Visceral organ weights, digestion and carcass characteristics of beef bulls differing in residual feed intake offered a high concentrate diet

Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle

BACKGROUND

Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage.

RESULTS

By analysing longitudinal body weights during the finishing period and genomic and metagenomic data from 359 beef cattle, our study demonstrates that the influence of the host genome on the functional rumen microbiome contributes to the temporal variation in average daily gain (ADG) in different months (ADG1, ADG2, ADG3, ADG4). Five hundred and thirty-three additive log-ratio transformed microbial genes (alr-MG) had non-zero genomic correlations (rg) with at least one ADG-trait (ranging from |0.21| to |0.42|). Only a few alr-MG correlated with more than one ADG-trait, which suggests that a differential host-microbiome determinism underlies ADG at different stages. These alr-MG were involved in ribosomal biosynthesis, energy processes, sulphur and aminoacid metabolism and transport, or lipopolysaccharide signalling, among others. We selected two alternative subsets of 32 alr-MG that had a non-uniform or a uniform rg sign with all the ADG-traits, regardless of the rg magnitude, and used them to develop a microbiome-driven breeding strategy based on alr-MG only, or combined with ADG-traits, which was aimed at shaping the rumen microbiome towards increased ADG at all finishing stages. Combining alr-MG information with ADG records increased prediction accuracy of genomic estimated breeding values (GEBV) by 11 to 22% relative to the direct breeding strategy (using ADG-traits only), whereas using microbiome information, only, achieved lower accuracies (from 7 to 41%). Predicted selection responses varied consistently with accuracies. Restricting alr-MG based on their rg sign (uniform subset) did not yield a gain in the predicted response compared to the non-uniform subset, which is explained by the absence of alr-MG showing non-zero rg at least with more than one of the ADG-traits.

CONCLUSIONS

Our work sheds light on the role of the microbial metabolism in the growth trajectory of beef cattle at the genomic level and provides insights into the potential benefits of using microbiome information in future genomic breeding programs to accurately estimate GEBV and increase ADG at each finishing stage in beef cattle.

Protein quality of a small mammal prey and its body organs for felids

This study evaluated the protein quality of small mammalian prey and its body organs by analyzing amino acid (AA) composition and digestibility of wild adult rats and their body organs (skin/fur, bone, muscle, intestine, liver, kidney, spleen, brain, heart, and lung) utilizing an in vitro digestion method. The average dry matter (DM) digestibility of whole rats was 89.9%. The digestibility of total AA (TAA), total indispensable AA (TIAA), and total dispensable AA (TDAA) in whole rats was 85.6, 87.0, and 87.6%, respectively. Differences in DM digestibility were observed among rat organs, ranging from 59.0% in bone to 99.8% in muscle (P < 0.001). Highly digestible organs generally exhibited AA digestibility exceeding 90%, except for cysteine (Cys) in the intestine and kidney (83.8% and 88.9%, respectively). The digestibility of AAs in skin/fur ranged from 19.7% for Cys to 81.0% for glycine (Gly). In bone, the digestibility spanned from 56.9% for Gly to 81.1% for tyrosine (Tyr). Additionally, examining the digestible indispensable AA score (DIAAS) gives us an idea of the protein quality of small mammalian prey and their body organs. Our results complement information on AA supply and digestion during prey ingestion by felids.

Relationship between residual feed intake and digestive traits of fattening bulls fed grass silage- or maize silage-based diets

