Feed Efficiency In Cattle Research Articles

Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes

We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = − 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.

An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle

BackgroundProvision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network.ResultsOf the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts.ConclusionsAlthough similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.

Feed efficiency of dairy cattle as genetic trait

This review article is devoted to the use of feed efficiency traits in dairy cattle breeding. An efficient cow is defined as the one that produces the same amount of milk and milk solids while consuming less feed and remaining healthy and fertile; thus, allowing to reduce costs without decrease in production. Improving feed efficiency is economically important due to the increasing price of fodder. Feed efficiency is a genetically complex trait that can be described as units of product output (e.g., milk yield) per unit of feed input. Nowadays genetic evaluation of dairy cattle for feed efficiency is routinely conducted in several countries, including Australia, USA, Canada, Netherlands, Denmark, Sweden, Finland, Norway and United Kingdom. Different countries use different measures of feed efficiency of dairy cows. The main feed efficiency traits are dry matter intake, gross feed efficiency, residual feed intake, energy balance and feed saved. Genome-wide association studies demonstrated that feed efficiency in polygenic trait. Nevertheless, several genes with large effects on feed efficiency were identified. Estimates of heritability of these traits vary from 0.07 to 0.49 and show the presence of considerable genetic variation of these traits and therefore, the possibility of their genetic improvement under the conditions of inclusion in breeding programs. Changes in diet and rumen microbiome substantially impact feed efficiency of dairy cows. Feed efficiency is related to methane emissions and excess nitrogen excretion. Genetic improvement of feed efficiency requires recording of individual data on feed intake in cows. Such data are limited. Two options exist to solve this problem: use of indirect predictors and genomic prediction. Accuracy of genomic prediction varies from 0.21 to 0.61 across countries. International cooperative pro­jects such as Efficient Dairy Genome Project in Canada were launched to establish large databases and to increase accuracy of feed efficiency traits genomic prediction. Future directions of research are the use of novel technologies: mid-infrared spectroscopy, artificial intelligence, holo-omics.

Predicting feed efficiency of Angus steers using the gastrointestinal microbiome

Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

BackgroundFeeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers’ profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.ResultsA total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.ConclusionsA total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Phenotypic relationships between meat quality parameters and residual feed intake in Japanese black Wagyu cattle.

Japanese black Wagyu cattle are renowned for producing some of the world's most highly valued and recognized beef with exceptional marbling. Therefore, the primary focus of genetic selection for Wagyu cattle has historically been on meat quality, particularly achieving high marbling levels. However, even when the price of the final product is high, production costs also remain high, especially considering that most of the feed has to be imported. The objective of this study was to evaluate phenotypic relationships between feed efficiency, specifically residual feed intake (RFI), as the most utilized efficiency index in cattle, and various meat quality parameters in Japanese black cattle in order to determine if a common phenotypic selection for these parameters could be feasible. For this, a total of 39 Wagyu cattle were evaluated for feed efficiency over their entire fattening period (900d), with a focus on RFI as a key indicator. Animals were fed high-starch diets with vitamin A deprivation to achieve the desired marbling. Results revealed positive correlations between feed efficiency and meat quality in Wagyu cattle. Specifically, animals with higher feed efficiency exhibited superior meat quality traits, including firmness, marbling, and overall meat rating. When comparing the 20 most extreme RFI individuals (10 most and 10 least efficient), we observed that efficient RFI animals showed increased marbling levels (+13.2%, P = 0.05) and ranking quality (+12%, P = 0.06) of the meat. In conclusion, this research contributes to understanding the interplay between feed efficiency and meat quality in Japanese black Wagyu cattle. Phenotypic correlations observed suggest the possibility of incorporating RFI criteria into genetic selection programs without compromising the prized meat quality traits of Wagyu beef.

- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality.

