Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality.

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

Effect of replacing concentrates with cassava root-top silage on feed utilization, rumen fermentation, blood parameters and growth performance in beef cattle.

OBJECTIVE: This experiment aimed to evaluate the effects of replacing concentrates with cassava root-top silage (CARTOS) on feed intake, digestibility, rumen fermentation, blood parameters, and growth performance of beef cattle. METHODS: Twenty crossbred bulls with a body weight (BW) of 226±56 kg were randomly assigned to one of five treatments for 90 d in a randomized complete block design having four blocks based on BW. The concentrates were replaced by CARTOS at levels of 0%, 25%, 50%, 75%, and 100% dry matter (DM). Animals were fed dietary treatments at 1.8% BW, with rice straw offered ad libitum. RESULTS: The DM and crude protein (CP) intake were decreased (p<0.01, p = 0.04) when the diet's CARTOS level was increased. The digestibility of DM, OM, and CP were not different among treatments, while fiber digestibility was increased with the inclusion of CARTOS (p = 0.03). The addition of CARTOS to replace concentrates did not change ruminal pH or volatile fatty acid proportions except for acetic acid, which increased with the addition of CARTOS (p = 0.03). The ruminal ammonia-nitrogen (NH3-N) was decreased (p<0.01) with increasing levels of CARTOS. The blood glucose and blood urea nitrogen decreased (p = 0.01) with the addition of CARTOS at 100%, whereas total protein and hematological parameters did not change with increasing levels of CARTOS. The use of CARTOS to substitute concentrates at 75% and 100% decreased average daily gain (ADG) and gain to feed ratio (G:F) (p<0.01); therefore, the addition of CARTOS up to 50% maintained ADG and G:F in beef cattle. CONCLUSION: CARTOS can replace concentrates up to 50% in beef cattle diets without adversely affecting feed intake, nutrient digestibility, rumen fermentation characteristics, blood parameters, or growth performance of beef cattle.

Proteomic changes of the bovine blood plasma in response to heat stress in a tropically adapted cattle breed.

Background: Identifying molecular mechanisms responsible for the response to heat stress is essential to increase production, reproduction, health, and welfare. This study aimed to identify early biological responses and potential biomarkers involved in the response to heat stress and animal's recovery in tropically adapted beef cattle through proteomic analysis of blood plasma. Methods: Blood samples were collected from 14 Caracu males during the heat stress peak (HSP) and 16 h after it (heat stress recovery-HSR) assessed based on wet bulb globe temperature index and rectal temperature. Proteome was investigated by liquid chromatography-tandem mass spectrometry from plasma samples, and the differentially regulated proteins were evaluated by functional enrichment analysis using DAVID tool. The protein-protein interaction network was evaluated by STRING tool. Results: A total of 1,550 proteins were detected in both time points, of which 84 and 65 were downregulated and upregulated during HSR, respectively. Among the differentially regulated proteins with the highest absolute log-fold change values, those encoded by the GABBR1, EPHA2, DUSP5, MUC2, DGCR8, MAP2K7, ADRA1A, CXADR, TOPBP1, and NEB genes were highlighted as potential biomarkers because of their roles in response to heat stress. The functional enrichment analysis revealed that 65 Gene Ontology terms and 34 pathways were significant (P < 0.05). We highlighted those that could be associated with the response to heat stress, such as those related to the immune system, complement system, hemostasis, calcium, ECM-receptor interaction, and PI3K-Akt and MAPK signaling pathways. In addition, the protein-protein interaction network analysis revealed several complement and coagulation proteins and acute-phase proteins as important nodes based on their centrality and edges. Conclusion: Identifying differentially regulated proteins and their relationship, as well as their roles in key pathways contribute to improve the knowledge of the mechanisms behind the response to heat stress in naturally adapted cattle breeds. In addition, proteins highlighted herein are potential biomarkers involved in the early response and recovery from heat stress in tropically adapted beef cattle.

Signatures of selection in Angus and Hanwoo beef cattle using imputed whole genome sequence data.