Several studies tried to identify digestive determinants of individual variation in feed efficiency between fattening bulls, because of their importance for breeding and management strategies. Most studies focused on single traits or single diet. Little is known about diet-dependent differences in digestive determinants and on their relative importance in distinguishing divergent residual feed intake (RFI) bulls. This research aimed (i) to identify digestive traits that differed between bulls diverging in RFI and fed a maize silage- or a grass silage-based diets; (ii) to highlight the relationships between RFI and digestive traits, and (iii) to explore the hierarchy among digestive traits in discriminating RFI divergent bulls. After an initial RFI test of 84 days on 100 Charolais growing bulls fed two different diets based on grass silage (GS), or maize silage (MS), the 32 most RFI divergent bulls were selected (eight efficient RFI- and eight inefficient RFI+ bulls per diet) and measured thereafter for total tract apparent digestibility and transit rate, enteric gas emissions (CH4 and H2), rumen pH, and feeding behaviour. Rumen particle size and visceral organ and reticulo-omasal orifice (ROO) sizes and rumen and ileum histology were measured at slaughter on the 32 selected extreme RFI bulls. Irrespective of the diet, efficient bulls (RFI-) had lower rumen size, CH4 yield (g/kg DM intake; tendency), lower number of cells in the ileal crypts, tended to have longer time of rumen pH below 5.8 and lower proportion of small size particles in rumen content than non-efficient bulls (RFI+). A long-term test for feed efficiency (197 d on average) was performed on the whole experimental period until slaughter for the 100 animals. The long-term RFI value was negatively related to time spent in activity other than ingestion, rumination, and resting, and positively related (tendency) to the duration of ingestion events, to rumen and abomasum size, irrespective of the diet. Diet-dependent effects were noted: with GS, efficient (RFI-) bulls showed a slower transit rate, whereas with MS, efficient (RFI-) bulls tended to have shorter resting events and a smaller ROO than inefficient bulls (RFI+). The transit rate and the ROO size tended to be positively related, while total tract apparent digestibility of nitrogen was negatively related to long-term RFI value, but only in GS. Rumen size appeared as the most discriminating digestive variable between RFI divergent bulls, but this result should be validated on a larger number of animals and diets.

Effects of Alternative Cassava and Taro Feed on the Carcass and Meat Quality of Fattening Pigs Reared under Ecuadorian Backyard Systems

Ecuadorian small producers use crossbred animals with a low level of genetic improvement, which are fed with alternative feeds to decrease production costs. The objective of this study was to evaluate the effects of geographical location and three diets according to the amount of cassava and taro incorporated into the feed (T1 conventional feed; T2 and T3 with 32% and 42% of cassava and taro, respectively) in pigs reared under the backyard system. The results did not show many differences between the treatments for morphological traits; however, between geographical locations, significant differences were evidenced. The fat content from the first rib was higher in the T1 group. The intramuscular fat percentage was higher in the T1 group, contrary to the protein levels, which were higher in the T3 group in Esmeraldas and the T2 group in Ro Chico. In the gastrointestinal tract (GIT) and its attached organs, differences were found in the empty stomach weight, full and empty small intestine weight, liver weight, and total GIT weight, with the T2 and T3 groups having the largest and heaviest. Cassava and taro did not affect the morphometric behavior and quality of the carcass but increased the amount of protein in the meat and the weight of the GIT. Geographical location was also observed to have a significant effect.

Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake

Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is necessary for the accurate identification of feed efficient animals and will underpin accelerated genetic improvement of the trait. The aim of this study was to determine genes and biological processes contributing to RFI across varying breed type and dietary sources in skeletal muscle tissue. Residual feed intake was calculated in Charolais and Holstein-Friesian steers across multiple dietary phases (phase-1: high concentrate (growing-phase); phase-2: zero-grazed grass (growing-phase); phase-3: high concentrate (finishing-phase). Steers divergent for RFI within each breed and dietary phase were selected for muscle biopsy collection, and muscle samples subsequently subjected to RNAseq analysis. No gene was consistently differentially expressed across the breed and diet types examined. However, pathway analysis revealed commonality across breeds and diets for biological processes including fatty acid metabolism, immune function, energy production and muscle growth. Overall, the lack of commonality of individual genes towards variation in RFI both within the current study and compared to the published literature, suggests other genomic features warrant further evaluation in relation to RFI.