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

Energy efficiency, reproductive performance, and metabolic parameters of grazing Hereford heifers

Feed and energy efficiency have been topics of extensive research in recent years, with residual feed intake (RFI) being the preferred index to determine feed efficiency in beef cattle. Nevertheless, the biggest downside of RFI is that its measurement requires accurately determining individual feed intake, which leads to the need to carry out RFI trials in confinement conditions. In this context, residual heat production (RHP), defined as the difference between observed and predicted heat production, presents an alternative to determine efficiency in grazing conditions as it is independent of feed intake. This work aimed to evaluate the repeatability of RHP and study its relationship with metabolic, endocrine, and reproductive variables. Seventy-four Hereford heifers were used, and at the beginning of the experimental period, heifers were 18 ± 0.7-month-old and weighed on average 278 ± 26 kg. Heat production (HP) was determined at the beginning (March to May; fall) and at the end (September to November; spring) of the experiment using the heart rate-O2 pulse technique to classify heifers according with the residual heat production (RHP). Efficient heifers showed lower HP (P < 0.01), ME (P < 0.01), and DM intake (P < 0.01) without differences in retained energy (RE; only in spring). During fall, average daily gain (ADG) was not included in the estimated HP model; therefore, although, as in RFI, RHP should be independent of BW and ADG, a trend for greater ADG and RE was found for efficient when compared with inefficient heifers. Decreased maintenance requirements (NEm and MEm) as well as higher partial efficiency of use of consumed ME (k) were estimated for more efficient heifers (low RHP; HH), while efficient heifers showed an earlier luteal phase and a shorter service-conception interval and calved earlier in the season, probably associated to an earlier development of fat tissue. Excluding glucose, no major differences were found in the plasma metabolites between groups. However, high-efficiency animals showed positive correlations with cholesterol and negative ones with NEFA plasma concentrations during fall.

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. Here, we explore the epigenetic basis of FE to provide base knowledge for the development of genomic tools to improve FE in cattle. The methylation level of 37,554 CpG sites was quantified using a mammalian methylation array (HorvathMammalMethylChip40) for 48 Holstein cows with extreme residual feed intake (RFI). We identified 421 CpG sites related to 287 genes that were associated with RFI, several of which were previously associated with feeding or digestion issues. Activator of transcription and developmental regulation (AUTS2) is associated with digestive disorders in humans, while glycerol-3-phosphate dehydrogenase 2 (GPD2) encodes a protein on the inner mitochondrial membrane, which can regulate glucose utilization and fatty acid and triglyceride synthesis. The extensive expression and co-expression of these genes across diverse tissues indicate the complex regulation of FE in cattle. Our study provides insight into the epigenetic basis of RFI and gene targets to improve FE in dairy cattle.

PSXIV-10 Estimation of Genetic Parameters of Traits Associated with Water Efficiency, Feed Efficiency and Growth in Beef Cattle

Abstract Concerns about water availability, quality and accessibility have intensified. The livestock industry, particularly the beef sector, is under pressure to adopt more sustainable practices that optimize water usage while improving growth and feed efficiency. The objective of this study was to estimate the genetic parameters of traits associated with water efficiency, feed efficiency and growth in beef cattle. The data were collected from 916 seedstock bulls and heifers representing six breeds (Angus, Charolais, Hereford, Limousin, Simmental and Sim-Angus) in a facility equipped with Vytelle SENSE feed intake, water intake and in-pen body weight recording systems, located at the West Virginia University central testing facility in Wardensville, WV. The animals were part of six performance tests between November 2019 and September 2022, with an average age at the start of the test of 284 days, and an average test duration of 73 days. The rations were formulated to achieve 1.5 to 1.6 kg/d ADG (depending on the test) and had a high forage inclusion (&amp;gt;75% corn silage and &amp;gt;15% dry hay, as fed). The facility consists of 5 pens and animals were rotated every two weeks through the pens, so all animals are exposed to all pens. The phenotypes analyzed were average daily water intake (DWI), residual water intake (RWI), average daily dry matter intake (DMI), residual feed intake (RFI), and average daily gain (ADG). RWI and RFI were used to measure the water and feed efficiency of the animals. The genetic parameters were estimated with multi-trait animal models using Echidna mixed model software. In all models, breed, sex and the contemporary group (trial number and pen group) were included as fixed effects, the age at the start of the test was added as a covariate, and the animal was treated as a random effect. RWI and RFI were analyzed by adding ADG and metabolic mid-weight as additional covariates. The estimates of heritability for DWI, RWI, DMI, RFI and ADG were 0.49 (± 0.11), 0.40 (± 0.10), 0.35 (± 0.11), 0.16 (± 0.07) and 0.47 (± 0.11) respectively. Average daily water intake exhibited a positive genetic correlation with RWI (0.90), DMI (0.71), and ADG (0.76). On the other hand, the genetic correlation between RWI and RFI was not significantly different from zero, and genetic correlation between RWI and ADG was slightly positive. These results suggest that selecting for enhanced water efficiency in beef cattle can effectively decrease the daily water consumption without any adverse effect on feed efficiency, although it may have a small impact on growth. The complete genetic and phenotypic correlations are in Table 1. In conclusion, the traits associated with water intake and efficiency in beef cattle have a sizable genetic component and show potential for genetic improvement.

133 Genetic Parameter Estimation for Dry Matter Required in Angus Cattle

Abstract Dry matter intake (DMI) is critical to determine feed efficiency in cattle. However, this trait is expensive and difficult to measure on an individual basis. An alternative to overcome such limitations is to approximate DMI by using mathematical models to estimate the dry matter required (DMR) for animals originally fed in groups. High genetic correlations (e.g., rg&amp;gt;0.95) have been informed between DMI and DMR. Thus, DMR has been proposed as an indicator trait for DMI in genetic evaluations. Few reports exist about genetic parameters associated to DMR and, when available, estimates have been obtained with datasets of limited size (~1,500 animals with phenotypes). Additionally, previous reports have focused on older animals during the finishing phase, such that mathematical models employed to derive DMR have not explicitly accounted for the presence of weaner calves on the data. Therefore, the objective was to estimate genetic parameters for DMR using a moderately large dataset that included weaning and yearling Angus bulls. A total of 8,121 records of estimated DMR were available for analyses. From these records, 6,324 belonged to weaned males whose phenotype was obtained using an equation proposed by NRC to predict DMR for calves. The 1,797 remaining records pertained to yearling bulls for which a different NRC equation was employed. First, a single-trait animal model was implemented to estimate genetic parameters for DMR, with contemporary group (defined as year of test and pen within the testing facility), test length and age of the animal when entering to the test (linear covariate) being included as fixed effects, while animal was considered a random effect. Afterwards, a bivariate model that included weaning weight (WW) as a correlated trait was implemented. In this model, the same effects were included for DMR but for WW, fixed effects included sex, weaning contemporary group and age of dam (BIF classes), while direct genetic, maternal genetic, and maternal permanent environmental effects were considered as random. For both models, a reduced pedigree was used to estimate variance components by tracing back 5 generations from animals having phenotypes. A total of 12,212 and 56,023 animals were included in the univariate analysis and the bivariate analysis, respectively. Heritability (h2) estimates (± SE) for DMR were 0.43 (± 0.04) and 0.49 (± 0.03) under univariate and bivariate model, respectively. Genetic correlation between DMR and WW was 0.69 (± 0.03), with a h2 estimate of 0.29 (± 0.01) for WW. Heritability estimates for DMR obtained with both models resembled those of DMR reported in literature. Results suggested that substantial additive genetic variation exists for DMR and, consequently, indirect genetic progress for DMI can be attained if selecting for DMR. Further studies are required to validate DMR as an indicator trait for DMI in larger Angus populations.

325 Understanding Variation in Residual Feed Intake of Brahman Steers Fed Two Different Diets

Abstract Improving feed efficiency in cattle is a long-standing aim of the beef industry. However, discrepancies in the ranking of bulls based on the diets used and calculation methods employed for defining feed efficiency have been observed. Hence, the objective of this research was to assess the extent to which different factors influence feed efficiency in Brahman steers. Individual DMI and ADG were measured, and residual feed intake (RFI) calculated using linear regression of DMI on ADG and midtest metabolic body weight. Eight-nine steers were initially fed a low-protein diet (LP, 8.8% CP) for 70 days, followed by a high-protein (HP, 13.5% CP) diet for another 70 days. The genetic variation among steers and the proportion of Bos indicus genes were determined using the GGP Indicus 50K assay (Neogen Corporation, Ipswich, Australia). Rumen bacteriome variation was determined with 16S rRNA gene sequencing of rumen fluid collected before and after feeding. Daily diet refusals were visually scored for the proportion of pellets versus hay and expressed as a diet selection index (1 to 3). Organic matter digestibility (OMD) was determined using total feces collection in metabolism crates. Plasma urea nitrogen (PUN) was measured in blood samples collected at four time points. The diet-animal fractionation of nitrogen isotopes (Δ15Ntail hair) was quantified in tail hair using isotope-ratio mass spectroscopy to indicate differences in nitrogen metabolism. Finally, carcass characteristics were determined at slaughter. Including carcass fat depth improved (P = 0.01) DMI prediction (R2 increased from 78.4 to 80.4%) in the LP diet but had a smaller effect (P = 0.39) in the HP diet (R2 increased from 75.0 to 75.2%). In the LP diet, the variation in carcass fat-correct RFI (RFIc) could be explained by DMI (14.5% of the variation), rumen bacteriome (5.89%), diet selection index (3.08%), PUN (1.88%), genetic distance (0.76%) and OMD (0.50%), accounting for a total of 26.6% of the RFIc variation. In the HP diet, the regression model explained 35.3% of the RFIc variation, with DMI explaining 25.9%, diet selection index 7.19%, rumen bacteriome 1.02%, genetic distance 0.73% and Δ15Ntail hair 0.50%. In conclusion, this study highlights the importance of measuring diet selection to accurately determine RFI in cattle. The results also suggest that variations in the rumen bacteriome and nitrogen metabolism parameters play a role in individual variations of feed efficiency. However, most of the variation in feed efficiency remained unexplained.

89 Physiological Mechanisms Related to Feed Efficiency of Beef Cattle

Abstract Improving feed efficiency is essential for the sustainability of the US beef production system. However, achieving this goal is challenging due to various factors such as diet types, genetics, environments, and industry segmentation. To address these difficulties, it is critical to have a fundamental understanding of what contributes to efficient nutrient utilization and feed resources, which can guide future genetic selection and production practices. Despite recent progress, the regulation of feed intake in growing and finishing cattle remains incompletely understood, hindering advances in feed efficiency. Recent research has aimed to advance the hepatic oxidation theory to growing and finishing cattle fed high-concentrate diets and explored the control of appetite by gut peptide hormones. Other factors contributing to variation in feed efficiency include nutrient metabolism and hormonal control of metabolism. Previous research is limited by a lack of in-depth analysis of metabolism due to the inability to time sample collection relative to feed consumption and account for correlations among metabolites. The role of fat metabolism in the rumen has been associated with epithelial inflammation, while inflammation of the gut has been identified as a contributing factor to inefficiencies in nutrient utilization. However, there is still a need to further understand the role of fatty acid metabolism in the induction of inflammation. An issue that limits the further understanding of efficiency is that a wide variety of feedstuffs are utilized by the industry and small changes in the nutrient composition of a diet can have large impacts on efficiency. Therefore, it is important to consider the utilization efficiency of specific nutrients rather than general feed efficiency. Nitrogen utilization efficiency is becoming increasingly important due to the significant economic and environmental ramifications of inefficiencies in nitrogen utilization. There is growing evidence that precision feeding of protein to match requirements can reduce nitrogen excretion without compromising growth and efficiency. In conclusion, a better understanding of the underlying biology contributing to nutrient utilization is crucial for improving feed utilization efficiency in the US beef production system, which will enhance the sustainability of the US beef production system.

PSII-27 Inflammation- and Immunity-Associated Gene Expression in the Liver and Whole Blood of Crossbred Beef Cattle with Divergent Residual Feed Intake Phenotype

Abstract We investigated the inflammation- and immunity-associated gene expression in the liver and whole blood of crossbred beef cattle with divergent residual feed intake phenotype to identify relevant immune-related biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 8; RFI = - 1.93 kg/d) and high-RFI beef steers (n = 8; RFI = + 2.01kg/d) were selected from a group of 56 growing crossbred beef steers (average BW = 261 ± 18.5 kg) fed a high-forage total mixed ration after a 49-d performance testing period. At the end of the 49-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. The mRNA expression of 84 genes each related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. The mRNA expressions of genes with fold change ≥ (-) 2.0 and FDR ≤ 0.05 in the blood and liver were determined to be differentially expressed. Out of the 84 immune genes analyzed, the expression of 8 genes in the blood and 20 genes in the liver were upregulated in low-RFI, compared with high-RFI steers. Gene ontology analysis of all the differentially expressed genes in the blood and liver revealed that pathways related to pattern recognition receptor activity, detection of lipopolysaccharide, detection of external biotic stimulus, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were enriched (FDR &amp;lt; 0.05) in Low-RFI beef steers. These results suggest that low-RFI steers have a robust immune repertoire that is capable of prompt response to inflammatory stimuli. This prompt response to inflammation in the Low-RFI group may be characterized by greater protein turnover and increased epithelial cell differentiation, whereby an enhanced quantity of invariant natural killer T-cells and viability of natural killer cells could induce a quicker and more effective response to inflammatory stimuli and consequently contribute to more efficient partitioning of nutrients for growth in these animals.

302 Incremental Variables in Predicting Beef Cattle Dry Matter Intake

Abstract The great strain of increasing climate variability on animal agriculture necessitates improvement of current production processes, the development of methods to measure individual feed and water intakes, and the improvement of feed and water use efficiency in cattle. The use of machine learning (ML) approaches in predicting beef cattle dry matter intake (DMI) have provided groundwork for improvement of beef cattle production using big data and ML. However, despite wide variation between daily feed intakes, typical variables in animal intake-based ML approaches are not incremental, not allowing for daily prediction of intake. Our work introduces first-differenced intake, climate, and animal performance variables into a ML algorithm to predict beef cattle DMI and increase the immediacy of prediction applications. A total of 745 animals were evaluated in eight test groups from 11/25/2019 to 9/2/2021 in a dry lot equipped with In-Pen Weighing Positions and Feed and Water-Intake Nodes. Relationships among average daily gain (ADG), DMI, residual feed intake (RFI), water intake (WI), residual water intake (RWI), animal performance variables, and environmental variables at the individual animal level were investigated on a first test group of 125 Angus bulls and 53 crossbred steers. Out-Of-Bag root mean square error (OOB RMSE), an internal measure of Random Forest (RF) prediction accuracy, was used as a measure of error between model-predicted and observed DMI. Input variables were first-differenced by differencing a variable’s value between sequential test days for the entire test period. Two models were run using the RF package in R (ntree = 500, mtry = 11), with the first model (M1) using a standard test-train data split and the second model (M2) using all first-differenced and non-incremental observations to train the model. The model incorporating the test-train split performed marginally better than M2 (OOB RMSE = 1.39 and 1.44, respectively), indicating that first-differenced input variables can be used to predict daily individual DMI by within 1.39 kg by using M1. Using percent-increase in MSE (%IncMSE), first-differenced variables were found to be of less overall predictive value than non-incremental variables, with incremental daily gain and first-differenced water intake being ~55 and 45% less predictive than ADG and overall water intake in both M1 and M2. Though first-differenced variables were less predictive than non-incremental variables, inclusion of first-differenced variables allowed for prediction of individual DMI by within 1.39 kg. Our work demonstrates critical preliminary steps in the development of a deployable algorithm for the efficient prediction of DMI and the improvement of beef cattle intake efficiencies for the continued sustainability of animal agriculture.

220 Assessment of the Rumen Bacterial Community in Beef Cows Differing in Feed Efficiency Across Four Feeding and Grazing Scenarios

Abstract In Alberta Canada, the mature cow-herd consumes a variety of forage-based diets; whether that be grazing pastures in spring, summer, and into the fall and winter, or preserved forage during late winter and very early spring. Residual feed intake (RFI) is a measure of the feed efficiency of individual cattle and is typically measured in a feedlot setting. We sought to evaluate how rumen bacterial communities fluctuate when animals progressed through several forage and grazing scenarios throughout the year and whether cattle with different feed efficiency have varied shift patterns of rumen bacteria. Rumen fluid samples were collected from thirty-seven Kinsella composite hybrid beef cows at the end of different feeding or grazing regimes (March: silage fed in the feedlot, June: grazing on seeded pasture, August: grazing on native grassland, and November: grazing on stockpiled native grassland). RFI values of the beef cows were measured during the feedlot period and cows were divided into three groups: high-RFI (inefficient; RFI &amp;gt; 0.33), medium-RFI (0.33 &amp;gt; RFI &amp;gt; -0.33), and low-RFI (efficient; RFI &amp;lt; -0.33). Volatile fatty acid (VFA) profiles and total bacterial populations were analyzed using gas chromatography and qPCR with universal bacteria primers, respectively. Bacterial communities were assessed using 16S rRNA gene amplicon sequencing, and the data were analyzed using QIIME2 (version 2022.11) with the SILVA 138.1 database. Rumen samples collected in June (seeded pasture) had greater (P &amp;lt; 0.05) concentrations of total VFAs, acetate, propionate, butyrate, isobutyrate, valerate, and isovalerate, compared with those collected at later dates while grazing native grassland. Rumen samples collected in March (feedlot) and June (seeded pasture) had greater (P &amp;lt; 0.05) total bacterial populations compared with samples collected in August (native grassland) and November (stockpiled native grassland). Higher microbial species richness (P &amp;lt; 0.05) was observed for rumen samples collected in March (feedlot) than those under other feeding regimens. Beta-diversity analysis revealed the rumen bacterial community of cows during the feedlot period was clearly separated (P &amp;lt; 0.05) from those grazed on pasture. A total of 22 phyla and 279 genera were identified from the rumen bacteriome. The relative abundances of five genera: Anaerosporobacter, Oribacterium, Pirellula, Robinsoniella, and uncultured taxa in Absconditabacteriales_SR1 were significantly different (P &amp;lt; 0.05) in the rumen during the different feeding or grazing periods. There were no differences in the rumen bacterial diversity and composition between RFI groups. The findings imply that feeding a homogenous diet in seeded pasture may enhance rumen fermentation and bacterial proliferation, and different grazing regimens could affect rumen bacterial diversity and abundance. Further studies are needed to identify major factors that drive the changes between different feeding and grazing regimes and to find ecological indicators of the rumen bacterial community related to feed efficiency.