In this study, we detected signatures of selection in Hanwoo and Angus beef cattle using allele frequency and haplotype-based methods based on imputed whole genome sequence variants. Our dataset included 13,202 Angus animals with 10,057,633 imputed SNPs and 10,437 Hanwoo animals with 13,241,550 imputed SNPs. The dataset was subset down to 6,873,624 SNPs in common between the two populations to identify within population (runs of homozygosity, extended haplotype homozygosity) and between population signals of selection (allele fixation index, extended haplotype homozygosity). Assuming these selection signals were complementary to each other, they were combined into a decorrelated composite of multiple signals to identify regions under selection for each of the breeds. 27 genomic regions spanning 25.15 Mb and harboring 360 genes were identified in Angus on chromosomes 1,3, 4, 5, 6, 7, 8, 12, 13, 14, 16, 20, 21 and 28. Similarly, in Hanwoo, 59 genes and 17 genomic regions spanning 5.21 Mb on chromosomes 2, 4, 5, 6, 7, 8, 9, 10, 13, 17, 20 and 24 were identified. Apart from a small region on chromosome 13, there was no major overlap of selection signals between the two breeds reflecting their largely different selection histories, environmental challenges, breeding objectives and breed characteristics. Positional candidate genes identified in selected genomic regions in Angus have been previously associated with growth, immunity, reproductive development, feed efficiency and adaptation to environment while the candidate genes identified in Hanwoo included important genes regulating meat quality, fat deposition, cholesterol metabolism, lipid synthesis, neuronal development, and olfactory reception.

Raising double-muscled breed cattle and their crossbreds in the tropics: insight from growth models.

Background and Aim: In tropical conditions, modeling the predictive parameters of live weight, including those at birth, pre-weaning, post-weaning, finishing, and maturing, and the average daily gain, is challenging. The heat load significantly influences the growth rate and final mature weights in the tropics. The study compared the growth rates of Kedah-Kelantan (KK), Brahman (BRAH), and Belgian Blue (BB) crossbred calves. Materials and Methods: The study conducted growth analysis using the non-linear regression growth models as it approximates the sex, breed, and growth physiology changes in beef cattle. It is supported by the utility of the most common growth functions (Brody, Logistic, von Bertalanffy, and Richard's model) in normal-muscled tropical breeds and double-muscled crossbred beef cattle in the tropics. Results: The BB crossbreds outperformed the KK and BRAH breeds by 50%-100% in live weight gains under tropical conditions. The crossbreds display the double-muscled effect and highlight the advantages of heterosis, making them suitable for upgrading local herds. The study's findings on the growth characteristics of BB crossbred cattle were best described by the von Bertalanffy growth model, which had a high coefficient of determination (R2 > 0.8) and yielded estimated mature weights of 527.5 kg for males and 518.5 kg for females. Conclusion: According to results, raising BB crossbreds in the tropics as a solution to ensure a sustainable beef supply could yield significant growth and economic benefits.

Licorice Extract Supplementation Benefits Growth Performance, Blood Biochemistry and Hormones, Immune Antioxidant Status, Hindgut Fecal Microbial Community, and Metabolism in Beef Cattle.

This study aimed to evaluate the effects of licorice extract (LE) on growth performance, nutrient apparent digestibility, serum index (biochemistry, hormones, humoral immunity, and antioxidant function), hindgut fecal microbiota, and metabolism in beef cattle. In total, 12 male yellow cattle aged 12 months were divided into two groups (6 cattle per group): the basal diet (CK group) and the basal diet supplemented with 2 g/kg LE (CHM group). The entire experimental phase lasted for 120 days, including a 30-day pre-feeding period. Compared to the CK group, the average daily gain, crude fiber, calcium, and crude protein nutrient digestibility were greater on d 30 than d 60 (p < 0.05) and the feed meat ratio was lower for LE addition (p < 0.01). In terms of serum indexes, the insulin and nitric oxide contents were enhanced on d 30, the alkaline phosphatase level was improved on d 60, and the levels of albumin, immunoglobulin A, and catalase were increased on d 90 (p < 0.05). In contrast, the cholesterol content was lower on d 60 for LE addition compared with the CK group (p < 0.05). The higher enrichment of [Eubacterium]-oxidoreducens-group, p-2534-18b5-gut-group, and Ileibacterium were observed in the CHM group (p < 0.05), while the relative abundances of Gallibacterium and Breznakia in the CHM group were lower compared with the CK group (p < 0.05). In addition, the differential metabolites related to healthy growth in the CHM group were increased compared with the CK group. And there was a close correlation between hindgut microbiota and metabolic differentials. In general, LE has a promoting effect on the growth performance and health status of beef cattle over a period (30 to 60 days).