Effects of substituting noug seed cake with pigeon pea leaves or desmodium hay on performance of male dairy calves

This experiment was conducted to evaluate the effects of substituting 50% of noug seed cake (NSC) in a concentrate mixture with pigeon pea leaves (PPL) or desmodium hay (DH) on feed intake, digestibility, body weight gain, carcass composition, and meat quality of crossbred male dairy calves. Twenty-seven male dairy calves at 7-8 months of age with an average initial body weight of 150 ± 31 kg (mean ± SD) were assigned to 3 treatments in a randomized complete block design with 9 replications. Calves were blocked based on their initial body weight and assigned to the 3 treatments. All calves were fed native pasture hay ad libitum (at ⁓10% refusal) supplemented with a concentrate containing 24% NSC (treatment 1) or supplemented with a concentrate where 50% of NSC was replaced with PPL (treatment 2) or a concentrate where 50% of NSC was replaced with DH (treatment 3). Feed and nutrient intake, apparent nutrient digestibility, body weight gain, feed conversion ratio, carcass composition, and meat quality (except texture) were similar (P > 0.05) among treatments. Treatments 2 and 3 had more (P < 0.05) tender loin and rib meat than treatment 1. It can be concluded that 50% of NSC in the concentrate mixture can be replaced with either PPL or DH in growing male crossbred dairy calves to achieve similar growth performance and carcass characteristics. Since the substitution of 50% NSC either with PPL or DH resulted in similar outcomes in almost all responses measured, it is recommended to evaluate the complete substitution of NSC either with PPL or DH on the performance of calves.

Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups

The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.

Effect of weaning strategy and backgrounding management on growth performance, carcass characteristics, and mRNA expression in the longissimus muscle of beef steers

We evaluate the effect of the weaning strategy (WS; early, 130 ± 21 d vs. normal, 187 ± 20 d) and backgrounding management (BGM) on growth, carcass characteristics, and relative mRNA expression in the longissimus muscle (LM) of beef steers. One hundred and twenty Angus × SimAngus-crossbred steers (body weight (BW) = 130 ± 11.2 kg) were used in a randomized complete block design. Steers, blocked by age and BW, were randomly assigned to one treatment (2 × 2 factorial). Treatments consisted of early weaned (EW) or normal weaned (NW) steers subsequently backgrounded (BG) on either a forage-based (FB) or concentrates-based (CB) diet. The EW steers (d 0) were ad libitum-fed a grain-based diet for 49 d until nursing calves were NW. Steers were ad libitum-fed either a FB diet for 214 d or a CB diet for 95 d afterward. Steers were finished on a high-grain diet until harvested at an estimated constant 12th-rib fat thickness (1.5 cm). Expression of mRNA in the LM was measured over time. Data were analyzed using PROC MIXED in SAS. The EW steers were heavier (P ˂ 0.01) at the beginning of the backgrounding and finishing period. When the finishing phase began, steers FB were heavier (P ˂ 0.01) than CB steers. There was a tendency for a WS × BGM interaction (P = 0.08) for final BW, where NW-FB steers were heavier than the steers on the other three treatments, which do not differ between them. In the finishing phase, steers BG on a FB diet had greater dry matter intake and average daily gain, but lower gain-to-feed ratio (P ˂ 0.01). There was a WS × BGM interaction (P = 0.03) for days on feed (DOF) in the finishing diet, where backgrounding steers in a FB diet decreased DOF required to reach the harvesting target among EW steers, but not within NW steers. No interactions or treatment effects (P ≥ 0.17) were detected for marbling score (MS). For ZFP423, EW steers showed a greater mRNA expression on d 112 and a lower expression on d 255 than NW steers (P ˂ 0.01). In d 57, steers BG on a CB diet presented a greater delta-like homolog 1 mRNA expression than steers BG on a FB diet, whereas in d 255, this was inverted (P ˂ 0.01). For CCAAT/enhancer binding protein D (C/EBPD) mRNA expression, a tendency for a WS × BGM interaction was observed (P = 0.06), where a greater expression of C/EBPD was observed in steers BG on a FB diet among EW steers, but not within NW steers. In this study, early grain feeding followed by different BGM does not support MS improvements of beef carcasses.

The effect of feed efficiency classification on visceral organ mass in finishing steers

Individual feed intake of crossbred beef steers (one contemporary group/year, 2 yr) was recorded during finishing to investigate visceral organ mass in steers divergent for feed efficiency. Based on residual feed intake (RFI), the 20% most efficient (HE, n = 8/year) and 20% least efficient (LE; n = 8/year) steers with 12th rib fat ≥1.02 cm were slaughtered. High efficiency steers had less DM intake (P < 0.001), greater G:F (P < 0.001), and similar ADG and hot carcass weight (HCW). High efficiency steers tended to have less (P ≤ 0.10) small intestinal mass (actual and relative to BW and HCW) in year 1. In year 2, HE steers tended to have greater (P ≤ 0.10) large intestinal actual and relative masses. Low efficiency steers tended to have greater (P = 0.06) actual omasum mass and had greater (P ≤ 0.03) relative omasum masses compared with HE. Stomach complex, total gastrointestinal tract, liver, and kidney masses tended to be greater (P ≤ 0.10) relative to BW, and were greater (P ≤ 0.05) relative to HCW, in LE. Data suggest that visceral organ mass, especially of the gastrointestinal tract, plays a role in overall metabolic efficiency of finishing steers.

Association of Residual Feed Intake With Blood Metabolites and Reproduction in Holstein Cows

The objectives of this study were to evaluate the associations between residual dry matter (DM) intake or residual feed intake (RFI) from 1 to 15 weeks postpartum and concentrations of metabolites in plasma in early lactation and reproduction in Holstein cows. Data from 9 experiments, including 851 cows, were used. Intake of DM, milk yield, and body weight were evaluated daily, whereas milk composition and body condition were evaluated twice weekly for the first 105 days postpartum. Blood was sampled on the day of calving and again on days 7, 14, and 21 postpartum and analyzed for concentrations of non-esterified fatty acids (FA), β-hydroxybutyrate (BHB), and glucose. Reproduction was evaluated for the first 300 days postpartum. Residual DM intake was calculated as the observed minus the predicted intake, with intake predicted based on a model that accounted for major energy sinks. Cows were ranked and categorized into RFI quartiles, from the smallest (Q1) to the largest (Q4) RFI (−1.87, −0.46, 0.39, and 1.90 kg/day). Increasing efficiency (i.e., from Q4 to Q1) resulted in linear decreases in DM intake (Q1 to Q4; 18.9, 20.4, 21.3, and 22.7 kg/day), and median days open (132, 125, 135, and 147 d). Conversely, improving efficiency was associated with a linear increase in pregnancy per artificial insemination (AI, 31.4, 30.6, 31.2, and 24.5%) and quadratic increases in the 21-day cycle pregnancy rate (21.2, 21.1, 22.0, and 16.6%) and the proportion of pregnant cows (79.0, 80.7, 82.4, and 71.5%). The estimated net energy for lactation (NEL) content of diets increased linearly with improved RFI (1.88, 1.76, 1.71, and 1.58 Mcal/kg), resulting in no association between RFI and energy-corrected milk yield or body energy change. Nevertheless, increased feed efficiency was associated with a linear increase in concentrations of blood FA (0.68, 0.63, 0.60, and 0.59 mM), but a quadratic association with BHB (0.75, 0.64, 0.64, and 0.65 mM), with no association with glucose. Collectively, the most feed efficient cows ate 3.8 kg/day less DM, produced the same amount of energy-corrected milk, and had improved reproductive performance compared with the least efficient cows, thus suggesting that the underlying mechanisms responsible for improved feed efficiency might also be linked with improvements in reproduction.