90 Leveraging the Potential of Molecular and Genetic Markers to Improve Feed Efficiency in Beef Cattle

Abstract Genetic and other molecular markers are powerful tools with the potential to improve livestock production traits, like feed efficiency. Feed efficiency is a complex biological trait mediated by many genes. Molecular based research, including transcriptome studies to evaluate gene expression profiles to determine the genes and pathways that contribute to feed efficiency in beef cattle have been widely performed over the last decade. Despite its widespread use, challenges remain in transcriptomic data analysis, in particular non-reproducibility of results between studies. These discrepancies exist for a number of reasons including small numbers of replicates, technical differences (e.g. sample preparation, sequencing platform), and biological differences (e.g., environmental, management, and genetic effects). Recent developments in technology and analytic tools provide an opportunity to integrate and synthesize the results of existing and future data. The potential to utilize these tools to have greater impact on feed efficiency will also be discussed. USDA is an equal opportunity provider and employer.

403 Awardee Talk: Characterization of Rumen Microbiome and Immune Genes Expression of Crossbred Beef Steers with Divergent Residual Feed Intake Phenotypes

Abstract We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake (RFI) phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were selected from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR &amp;lt; 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. Our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared with high-RFI steers.

PSXII-18 The Probiotic Containing Bacillus Licheniformis and Bacillus Subtilis Improves Feed Efficiency in Beef Cattle

Abstract The aim of this study was to investigate the effects of a probiotic containing B. licheniformis and B. subtilis on fecal characteristics, blood parameters, and performance in feedlot cattle. One hundred and forty-four single-sourced Angus x Nellore bulls (initial shrunk BW = 401 ± 45.5 kg) were randomly assigned to 1 of 2 treatments (4 bulls per pen; 18 pen replicates per treatment). Treatments consisted of a finishing diet containing no probiotic (CONTROL) or a diet with 2 g of probiotic/bull/d (PROB). The probiotic was composed of B. licheniformis CH200 and B. subtilis CH201 (3.2 x 109 CFU/g; BOVACILLUS). The diet was formulated using NASEM (2016) to provide an ADG of 1.9 kg/d (23% of corn silage, 65% of ground corn, 8% of soybean meal, 1% of urea, and 3% of mineral mix; DM basis). Bulls were adapted to the finishing diet over a 15-d period and fed for a total of 84 d. Fecal samples were collected on d 33 and 63. Blood samples were collected on the day of shipping to slaughter. Statistical analysis of experimental data was performed using the MIXED procedure of SAS 9.4. An α of 0.05 determined significance and an α of 0.06 to 0.10 was considered a tendency. No differences were obtained for initial BW, final BW, ADG, hot carcass, and dressing. Dry matter intake was reduced by 4% (P = 0.002) and G:F was increased by 6.3% (P = 0.036) in bulls consuming PROB diet. Regarding blood parameters, no differences were observed for glucose, haptoglobin, and LBP. There was a tendency of greater plasma urea (P = 0.09) in bulls consuming CONTROL diets. Fecal characteristics (DM, starch, N, pH, and scoring) were not different between treatments. Overall, dietary supplementation with B. licheniformis and B. subtilis improves feed efficiency in feedlot cattle.

Characterization of feed efficiency-related key signatures molecular in different cattle breeds.

Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.