Probabilistic Risk Assessment of Polioencephalomalacia from Texas Beef Consuming Rations Containing Multiple Sources of Dietary Sulfur.

The purpose of this probabilistic assessment was to estimate the risk of sulfur-induced polioencephalomalacia (S-PEM) for beef raised across Texas, from a dietary perspective. Ruminant nutritionists in Amarillo, TX, formulated two typical nutritional regimens based on cattle production stages, each containing six feed ingredients and well water. The Office of the Texas State Chemist (OTSC), National Research Council (NRC), and the published literature provided S data for feed ingredients. The Texas Water Development Board provided data for S content in Texas well water, categorized into twelve districts established by the Texas A&M AgriLife Research Extension Service. The S-PEM risk was estimated at five different eNDF levels ranging from 0% to 8% in 2% increments, using rumen degradable S (RDS) as an input value. Findings identified cattle raised in the South Plains district as the most susceptible population to S toxicity, with beef in the finishing production stage experiencing increased sensitivity. The most potential (MP) risk scenario suggested that the S-PEM risk could reach 28.5% for growers and 100% for finishers. Results further revealed that when S concentrations in well water exceeded 14.5 mg/L, water became the greatest contributor to RDS content for Texas beef, suggesting that high S content in well water is the most prominent concern for Texas beef.

The Use of Pulmonary Arterial Pressure (PAP) for Improved Beef Cattle Management.

Pulmonary arterial pressure (PAP) determines cattle's susceptibility to High Altitude Disease (HAD), also known as Brisket Disease, High Mountain Disease, and right-sided heart failure (RHF). This non-infectious disease causes pulmonary hypertension due to hypoxia. PAP measures the resistance of blood flow through the lungs. It is estimated that 1.5 million head of cattle are raised in high-altitude environments (above 1500 m), and HAD accounts for 3-5% of calf death loss yearly. In addition, there have been increasing concerns about feedlot cattle succumbing to RHF at moderate elevations. This review focuses on the historical background, explanation of PAP measurement and scores, genetic implications, and the relationship between PAP and economically relevant traits. Specifically, traits such as gestation length, birth weight, weaning weight, and yearling weight may impact PAP scores. In addition, environmental effects and other factors impacting PAP score variations are discussed. Information gaps and research needs are addressed to determine where missing information could improve the understanding of PAP while also benefiting beef cattle producers in high-elevation production systems.

Behavioural Responses of Beef Cattle to Hot Conditions.

Cattle are increasingly exposed to hot temperatures as a result of climate change, and a better understanding of behavioural responses could be beneficial for the diagnosis of heat loads. The changes in the positioning of key body parts, feeding behaviour, body maintenance, and respiratory dynamics were assessed in 24 Black Angus steers individually exposed to hot conditions and fed a finisher diet based on cereal grain or a substituted diet (8% of the grain replaced by an isoenergetic amount of lucerne hay). Increased respiration rate during the heat load period, compared to the recovery period, was associated with increased stepping, especially by left limbs. Cattle also reduced eating, grooming, and scratching during the heat load period. The lowered head, backward ear, vertical or raised tail, and increased respiration rate and panting persisted in cattle during the heat load period. Cattle on the cereal grain diet stood for longer and were more likely to hold their ears backward and tail vertical than those on the substituted diet. We conclude that these behaviours could be used to detect animals that are most affected and that changing from a cereal-based diet to a substituted diet containing a higher amount of fibre, such as lucerne hay, can reduce hyperthermic behavioural responses to a heat load.