Residual Feed Intake and Rumen Metabolism in Growing Pelibuey Sheep

This study was carried out to evaluate the residual feed intake (RFI), volatile fatty acid (VFA) production and enteric methane (CH4) from growing Pelibuey sheep. In this case, 12 non-castrated Pelibuey with an initial average live weight (LW) of 21.17 ± 3.87 kg and an age of 3 months, were housed in individual pens and fed a basal diet with 16% of crude protein and 11 MJ ME for 45 days. Dry matter intake (DMI) was measured and the daily weight gain (DWG) was calculated using a linear regression between the LW and experimental period. Mean metabolic live weight (LW0.75) was calculated. RFI was determined by linear regression with DWG and LW0.75 as independent variables. Lambs were classified as low, medium, and high RFI. Feed efficiency was determined as DWG/DMI. For determining rumen pH, ammonia nitrogen concentration NH3-N), and VFA, ruminal fluid was obtained using an esophageal probe on day 40. Feed intake of low RFI lambs was approximately 16% lower (p < 0.05) while growth rate was not significantly different. Their average energy loss, expressed as CH4 production per kilogram of metabolic weight, was 17% lower (p < 0.05).

Individual Feed Efficiency Monitoring of Charolaise Candidate Young Bulls in Relation to Feeding Behavior and Self-Performance Test Results

This study evaluated the effect of differences in residual feed intake (RFI) of Charolaise candidate young bulls on feeding behavior and self-performance test results. Bulls were classified into high and low RFI (H-RFI, L-RFI) groups. Bulls were fed in a HOKOFARM system to measure individual animal intake and behavior. L-RFI bulls had significantly lower feed intakes (p = 0.002) and higher gain to feed ratio (p = 0.001), lower intake per day/kg DM (dry matter) (p = 0.002) and lower intake g/body weight/day (p < 0.001). L-RFI animals had lower visits number per day (p = 0.02), but spent longer time per visit (p = 0.02), and tended to have higher intake g/visit (p = 0.06) on feeders. The correlation between RFI and DMI (dry matter intake)/bodyweight/day as well as intake per day/kg were large and positive. Back-loin length and rump length, and moreover muzzle width and frame, showed negative correlations with RFI value. However, bulls with better RFI values associated with lower legs score. Results reveal that RFI was shown beneficial correlations with economically relevant self-performance traits. Further investigations are needed to seek additional indicator traits that are predictive for RFI.

How Divergence for Feed Efficiency Traits Affects Body Measurements and Metabolites in Blood and Ruminal Parameters on Pre-Weaning Dairy Heifers

The objectives of this study were: (1) to evaluate feed efficiency indexes and their relationships with body measurements and blood and ruminal metabolites in the pre-weaning period; (2) to determine if such measurements can be used as feed-efficiency markers during the pre-weaning period. Holstein-Gyr heifer calves (n = 36), enrolled between 4 and 12 weeks of age, were classified into two residual feed intake (RFI) and residual body weight gain (RG) groups: high efficiency (HE; RFI, n = 10; and RG, n = 9), and low efficiency (LE; RFI, n = 10; and RG, n = 8). Calves were fed whole milk (6 L/day) and solid feed ad libitum. Body developments were measured weekly and feed intake (milk and solid feed) daily during the whole period. Blood samples were collected at 12 weeks of age and analyzed for glucose, insulin and β-hydroxybutyrate (BHB). Samples of ruminal content were collected on the same day and analyzed for pH, NH₃-N, and volatile fatty acids (VFA). Among the growth characteristics, only the initial hip width differed between the RFI groups, and withers height differed between the RG groups. Concentration of BHB was greater and glucose: insulin ratios tended to be greater in LE-RG animals. Butyric acid proportions were similar among RFI groups, but tended to be greater for HE-RG than for LE-RG. Overall, correlation coefficients between RFI or RG and blood, rumen, or morphometric markers were low. Thus, it is unlikely that measurements of metabolic indicators, per se, will be useful in the early identification of more efficient animals. Understanding the underlying physiological basis for improved feed efficiency in dairy heifers requires further investigation.

Plasma proteins δ15N vs plasma urea as candidate biomarkers of between-animal variations of feed efficiency in beef cattle: Phenotypic and genetic evaluation

Identifying animals that are superior in terms of feed efficiency may improve the profitability and sustainability of the beef cattle sector. However, measuring feed efficiency is costly and time-consuming. Biomarkers should thus be explored and validated to predict between-animal variation of feed efficiency for both genetic selection and precision feeding. In this work, we aimed to assess and validate two previously identified biomarkers of nitrogen (N) use efficiency in ruminants, plasma urea concentrations and the ¹⁵N natural abundance in plasma proteins (plasma δ¹⁵N), to predict the between-animal variation in feed efficiency when animals were fed two contrasted diets (high-starch vs high-fibre diets). We used an experimental network design with a total of 588 young bulls tested for feed efficiency through two different traits (feed conversion efficiency [FCE] and residual feed intake [RFI]) during at least 6 months in 12 cohorts (farm × period combination). Animals reared in the same cohort, receiving the same diet and housed in the same pen, were considered as a contemporary group (CG). To analyse between-animal variations and explore relationships between biomarkers and feed efficiency, two statistical approaches, based either on mixed-effect models or regressions from residuals, were conducted to remove the between-CG variability. Between-animal variation of plasma δ¹⁵N was significantly correlated with feed efficiency measured through the two criteria traits and regardless of the statistical approach. Conversely, plasma urea was not correlated to FCE and showed only a weak, although significant, correlation with RFI. The response of plasma δ¹⁵N to FCE variations was higher when animals were fed a high-starch compared to a high-fibre diet. In addition, we identified two dietary factors, the metabolisable protein to net energy ratio and the rumen protein balance that influenced the relation between plasma δ¹⁵N and FCE variations. Concerning the genetic evaluation, and despite the moderate heritability of the two biomarkers (0.28), the size of our experimental setup was insufficient to detect significant genetic correlations between feed efficiency and the biomarkers. However, we validated the potential of plasma δ¹⁵N to phenotypically discriminate two animals reared in identical conditions in terms of feed efficiency as long as they differ by at least 0.049 g/g for FCE and 1.67 kg/d for RFI. Altogether, the study showed phenotypic, but non-genetic, relationships between plasma proteins δ¹⁵N and feed efficiency that varied according to the efficiency index and the diet utilised.

Relationships among feed efficiency traits across production segments and production cycles in cattle

Understanding the relationships between feed efficiency traits measured in different stages of production is necessary to improve feed efficiency across the beef value chain. The objective of this study was to evaluate relationships among feed efficiency traits measured as growing heifers and breeding females and in their progeny in three full production cycles, and relationships of dam residual feed intake (RFI) with lifetime and lifecycle cow efficiency traits. Data were collected on 160 mixed-breed heifers from 240 d of age to weaning of their third progeny, and postweaning performance of progeny until harvest in experiments initiated in 1953, 1954, 1959, 1964, 1969, and 1974. Individual feed offered was recorded daily, and feed refusals measured every 28 d. Milk yield was measured at 14-d intervals throughout lactation by machine or hand milking. Females and progeny were weighed at 28-d intervals and progeny were harvested at a constant endpoint of live grade or age depending upon the experiment. Feed efficiency traits of RFI and residual BW gain (RG) were computed as the residual from linear regression for developing heifers, dams (RFI and residual energy-corrected milk [RECM]), and postweaning progeny. Feed:gain ratio (FCR) was computed for developing heifers and postweaning progeny, and feed:milk energy ratio (FME) was computed for dams. Various measures of cow efficiency were calculated on either a life cycle or lifetime basis using ratios of progeny and dam weight outputs to progeny and dam feed inputs. Pearson correlations were computed among traits adjusted for a random year-breed-diet group effect. Heifer RFI (0.74) and RG (-0.32) were correlated (P ≤ 0.05) with dam RFI in parity 1 only, but were not correlated (P > 0.05) with dam RECM in any parity. Heifer RFI was correlated (P ≤ 0.05) with progeny RFI (0.17) in parity 3 only. Heifer FCR was not correlated with dam FME or progeny FCR in any parity. Dam RFI was weakly correlated (r = 0.25 to 0.36; P ≤ 0.05) among parities, whereas dam FME and RECM were strongly correlated (r = 0.49 to 0.72; P ≤ 0.05) among parities. Dam RFI in parity 1 and 2 was weakly correlated (r = -0.20 to -0.33; P ≤ 0.05) with cow efficiency ratios that included dam weight as an output, whereas dam RFI in parity 3 was not correlated with any cow efficiency ratio. In conclusion, feed efficiency traits were poorly correlated across production segments, but moderately repeatable across production cycles.

