the location and the detectability of the plume. Despite their importance, the natural statistics of such variables are difficult to reproduce in the laboratory and hence few studies have investigated strategies of olfactory orientation by mobile animals under different meteorological conditions. Using trained search and rescue dogs, we quantified the olfactory orientation behaviors of dogs searching for a trail (aged 1-3 h) of a hidden human subject in a natural landscape, under a range of meteorological conditions.

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns.

Background: Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date.

Establishment and transcriptomic analyses of a cattle rumen epithelial primary cells (REPC) culture by bulk and single-cell RNA sequencing to elucidate interactions of butyrate and rumen development.

As a critical and high-value tool to study the development of rumen, we established a stable rumen epithelial primary cell (REPC) culture from a two-week-old Holstein bull calf rumen epithelial tissue. The transcriptomic profiling of the REPC and the direct effects of butyrate on gene expression were assessed. Correlated gene networks elucidated the putative roles and mechanisms of butyrate action in rumen epithelial development.

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations.

Background: The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively utilizing the increased amount of genome sequences reported. However, while such annotation has been well explored in a diverse set of tissues and cell types in human and model organisms, relatively little data are available for livestock genomes, hindering our understanding of complex trait variation, domestication, and adaptive evolution. Here, we present the first complete global landscape of regulatory elements in cattle and explore the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator-butyrate.

Olfactory Navigation and the Receptor Nonlinearity.

The demands on a sensory system depend not only on the statistics of its inputs but also on the task. In olfactory navigation, for example, the task is to find the plume source; allocation of sensory resources may therefore be driven by aspects of the plume that are informative about source location, rather than concentration per se. Here we explore the implications of this idea for encoding odor concentration.

Elementary sensory-motor transformations underlying olfactory navigation in walking fruit-flies.

Odor attraction in walking is commonly used to relate neural function to behavior, but the algorithms underlying attraction are unclear. Here, we develop a high-throughput assay to measure olfactory behavior in response to well-controlled sensory stimuli. We show that odor evokes two behaviors: an upwind run during odor (ON response), and a local search at odor offset (OFF response).

Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?

Many species rely on olfaction to navigate towards food sources or mates. Olfactory navigation is a challenging task since odor environments are typically turbulent. While time-averaged odor concentration varies smoothly with the distance to the source, instaneous concentrations are intermittent and obtaining stable averages takes longer than the typical intervals between animals' navigation decisions.

Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle.

Background: Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been applied in livestock, although few studies have focused on Holstein cattle.

Results: We describe 191 CNV detected using intensity data from over 700,000 SNP genotypes generated with the BovineHD Genotyping BeadChip (Illumina, San Diego, CA) in 528 Holstein cows.

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm.

Background: Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown.

Results: Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats.

The essence of appetite: does olfactory receptor variation play a role?

Olfactory receptors are G-protein-coupled chemoreceptors expressed on millions of olfactory sensory neurons within the nasal cavity. These receptors detect environmental odorants and signal the brain regarding the location of feed, potential mates, and the presence of possible threats (e.g.

Rumen Function and Development.

The ruminal epithelium is a complex tissue that serves as an important protective barrier as well as a metabolically important tissue for whole-animal energy metabolism. Up to 70% of the energetic needs of mature animals are absorbed as short-chain fatty acids through the stratified squamous epithelium, and it serves as the primary producer of ketones in fed animals. Both physical and metabolic development are incomplete at birth and are triggered by short-chain fatty acids.

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium.

The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following introduction of solid feed to the weaning neonate as well as affecting the metabolism of other nutrients and absorption of nutrients in in vitro experiments. The objective of the present study was to validate expression stability of eight putative reference genes bovine rumen, considering the intrinsic heterogeneity of bovine rumen with regard to different luminal characteristics due to direct infusion of butyrate to double the intra-ruminal content of the rumen liquor.

Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression.

Background: As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle.

Results: Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues.

Gene expression in bovine rumen epithelium during weaning identifies molecular regulators of rumen development and growth.

During weaning, epithelial cell function in the rumen transitions in response to conversion from a pre-ruminant to a true ruminant environment to ensure efficient nutrient absorption and metabolism. To identify gene networks affected by weaning in bovine rumen, Holstein bull calves were fed commercial milk replacer only (MRO) until 42 days of age, then were provided diets of either milk + orchardgrass hay (MH) or milk + grain-based calf starter (MG). Rumen epithelial RNA was extracted from calves sacrificed at four time points: day 14 (n = 3) and day 42 (n = 3) of age while fed the MRO diet and day 56 (n = 3/diet) and day 70 (n = 3/diet) while fed the MH and MG diets for transcript profiling by microarray hybridization.

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake.

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of copy number variations (CNVs) using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intake (RFI). We detected 443 candidate CNV regions (CNVRs) that represent 18.