Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake.

The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 ( = 16) were selected for high and low RFI.

Disrupted one-carbon metabolism in heifers negatively affects their health and physiology.

The objective of this study was to determine the dose-dependent response of one-carbon metabolite (OCM: methionine, choline, folate, and vitamin B12) supplementation on heifer dry matter intake on fixed gain, organ mass, hematology, cytokine concentration, pancreatic and jejunal enzyme activity, and muscle hydrogen peroxide production. Angus heifers (n = 30; body weight [BW] = 392.6 ± 12.

Effects of protein concentration and beta-adrenergic agonists on ruminal bacterial communities in finishing beef heifers.

To improve animal performance and modify growth by increasing lean tissue accretion, beef cattle production has relied on use of growth promoting technologies such as beta-adrenergic agonists. These synthetic catecholamines, combined with the variable inclusion of rumen degradable (RDP) and undegradable protein (RUP), improve feed efficiency and rate of gain in finishing beef cattle. However, research regarding the impact of beta-adrenergic agonists, protein level, and source on the ruminal microbiome is limited.

Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet.

Most of the research addressing feed efficiency and the microbiota has been conducted in cattle fed grain diets, although cattle evolved to consume forage diets. Our hypothesis was that the bacteria in the rumen and cecum differed in cattle that have a common feed intake but had different ^average daily body weight gains (ADG) on a forage diet. Heifers (n = 134) were 606 ± 1 d of age and weighed 476 ± 3 kg at the start of the 84-d feeding study.

Effects of adding ruminal propionate on dry matter intake and glucose metabolism in steers fed a finishing ration.

The objective of this experiment was to determine if supplying additional propionate to the rumen alters dry matter intake (DMI), feeding behavior, glucose metabolism, and rumen fluid metabolites in steers fed a finishing diet. Ruminally cannulated steers (n = 6) were fed a finishing diet ad libitum. Steers were randomly assigned to one of three treatments in a 3 × 6 Latin rectangle design with three 15 d periods.

One-carbon metabolite supplementation to heifers for the first 14 d of the estrous cycle alters the plasma and hepatic one-carbon metabolite pool and methionine-folate cycle enzyme transcript abundance in a dose-dependent manner.

The objective of this study was to determine the dose of folate and vitamin B12 in beef heifers fed rumen protected methionine and choline required to maintain increased B12 levels and intermediates of the methionine-folate cycle in circulation. Angus heifers (n = 30; BW = 392.6 ± 12.

Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq.

Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates. Meta-analysis procedures can be used to integrate and jointly analyze data from multiple independent studies.

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers.

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging.

DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply.

Fetal programming is established early in life, likely through epigenetic mechanisms that control gene expression. Micronutrients can act as epigenetic modifiers (EM) by modulating the genome through mechanisms that include DNA methylation and post-translational modification of chromatin. Among the EM, methionine, choline, folate, and vitamin B have been suggested as key players of DNA methylation.

Epigenetic Modifier Supplementation Improves Mitochondrial Respiration and Growth Rates and Alters DNA Methylation of Bovine Embryonic Fibroblast Cells Cultured in Divergent Energy Supply.

Epigenetic modifiers (EM; methionine, choline, folate, and vitamin B) are important for early embryonic development due to their roles as methyl donors or cofactors in methylation reactions. Additionally, they are essential for the synthesis of nucleotides, polyamines, redox equivalents, and energy metabolites. Despite their importance, investigation into the supplementation of EM in ruminants has been limited to one or two epigenetic modifiers.

Global analysis of differential gene expression within the porcine conceptus transcriptome as it transitions through spherical, ovoid, and tubular morphologies during the initiation of elongation.

This study aimed to identify transcriptome differences between distinct or transitional stage spherical, ovoid, and tubular porcine blastocysts throughout the initiation of elongation. We performed a global transcriptome analysis of differential gene expression using RNA-Seq with high temporal resolution between spherical, ovoid, and tubular stage blastocysts at specific sequential stages of development from litters containing conceptus populations of distinct or transitional blastocysts. After RNA-Seq analysis, significant differentially expressed genes (DEGs) and pathways were identified between distinct morphologies or sequential development stages.

Hematology parameters as potential indicators of feed efficiency in pigs.

The identification of an inexpensive, indirect measure of feed efficiency in swine could be a useful tool to help identify animals with improved phenotypes to supplement expensive phenotypes including individual feed intakes. The purpose of this study was to determine whether hematology parameters in pigs at the beginning and end of a feed efficiency study, or changes in those values over the study, were associated with average daily gain (ADG), average daily feed intake (ADFI), or gain-to-feed (G:F). Whole blood samples were taken at days 0 and 42 from pigs ( = 178) that were monitored for individual feed intakes and body weight gain during a 6-week study.

Effects of increasing calcium propionate in a finishing diet on dry matter intake and glucose metabolism in steers.

The objective of this study was to determine whether increasing propionate alters dry matter intake (DMI), glucose clearance rate, blood metabolites, insulin concentrations, and hepatic gene expression in steers fed a finishing diet. Holstein steers (n = 15; BW = 243 ± 3.6 kg) were individually fed a finishing diet ad libitum.

Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation.

Objective: Realimentation can compensate for weight loss from poor-quality feedstuffs or drought. Mature cows fluctuate in body weight throughout the year due to nutrient availability. The objective of this study was to determine whether cows that differ in weight gain during realimentation also differ in the abundance of transcripts for enzymes associated with energy utilization in skeletal muscle.

Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities.

Background: Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell types, including mammary epithelial cells, neutrophils, macrophages, and lymphocytes, as well nanoparticles, such as milk exosomes. To-date, only a limited number of livestock transcriptomic studies have reported sequencing of milk.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses.

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F.

Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers.

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple and -influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence.

Associations of mucosal disaccharidase kinetics and expression in the jejunum of steers with divergent average daily gain.

The objective of this study was to quantify the differences in the activity of jejunal maltase and isomaltase between two groups of steers with average dry matter intake (DMI) and differing average daily gain (ADG). DMI and ADG were measured in crossbred steers (n = 69; initial body weight = 456 ± 5.0 kg) consuming a finishing diet containing 67.

Ruminal transcript abundance of the centromere-associated protein E gene may influence residual feed intake in beef steers.

A better understanding regarding the mechanisms by which the rumen processes feed may assist us in identifying animals with superior feed efficiency. Studies to evaluate the gene expression of rumen tissue have previously been performed to analyze their relationship with feed efficiency. Continuing this research is critical to determine whether the expression of the genes identified is associated with feed efficiency in additional populations of beef cattle to ensure that they are robust across breed and environment.

Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs.

The "large small " problem has posed a significant challenge in the analysis and interpretation of genome-wide association studies (GWAS). The use of prior information to rank genomic regions and perform SNP selection could increase the power of GWAS. In this study, we propose the use of gene expression data from RNA-Seq of multiple tissues as prior information to assign weights to SNP, select SNP based on a weight threshold, and utilize weighted hypothesis testing to conduct a GWAS.

Digestive tract microbiota of beef cattle that differed in feed efficiency.

We hypothesized cattle that differed in BW gain had different digestive tract microbiota. Two experiments were conducted. In both experiments, steers received a diet that consisted of 8.

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers.

Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake.

A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.

Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties.