Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard.

Targets for finished livestock are often determined by expected fat, either subcutaneous or intramuscular. These targets are used frequently to improve eating quality. Lower intramuscular fat, lack of product uniformity, and insufficient tenderness can negatively impact beef acceptability. This study aimed to investigate the differences in gene expression that alter metabolism and intercellular signaling in the muscle and adipose tissue in beef carcasses at different fat endpoints. In this study, longissimus thoracis muscle samples and adipose tissue were collected at harvest, and RNA was extracted and then sequenced using RNAseq. Differential expression was determined using edgeR, and p-values were adjusted using the Benjamini-Hochberg method. A corrected p-value of 0.005 and log2 (fold change) of >1 were the threshold to identify differential expression. Comparison between intermuscular and subcutaneous fat showed no differences in the genes activated in the two adipose tissue depots, suggesting that subcutaneous fat was an adequate sample. Carcass data allowed the classification of carcasses by USDA quality grades (marbling targets). In comparing muscle from Standard and Choice carcasses, 15 genes were downregulated, and 20 were upregulated. There were 49 downregulated and 113 upregulated genes comparing adipose tissue from Standard and Choice carcasses. These genes are related to the metabolism of fat and energy. This indicates that muscle transcript expression varies less than adipose. In addition, subcutaneous fat can be used to evaluate transcript changes in fat. However, it is unclear whether these fat tissues can be used as surrogates for marbling.

The recombinant Link module of human TSG-6 suppresses cartilage damage in models of osteoarthritis: A potential disease-modifying OA drug.

OBJECTIVE: To investigate the role of endogenous TSG-6 in human osteoarthritis (OA) and assess the disease-modifying potential of a TSG-6-based biological treatment in cell, explant and animal models of OA. DESIGN: Knee articular cartilages from OA patients were analyzed for TSG-6 protein and mRNA expression using immunohistochemistry and RNAscope, respectively. The inhibitory activities of TSG-6 and its isolated Link module (Link_TSG6) on cytokine-induced degradation of OA cartilage explants were compared. Human mesenchymal stem/stromal cell-derived chondrocyte pellet cultures were used to determine the effects of Link_TSG6 and full-length TSG-6 on IL-1α-, IL-1ß-, or TNF-stimulated ADAMTS4, ADAMTS5, and MMP13 mRNA expression. Link_TSG6 was administered i.a. to the rat ACLTpMMx model; cartilage damage and tactile allodynia were assessed. RESULTS: TSG-6 is predominantly associated with chondrocytes in regions of cartilage damage where high TSG-6 expression aligns with low MMP13, the major collagenase implicated in OA progression. Link_TSG6 is more potent than full-length TSG-6 at inhibiting cytokine-mediated matrix breakdown in human OA cartilage explants;>50% of donor cartilages, from 59 tested, were responsive to Link_TSG6 treatment. Link_TSG6 also displayed more potent effects in 3D pellet cultures, suppressing ADAMTS4, ADAMTS5, and MMP13 gene expression, which was consistent with reduced aggrecanase and collagenase activities in explant cultures. Link_TSG6 treatment reduced touch-evoked pain behavior and dose-dependently inhibited cartilage damage in a rodent model of surgically-induced OA. CONCLUSIONS: Link_TSG6 has enhanced chondroprotective activity compared to the full-length TSG-6 protein and shows potential as a disease modifying OA drug via its inhibition of aggrecanase and collagenase activity.

Identification of Genomic Regions for Carcass Quality Traits within the American Simmental Association Carcass Merit Program.

USDA quality and yield grade are primary driving forces for carcass value in the United States. Carcass improvements can be achieved by making selection decisions based on the results of genetic evaluations in the form of expected progeny differences (EPD), real-time ultrasound imaging, and physical evaluation of candidate breeding animals. In an effort to advance their ability to accurately predict the breeding value of potential sires for carcass traits, the American Simmental Association launched the Carcass Merit Program as a means to collect progeny sire group carcass information. All records were extracted from the American Simmental Association database. Progeny data were organized by sire family and progeny performance phenotypes were constructed. Sire genotypes were filtered, and a multi-locus mixed linear model was used to perform an association analysis on the genotype data, while correcting for cryptic relatedness and pedigree structure. Three chromosomes were found to have genome-wide significance and this conservative approach identified putative QTL in those regions. Three hundred ninety-three novel regions were identified across all traits, as well as 290 novel positional candidate genes. Correlations between carcass characteristics and maternal traits were less unfavorable than those previously reported.

Differential haptoglobin responsiveness to a Mannheimia haemolytica challenge altered immunologic, physiologic, and behavior responses in beef steers.

Indicator traits associated with disease resiliency would be useful to improve the health and welfare of feedlot cattle. A post hoc analysis of data collected previously (Kayser et al., 2019a) was conducted to investigate differences in immunologic, physiologic, and behavioral responses of steers (N = 36, initial BW = 386 ± 24 kg) that had differential haptoglobin (HPT) responses to an experimentally induced challenge with Mannheimia haemolytica (MH). Rumen temperature, DMI, and feeding behavior data were collected continuously, and serial blood samples were collected following the MH challenge. Retrospectively, it was determined that 9 of the 18 MH-challenged steers mounted a minimal HPT response, despite having similar leukocyte and temperature responses to other MH-challenged steers with a greater HPT response. Our objective was to examine differences in behavioral and physiological responses between MH-challenged HPT responsive (RES; n = 9), MH-challenged HPT nonresponsive (NON; n = 9), and phosphate-buffered saline-inoculated controls (CON; n = 18). Additionally, 1H NMR analysis was conducted to determine whether the HPT-responsive phenotype affected serum metabolite profiles. The RES steers had lesser (P < 0.05) cortisol concentrations than NON and CON steers. The magnitude of the increases in neutrophil concentrations and rumen temperature, and the reduction in DMI following the MH challenge were greatest (P < 0.05) in RES steers. Univariate analysis of serum metabolites indicated differences between RES, NON, and CON steers following the MH challenge; however, multivariate analysis revealed no difference between HPT-responsive phenotypes. Prior to the MH challenge, RES steers had longer (P < 0.05) head down and bunk visit durations, slower eating rates (P < 0.01) and greater (P < 0.05) daily variances in bunk visit frequency and head down duration compared with NON steers, suggesting that feeding behavior patterns were associated with the HPT-responsive phenotype. During the 28-d postchallenge period, RES steers had decreased (P < 0.05) final BW, tended (P = 0.06) to have lesser DMI, and had greater (P < 0.05) daily variances in head down and bunk visit durations compared with NON steers, which may have been attributed to their greater acute-phase protein response to the MH challenge. These results indicate that the HPT-responsive phenotype affected feeding behavior patterns and may be associated with disease resiliency in beef cattle.

Evaluating wildlife translocations using genomics: A bighorn sheep case study.

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

Blood lactate and rectal temperature can predict exit velocity of beef feedlot steers.

Interest in beef cattle temperament has increased due to growing consumer awareness of animal welfare and increased concern for handler safety. Temperament measures are based on behavioral responses to a perceived stressor. Subjective chute scoring has been used to give a numeric value to temperament; however, the subjectivity and variability among observers have been questioned. To deal with the perceived subjectivity and variability, other researchers have used exit velocity. Researchers have related faster exit velocities to increased cortisol and plasma lactate. The objectives of this study were to compare temperament between feedlot steers and heifers and to confirm chute side measures of temperament relationship to physiological responses to stress. Body temperature, blood and plasma lactate, serum glucose, salivary and serum cortisol concentrations were measured on Bos taurus commercial crossbred feedlot cattle (n = 197). Fast, medium, and slow classifications were developed from exit velocities. Plasma lactate was significantly different between all exit velocity classes. Exit velocity and physiological measures indicated that heifers were more excitable (faster exit velocities (P = 0.003), higher plasma lactate concentrations (P = 0.03), and cortisol concentrations (P = 0.001)). Simple correlations among these variables indicated body temperature (heifers r = 0.44, P < 0.0001; steers r = 0.45, P < .0001), plasma lactate (heifers r = 0.52, P < 0.0001; steers r = 0.63, P < 0.0001), blood lactate (heifers r = 0.53, P < 0.001; steers r = 0.59, P < 0.001), and glucose (heifers r = 0.54, P < 0.001; steers r = 0.32, P <0.003) were all related to exit velocity. Cortisol measures were not correlated to exit velocity in steers but were in heifers. Linear models constructed and evaluated using the Akaike information criterion indicated that blood lactate in combination with rectal temperature were strong candidates to predict exit velocity. Using the discriminate function analysis, the model correctly categorized fast and slow classifications 69.23% and 61.54%, respectively, indicating that in combination measures of body temperature and blood lactate can potentially increase accuracy of temperament identification or replace exit velocity as a measure of temperament. The plasma lactate and rectal temperature have the potential to become strong objective measures to augment or replace exit velocity.

Evaluating sample size to estimate genetic management metrics in the genomics era.

Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers.

Dairy heifers were subjected to a non-life-threatening challenge designed to induce ruminal acidosis by feeding grain and sugar. Large among animal variation in clinical signs of acidosis, rumen metabolite concentrations, and the rumen microbiome occurred. This exploratory study investigates sources of the variation by examining associations between the genome, metabolome, and microbiome, albeit with a limited population. The broader objective is to provide a rationale for a larger field study to identify markers for susceptibility to ruminal acidosis. Initially, heifers (n = 40) allocated to five feed additive groups were fed 20-days pre-challenge with a total mixed ration and additives. Fructose (0.1% of bodyweight/day) was added for the last 10 days pre-challenge. On day 21 heifers were challenged with 1.0% of bodyweight dry matter wheat + 0.2% of bodyweight fructose + additives. Rumen samples were collected via stomach tube weekly (day 0, 7, and 14) and at five times over 3.6 h after challenge and analyzed for pH and volatile fatty acid, ammonia, D-, and L-lactate concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Genotyping was undertaken using a 150K Illumina SNPchip. Genome-wide association was performed for metabolite and microbiome measures (n = 33). Few genome associations occurred with rumen pH, concentration of acetate, propionate, total volatile fatty acids, or ammonia, or the relative abundance of the Firmicutes, Bacteroidetes, and Spirochaetes phyla. Metabolites and microbial phyla that had markers associated and quantitative trait loci (QTL) were: acetate to propionate ratio (A:P), D-, L-, and total lactate, butyrate, acidosis eigenvalue, Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Planctomycetes, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Euryarchaeota, and Fibrobacteres and covered the region that codes for matrix extracellular phosphoglycoprotein (MEPE). Other overlapping regions were: (1) Chloroflexi, Tenericutes, and A:P, (2) L- and total lactate and Actinobacteria, and (3) Actinobacteria, Euryarchaeota, Fibrobacteres, and A:P. Genome-wide associations with the metabolome and microbiome occurred despite the small population, suggesting that markers for ruminal acidosis susceptibility exist. The findings may explain some of the variation in metabolomic and microbial data and provide a rationale for a larger study with a population that has variation in acidosis.

Immediate memory and electrophysiologic effects of prefrontal cortex transcranial direct current stimulation on neurotypical individuals and individuals with chronic traumatic brain injury: a pilot study.

Purpose/aim: Memory impairment post-TBI is common, frequently persistent, and functionally debilitating. The purposes of this pilot study were to assess and to compare immediate behavioral auditory working memory and electrophysiologic effects of three different, randomized, conditions of left dorsolateral prefrontal cortex (LDLPFC) transcranial direct current stimulation (tDCS) applied to four neurotypical adults and four adults with chronic traumatic brain injury (TBI). MATERIALS/METHODS: Pre- and post-anodal, cathodal, and sham tDCS auditory memory performance, auditory event-related potentials (P300 amplitude and latency) and power of alpha and theta EEG bands were measured across individuals in each group. RESULTS: Post-anodal tDCS only, the neurotypical and TBI groups both demonstrated significantly improved immediate auditory memory function. Also post-anodal tDCS, the TBI group demonstrated significantly increased P300 amplitude versus post-sham tDCS. The neurotypical group demonstrated no pre- post-tDCS electrophysiologic changes across conditions. CONCLUSIONS: These findings are consistent with findings of other studies of immediate tDCS effects on other types of memory in neurotypical individuals and in individuals with Parkinson's disease, Alzheimer's disease and stroke and suggest that individuals with memory impairments second to chronic TBI may benefit from LDLPFC anodal tDCS. Pairing tDCS with traditional behavioral memory interventions may facilitate TBI rehabilitation outcomes and warrants continued investigation.

The Effects of Visual Attention Span and Phonological Decoding in Reading Comprehension in Dyslexia: A Path Analysis.

Increasing evidence has shown visual attention span to be a factor, distinct from phonological skills, that explains single-word identification (pseudo-word/word reading) performance in dyslexia. Yet, little is known about how well visual attention span explains text comprehension. Observing reading comprehension in a sample of 105 high school students with dyslexia, we used a pathway analysis to examine the direct and indirect path between visual attention span and reading comprehension while controlling for other factors such as phonological awareness, letter identification, short-term memory, IQ and age. Integrating phonemic decoding efficiency skills in the analytic model, this study aimed to disentangle how visual attention span and phonological skills work together in reading comprehension for readers with dyslexia. We found visual attention span to have a significant direct effect on more difficult reading comprehension but not on an easier level. It also had a significant direct effect on pseudo-word identification but not on word identification. In addition, we found that visual attention span indirectly explains reading comprehension through pseudo-word reading and word reading skills. This study supports the hypothesis that at least part of the dyslexic profile can be explained by visual attention abilities. Copyright © 2016 John Wiley & Sons, Ltd.

Invited review: Recommendations for reporting intervention studies on reproductive performance in dairy cattle: Improving design, analysis, and interpretation of research on reproduction.

Abundant evidence from the medical, veterinary, and animal science literature demonstrates that there is substantial room for improvement of the clarity, completeness, and accuracy of reporting of intervention studies. More rigorous reporting guidelines are needed to improve the quality of data available for use in comparisons of outcomes (or meta-analyses) of multiple studies. Because of the diversity of factors that affect reproduction and the complexity of interactions between these, a systematic approach is required to design, conduct, and analyze basic and applied studies of dairy cattle reproduction. Greater consistency, clarity, completeness, and correctness of design and reporting will improve the value of each report and allow for greater depth of evaluation in meta-analyses. Each of these benefits will improve understanding and application of current knowledge and better identify questions that require additional modeling or primary research. The proposed guidelines and checklist will aid in the design, conduct, analysis, and reporting of intervention studies. We propose an adaptation of the REFLECT (Reporting Guidelines for Randomized Controlled Trials for Livestock and Food Safety) statement to provide guidelines and a checklist specific to reporting intervention studies in dairy cattle reproduction. Furthermore, we provide recommendations that will assist investigators to produce studies with greater internal and external validity that can more often be included in systematic reviews and global meta-analyses. Such studies will also assist the development of models to describe the physiology of reproduction.

Transcranial direct current stimulation modulates efficiency of reading processes.

Transcranial direct current stimulation (tDCS) is a neuromodulatory technique that offers promise as an investigative method for understanding complex cognitive operations such as reading. This study explores the ability of a single session of tDCS to modulate reading efficiency and phonological processing performance within a group of healthy adults. Half the group received anodal or cathodal stimulation, on two separate days, of the left temporo-parietal junction while the other half received anodal or cathodal stimulation of the right homologue area. Pre- and post-stimulation assessment of reading efficiency and phonological processing was carried out. A larger pre-post difference in reading efficiency was found for participants who received right anodal stimulation compared to participants who received left anodal stimulation. Further, there was a significant post-stimulation increase in phonological processing speed following right hemisphere anodal stimulation. Implications for models of reading and reading impairment are discussed.

Auditory temporal processing skills in musicians with dyslexia.

The core cognitive difficulty in developmental dyslexia involves phonological processing, but adults and children with dyslexia also have sensory impairments. Impairments in basic auditory processing show particular links with phonological impairments, and recent studies with dyslexic children across languages reveal a relationship between auditory temporal processing and sensitivity to rhythmic timing and speech rhythm. As rhythm is explicit in music, musical training might have a beneficial effect on the auditory perception of acoustic cues to rhythm in dyslexia. Here we took advantage of the presence of musicians with and without dyslexia in musical conservatoires, comparing their auditory temporal processing abilities with those of dyslexic non-musicians matched for cognitive ability. Musicians with dyslexia showed equivalent auditory sensitivity to musicians without dyslexia and also showed equivalent rhythm perception. The data support the view that extensive rhythmic experience initiated during childhood (here in the form of music training) can affect basic auditory processing skills which are found to be deficient in individuals with dyslexia.

TSG-6 inhibits neutrophil migration via direct interaction with the chemokine CXCL8.

TNF-stimulated gene/protein-6 (TSG-6) is expressed by many different cell types in response to proinflammatory cytokines and plays an important role in the protection of tissues from the damaging consequences of acute inflammation. Recently, TSG-6 was identified as being largely responsible for the beneficial effects of multipotent mesenchymal stem cells, for example in the treatment of animal models of myocardial infarction and corneal injury/allogenic transplant. The protective effect of TSG-6 is due in part to its inhibition of neutrophil migration, but the mechanisms underlying this activity remain unknown. In this study, we have shown that TSG-6 inhibits chemokine-stimulated transendothelial migration of neutrophils via a direct interaction (KD, ∼ 25 nM) between TSG-6 and the glycosaminoglycan binding site of CXCL8, which antagonizes the association of CXCL8 with heparin. Furthermore, we found that TSG-6 impairs the binding of CXCL8 to cell surface glycosaminoglycans and the transport of CXCL8 across an endothelial cell monolayer. In vivo this could limit the formation of haptotactic gradients on endothelial heparan sulfate proteoglycans and, hence, integrin-mediated tight adhesion and migration. We further observed that TSG-6 suppresses CXCL8-mediated chemotaxis of neutrophils; this lower potency effect might be important at sites where there is high local expression of TSG-6. Thus, we have identified TSG-6 as a CXCL8-binding protein, making it, to our knowledge, the first soluble mammalian chemokine-binding protein to be described to date. We have also revealed a potential mechanism whereby TSG-6 mediates its anti-inflammatory and protective effects. This could inform the development of new treatments for inflammation in the context of disease or following transplantation.

Characterization of the Vaginal Microbiota of Ewes and Cows Reveals a Unique Microbiota with Low Levels of Lactobacilli and Near-Neutral pH.

Although a number of common reproductive disorders in livestock involve bacterial infection, very little is known about their normal vaginal microbiota. Therefore, we sought to determine the species composition of sheep and cattle vaginal microbiota. Twenty Rambouillet ewes and twenty crossbred cows varying in age and reproductive status were sampled by ectocervicovaginal lavage. We amplified and sequenced the V3-V4 region of the 16S ribosomal RNA (rRNA) contents yielding a total of 907,667 high-quality reads. Good's Coverage estimates indicated that we obtained data on 98 ± 0.01% of the total microbial genera present in each sample. Cow and ewe vaginal microbiota displayed few differences. Cow microbiota exhibited greater (P ≤ 0.05) α-diversity compared to the ewe microbiota. Both livestock species differed (P ≤ 0.05) from all previously reported vaginal communities. While bacteria were numerically dominant, Archaea were detected in 95% of cow and ewe samples, mainly of the order Desulfurococcales. Both ewes and cows were predominately colonized by the bacterial phyla Bacteroidetes, Fusobacteria, and Proteobacteria. The most abundant genera were Aggregatibacter spp., and Streptobacillus spp. Lactobacillus spp. were detected in 80% of ewe and 90% of cow samples, but only at very low abundances. Bacteria previously described from culture-based studies as common to the cow and ewe vaginal tract, except for Escherichia, were variably present, and only in low abundance. Ewe and cow pH differed (P ≤ 0.05), with means (±SD) of 6.7 ± 0.38 and 7.3 ± 0.63, respectively. In conclusion, 16S rRNA sequencing of cow and ewe vaginal ectocervicovaginal lavages showed that cow and ewe vaginal microbiota differ from culture-led results, revealing a microbiota distinct from previously described vaginal ecosystems.

Impaired non-speech auditory processing at a pre-reading age is a risk-factor for dyslexia but not a predictor: an ERP study.

Impaired auditory sensitivity to amplitude rise time (ART) has been suggested to be a primary deficit in developmental dyslexia. The present study investigates whether impaired ART-sensitivity at a pre-reading age precedes and predicts later emerging reading problems in a sample of Dutch children. An oddball paradigm, with a deviant that differed from the standard stimulus in ART, was administered to 41-month-old children (30 genetically at-risk for developmental dyslexia and 14 controls) with concurrent EEG measurement. A second deviant that differed from the standard stimulus in frequency served as a control deviant. Grade two reading scores were used to divide the at-risks in a typical-reading and a dyslexic subgroup. We found that both ART- and frequency processing were related to later reading skill. We however also found that irrespective of reading level, the at-risks in general showed impaired basic auditory processing when compared to controls and that it was impossible to discriminate between the at-risk groups on basis of both auditory measures. A relatively higher quality of early expressive syntactic skills in the typical-reading at-risk group might indicate a protective factor against negative effects of impaired auditory processing on reading development. Based on these results we argue that ART- and frequency-processing measures, although they are related to reading skill, lack the power to be considered single-cause predictors of developmental dyslexia. More likely, they are genetically driven risk factors that may add to cumulative effects on processes that are critical for learning to read.

The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility.

Classical bovine spongiform encephalopathy is a transmissible prion disease that is fatal to cattle and is a human health risk due to its association with a strain of Creutzfeldt-Jakob disease (vCJD). Mutations to the coding region of the prion gene (PRNP) have been associated with susceptibility to transmissible spongiform encephalopathies in mammals including bovines and humans. Additional loci such as the retinoic acid receptor beta (RARB) and stathmin like 2 (STMN2) have also been associated with disease risk. The objective of this study was to refine previously identified regions associated with BSE susceptibility and to identify positional candidate genes and genetic variation that may be involved with the progression of classical BSE. The samples included 739 samples of either BSE infected animals (522 animals) or non-infected controls (207 animals). These were tested using a custom SNP array designed to narrow previously identified regions of importance in bovine genome. Thirty one single nucleotide polymorphisms were identified at p < 0.05 and a minor allele frequency greater than 5%. The chromosomal regions identified and the positional and functional candidate genes and regulatory elements identified within these regions warrant further research.

Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.

Development of management paradigms that enhance the rate of gain and qualitative characteristics of beef carcass development has the potential to impact production and nutrient use efficiency but also mitigate losses to the environment. We used eight Black Angus beef steers (272.5 ± 17.6 kg initial body wt) fed a forage-based pelleted diet alone (n = 4) or supplemented with sodium propionate included (n = 4) for 42 days. High-quality RNA was extracted from the longissimus lumborum and subjected to transcriptome sequencing using RNA-seq technology. Trimmed reads were aligned to the bovine reference genome (Btau4.0, release 63) and uniquely mapped reads from control and propionate treatment groups were subject to further analysis using edgeR. Candidates were filtered to account for multiple testing and differentially expressed genes (153 at a false discovery rate of <5%) were analyzed using Gene Ontology (GO) analysis (GOseq) to select terms where enrichment had occurred. Significant GO terms included regulation of cholesterol transport, regulation of sterol transport, and cellular modified amino acid metabolic process. Furthermore, the top four identified gene networks included lipid metabolism, small molecule biochemistry, carbohydrate metabolism, and molecular transport-related categories. Notably, changes in lipid metabolism specific genes reflect both increased oxidative and lipid synthetic capacities. Metabolism-related gene changes are reflective of expected enhancements in lean tissue accretion patterns exhibited in steers where high ruminal propionate relative to other short chain fatty acids is observed. Propionate feeding induced increased N retention in rapidly growing Angus cattle, and the observed alterations in LL tissue lipid metabolism-related gene networks are consistent with enhanced cell formation and function (protein synthesis, and lipogenic vs. lipolytic activities).