Chlorine dioxide may be an alternative to acidification and chlorination for drinking water chemical disinfection in dairy beef bulls.

Alternative water disinfectants to chlorination need to be identified because its effectiveness is limited by water pH and potentially carcinogen by-products resulted from chlorination and organic compound reaction. The first study aimed to evaluate the effect of different drinking water chemical disinfection treatments on water quality, its potential hazard effects on animal health, water and feed consumption, and apparent total tract digestibility in dairy beef bulls fed high-concentrate diets. For 224 days, 24 Holstein bulls (176 ± 16.3 kg BW, and 149 ± 5.8 days of age) were individually assigned to one of four treatments with different drinking water chemical disinfectants: without disinfection (CTR); acidification and chlorination (ACCHL; 0.65 mL/L H3PO4 and 0.14 mL/L NaClO 15%); hydrogen peroxide (PER; 0.15 mL/L); and chlorine dioxide (DIO; 2.50 mL/L). Data were analysed with a mixed-effects model. Treatments affected the chemical characteristics of the water: in ACCHL, pH was 6.60 and free residual chlorine was 0.75 mg/L; in PER, H2O2 was 10.6 mg/L; and in DIO, ClO2 was 0.52 mg/L. Water physicochemical quality parameters in all treatments were below maximal thresholds established for safe water consumption by the Water Safety Royal Decree (RD 140/2003). In addition, the total coliform count of treated waters was reduced (P = 0.01) compared with CTR; moreover, ACCHL and DIO treatments were more effective in reducing total coliform count than PER. Dry matter intake tended (P = 0.07) to increase in DIO compared with CTR. Treatments did not affect blood parameters nor apparent total tract digestibility. The second study aimed to evaluate the potential benefit on animal performance of two drinking water disinfectants under commercial conditions in dairy beef crossbred Holstein bulls fed high-concentrate diets. Ninety-six animals (307 ± 4.4 kg BW, and 224 ± 1.8 days of age) were allocated to six pens for 140 days and assigned to one of two treatments: ACCHL, most common water disinfectant, and DIO. Data were analysed with a mixed-effects model. Water total coliform count and water consumption were similar between treatments. Concentrate intake was greater (P = 0.02) in ACCHL for the last 14 study days. Growth performance and carcass quality were similar between treatments. In summary, acidification and chlorination, H2O2, and ClO2 as drinking water disinfectants in dairy beef bulls had good disinfecting activity without detrimental effects on health and nutrient digestibility, and performance.

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle.

BACKGROUND: Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted - 0.23 kg/d gain), and OCM supplementation (+ OCM vs - OCM; n = 8/treatment; except n = 9 for RES-OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d - 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3-V4) sequencing. RESULTS: Overall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota. CONCLUSION: Restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota.

Metabolic profile of Charolais young bulls transported over long-distance.

Long-distance transport can cause stress to beef cattle impairing health and growth performances. This study aimed to deepen the knowledge of the effects of long-distance transport on young bulls' metabolic profile to identify reliable blood parameters for monitoring their health and welfare. Eighty Charolais young bulls, transported for 12 hours to the final fattening unit, were weighed and blood sampled at three time intervals: before leaving the commingling centre (day -1), upon arrival at the fattening unit (day 0), and 7 days post-arrival (day 7). These bulls were part of a larger study aimed at testing whether the animals have some benefit from the supplementation of live yeast and selenium through slow-release rumen boluses that were administered to half of them before departure from France ('Yeast' vs 'Control' group). The effect of the supplementation on the parameters considered in this study was included in the statistical analysis to account for the structure of the experimental design. Transport affected the initial body weight of the animals, which dropped on day 0 and it was not fully recovered on day 7. Most plasma traits of protein, energy, hepato-muscle, and mineral profiles were affected by transport. Cortisol was also assessed and peaked at day 0. The footprint of the long-distance transport on bulls' metabolic profile indicated a combination of stress, energy deficit, and muscle damage, with a certain degree of dehydration and liver impairment. Plasma traits measured on day -1 highlighted that stressful conditions and physiological responses of the bulls to recover homeostasis already started during the commingling phase before departure. No effect of supplementation was detected, except for higher selenium plasma level in Yeast bulls at day 7. Among blood parameters, non-esterified fatty acids, total protein, cortisol, glucose, and iron were those responsible for most of the variation in metabolic profile of bulls undergoing long journey. Therefore, these traits might be used as major biomarkers to assess stress in transported beef cattle, helping to identify critical situations for which proper mitigating actions should be taken. The outcomes of this study suggested that preventive measures against transport stress in beef cattle should start at the commingling of the animals in the collection centers, thus before departure.

Innovating Beef Cattle Veterinary Practices: Leveraging Genetic and Genomic Tools.

In the evolving landscape of beef cattle management, veterinarians are transitioning from their traditional role of treating diseases to becoming proactive advisors. This article explores how veterinarians with knowledge of genetic tools are poised to be vital in addressing the fundamental industry challenges. It highlights the role of genetic selection in reducing calving difficulties, emphasizing its benefits for animal health and welfare. The article also surveys the genomic technologies available and discusses the importance of integrating these insights with veterinary expertise to support informed decisions in selection, mating, and marketing strategies.

Theileria orientalis Ikeda infection does not negatively impact growth performance or breeding soundness exam results in young beef bulls at bull test stations.

Introduction: Theileria orientalis Ikeda genotype is an emerging cattle disease in the US. Since 2017, when T. orientalis Ikeda was discovered in beef cattle in two counties in Virginia, cattle infections have risen to include ~67% of Virginia counties and 14 states. Consistent with New Zealand studies, many infected herds in Virginia were >90% positive upon initial testing without overt evidence of infection. Central bull tests present a unique opportunity to study the effects of T. orientalis Ikeda infections, as bulls from multiple source herds are consolidated. The objective of this study was to determine if infection with T. orientalis Ikeda affected the average daily gain (ADG), adjusted yearling weight (AYW) and breeding soundness of bulls at two test stations in Virginia over a period of years. Materials and methods: The bulls were fed and housed similarly to compare their growth performance and breeding soundness. For T. orientalis Ikeda testing, DNA was extracted from whole blood for quantitative polymerase chain reaction. Results: The number of bulls infected with T. orientalis Ikeda at initial delivery to the stations increased significantly over the years studied. Multivariable linear regression models, using Angus bulls from Virginia test stations, indicated no significant effect on ADG or AYW in bulls that became test positive during the test or were positive for the duration, compared to Angus bulls that were negative for the duration. At LOC A, the odds of passing a breeding soundness exam (BSE) were not significantly different for bulls that turned positive during the test or were positive for the duration, compared to bulls that were negative for the duration of the test. At LOC B, bulls that became positive during the test were 2.4 times more likely (95% CI: 1.165-4.995, p = 0.016) to pass their BSE compared to bulls that remained negative throughout the test. Discussion: We do not suppose that an obscured infection of T. orientalis Ikeda is protective for bulls to pass a BSE. However, this study demonstrates an obscured infection of T. orientalis Ikeda does not negatively affect weight gain or achievement of a satisfactory BSE rating at the central bull test stations in Virginia.

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data.

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

Integrated Blood Transcriptome and Multi-Tissue Trace Mineral Analyses of Healthy Stocker Cattle Fed Complexed or Inorganic Trace Mineral Supplement.

Supplementing trace minerals is common in managing bovine respiratory disease (BRD) in post-weaned cattle; however, its influence on host immunity and metabolism in high-risk cattle remains unclear. We aimed to assess the impact of three supplementation programs on liver and serum trace element concentrations and blood gene expression. Fifty-six high-risk beef steers were randomly assigned to one of three groups over 60 days: (1) sulfate-sourced Cu, Co, Mn, and Zn (INR), (2) amino acid-complexed Cu, Mn, Co, and Zn (AAC), or (3) AAC plus trace mineral and vitamin drench (COMBO). Serum and liver biopsies for Cu, Co, Mn, and Zn at d0, d28, and d60 were analyzed from cattle free of BRD (n = 9 INR; n = 6 AAC; n = 10 COMBO). Differences and correlations of mineral concentrations were analyzed via generalized linear mixed models and Spearman's rank coefficients, respectively (p < 0.05). Whole blood RNA samples from healthy cattle (n = 4 INR; n = 4 AAC; n = 4 COMBO) at d0, d13, d28, d45, and d60 were sequenced and analyzed for differentially expressed genes (DEGs) via glmmSeq (FDR < 0.05), edgeR (FDR < 0.10), and Trendy (p < 0.10). Serum and liver Cu and Co concentrations increased over time in all groups, with higher liver Cu in COMBO (487.985 µg/g) versus AAC (392.043 µg/g) at d60 (p = 0.013). Serum and liver Cu concentrations (ρ = 0.579, p = 6.59 × 10-8) and serum and liver Co concentrations (ρ = 0.466, p = 2.80 × 10-5) were linearly correlated. Minimal gene expression differences were found between AAC versus COMBO (n = 2 DEGs) and INR versus COMBO (n = 0 DEGs) over time. AAC versus INR revealed 107 DEGs (d13-d60) with increased traits in AAC including metabolism of carbohydrates/fat-soluble vitamins, antigen presentation, ATPase activity, and B- and T-cell activation, while osteoclast differentiation and neutrophil degranulation decreased in AAC compared to INR. Our study identifies gene expression differences in high-risk cattle fed inorganic or amino acid-complexed mineral supplements, revealing adaptive immune and metabolic mechanisms that may be improved by organically sourced supplementation.

Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation.

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

One-carbon metabolite supplementation increases vitamin B12, folate, and methionine cycle metabolites in beef heifers and fetuses in an energy dependent manner at day 63 of gestation.

One-carbon metabolites (OCM) are metabolites and cofactors which include folate, vitamin B12, methionine, and choline that support methylation reactions. The objectives of this study were to investigate the effects of moderate changes in maternal body weight gain in combination with OCM supplementation during the first 63 d of gestation in beef cattle on (1) B12 and folate concentrations in maternal serum (2) folate cycle intermediates in maternal and fetal liver, allantoic fluid (ALF), and amniotic fluid (AMF) and (3) metabolites involved in one-carbon metabolism and related metabolic pathways in maternal and fetal liver. Heifers were either intake restricted (RES) and fed to lose 0.23 kg/d, or fed to gain 0.60 kg/d (CON). Supplemented (+ OCM) heifers were given B12 and folate injections weekly and fed rumen-protected methionine and choline daily, while non-supplemented (-OCM) heifers were given weekly saline injections. These two treatments were combined in a 2 × 2 factorial arrangement resulting in 4 treatments: CON-OCM, CON + OCM, RES-OCM, and RES + OCM. Samples of maternal serum, maternal and fetal liver, ALF, and AMF were collected at slaughter on day 63 of gestation. Restricted maternal nutrition most notably increased (./ ≤ 0.05) the concentration of vitamin B12 in maternal serum, 5,10-methylenetetrahydrofolate and 5,10-methenyltetrahydrofolate in maternal liver, and cystathionine in the fetal liver; conversely, maternal restriction decreased (P = 0.05) 5,10-methylenetetrahydrofolate concentration in fetal liver. Supplementing OCM increased (P ≤ 0.05) the concentrations of maternal serum B12, folate, and folate intermediates, ALF and AMF 5-methyltetrahydrofolate concentration, and altered (P ≤ 0.02) other maternal liver intermediates including S-adenosylmethionine, dimethylglycine, cystathionine Glutathione reduced, glutathione oxidized, taurine, serine, sarcosine, and pyridoxine. These data demonstrate that OCM supplementation was effective at increasing maternal OCM status. Furthermore, these data are similar to previously published literature where restricted maternal nutrition also affected maternal OCM status. Altering OCM status in both the dam and fetus could impact fetal developmental outcomes and production efficiencies. Lastly, these data demonstrate that fetal metabolite abundance is highly regulated, although the changes required to maintain homeostasis may program altered metabolism postnatally.

Maternal stresses that occur during pregnancy, such as restricted nutrition, can impact the developmental outcomes of the offspring in a process known as developmental programming. This programming can occur through epigenetics, which involves changes in fetal gene expression and can occur through the addition of methyl groups to DNA. These changes regulate gene transcription in the offspring and can alter offspring health, efficiency, and life-long outcomes. One-carbon metabolites (OCM), which are nutrients like the amino acid methionine and the vitamins B12, folate, and choline, act as intermediates or cofactors for the donation of methyl groups to DNA. This study investigated the effects of differing maternal rates of gain along with OCM supplementation during early gestation on OCM and related metabolite concentrations in the dam and fetus. We found that supplementing OCM to beef heifers increased maternal OCM and related metabolite concentrations and fetal fluid OCM concentrations. We also found that low maternal gain increased maternal serum and liver OCM concentrations. We can conclude from these findings that both maternal rate of gain and OCM supplementation can impact maternal OCM concentrations at day 63 of gestation and further research is needed to see if those maternal impacts will affect the developing fetus or calf later in its life.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Effects of supplementation of grazing Nellore cows with ß-carotene and vitamins A + D3 + E + biotin on follicle diameter, oestrus, establishment of pregnancy, and foetal morphometry.

The objectives of this experiment were to evaluate the effects of supplementation of Nellore (Bos indicus) cows with ß-carotene + vitamins A + D3 + E + biotin on body condition score (BCS), oestrus, pregnancy, and foetal morphometry. Lactating cows (n = 497) from two herds were balanced for BCS and calving period [early calving (EC); late calving (LC)] and were assigned randomly to: Control (n = 251)-supplementation with a mineral supplement; and SUP (n = 246)-supplementation with the mineral supplement fed to control + ß-carotene (150 mg/day) + vitamin A (40,000 IU/day) + vitamin D3 (5000 IU/day) + vitamin E (300 mg/day) + biotin (20 mg/day). Cows were supplemented from Days -30 to 30 (Day 0 = timed artificial insemination; TAI). Pregnancy was diagnosed 30 days after TAI and foetal crown-rump distance and thoracic diameter were measured at 30 and 77 days of gestation. Cows in the SUP treatment were more likely to have BCS ≥3.0 on Day 0 (63.0 ± 3.1 vs. 60.2 ± 3.1; p < .01) and were more likely to gain BCS from Days -30 to 30 (57.7 ± 3.3 vs. 44.1 ± 3.3%; p < .01). Fewer LC cows in the SUP treatment were detected in oestrus at the time of the first TAI (Control: LC: 75.4 ± 4.4 vs. SUP: LC: 64.0 ± 5.2 vs. Control: EC: 65.3 ± 4.0 vs. SUP: EC: 71.8 ± 3.7; p = .04). There was a tendency for the SUP treatment to increase pregnancy to the first TAI (64.2 ± 3.0 vs. 56.6 ± 3.1%; p = .08). A greater percentage of SUP cows was detected in oestrus at the time of the second TAI (70.1 ± 5.0 vs. 52.3 ± 4.8%; p = .01). The SUP treatment increased pregnancy to the second TAI among LC cows (SUP: LC: 75.9 ± 8.0% vs. Control: LC: 50.0 ± 8.3% vs. Control: EC: 52.0 ± 5.9% vs. SUP: EC: 41.4 ± 6.5%; p = .02). The SUP treatment increased foetal size (crown-rump; p = .04 and thoracic diameter; p < .01) at 30 days of gestation and, despite decreasing crow-rump length at 77 days after the first TAI among EC cows (p < .01), it increased the thoracic diameter at 77 days after the first TAI independent of calving season. Our results support that pregnancy establishment and foetal growth can be improved when grazing Nellore cows are supplemented with ß-carotene and vitamins A + D3 + E + biotin.