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake

The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.

Grazing behavior and production for lactating cows differing in residual feed intake while grazing spring and summer rangeland

The objectives were to determine if previously classified, efficient (LRFI, low-residual-feed intake, n = 12 × 2 yr) vs. inefficient (HRFI, high-residual-feed intake, n = 12 × 2 yr) lactating 2-yr-old Hereford × Angus cows differed in grazing behavior, body weight (BW), body condition score (BCS), and calf weaning weight while grazing rugged rangeland pastures. Cows were fitted with grazing halters containing both an accelerometer and a global positioning system (GPS) data logger during June 14 to July 4, 2016, August 2 to 25, 2016, May 23 to June 12, 2017, and August 5 to 28, 2017. GPS data were recorded at 7-min intervals in 2016 and 4-min intervals in 2017 and accelerometer data recorded at 25 times/s. Grazing time (GT), resting, walking, bite rate (BR), daily travel distance (DTD), elevation, and slope were analyzed with a mixed model that included fixed effects of RFI group, day, and RFI group × day and cow within treatment as the random effect. Cow BW, BCS, and calf weaning weight were analyzed by analysis of variance with treatment as the main effect. There were no differences (P > 0.10) due to RFI detected for BW, BCS, or calf weaning weights. During periods of mild heat load (MHL), HRFI cows spent more (P < 0.05) time resting during the day at lower elevations (P < 0.05) than LRFI cows. During a 6-d period in spring with only 2 h MHL, HRFI cows grazed 1.7 h/d longer than LRFI cows (P < 0.05); commencing grazing earlier in the morning and extending the grazing bout later. During the summer with > MHL, LRFI cows grazed more than HRFI cows 18% of the time (P < 0.10). The HRFI cows had greater GT than LRFI cows only 3% of the time (P < 0.10) during summer. There was no difference (P > 0.10) in BR between HRFI and LRFI cattle. The DTD tended (P < 0.10) to be greater for LRFI cattle during summer 2017. Over all sample periods, HRFI had greater walking than LRFI 15% of the time and LRFI exceeded HRFI cattle for walking 3% of the time (P < 0.10). The greater walking for HRFI was assumed to be associated with more search grazing. Metabolic heat load on hot summer days for HRFI cattle is presumed to have contributed to differences observed in grazing behavior. These results suggest that lactating cows with low-RFI phenotypes appear to be better adapted to grazing rugged rangelands in late summer during periods of MHL.

Feeding behavior, water intake, and energy and protein requirements of young Nellore bulls with different residual feed intakes

This study aimed to determine feeding behavior, water intake (WI), and energy requirements of high- and low-residual feed intake (RFI) Nellore bulls. Data were collected from 42 weaned Nellore bulls (initial body weight [BW] 260 ± 8.1 kg; age 7 ± 1.0 mo) housed in a feedlot in group pens that contained electronic feeders, waterers, and a scale connected to the waterers. The individual dry matter intake (DMI), WI, and BW were recorded daily. The indexes of average daily gain (ADG), feed efficiency (gain to feed ratio), and RFI were calculated based on the data collected. The number of feeder and waterer visits and the time spent feeding or drinking water per animal per day were recorded as feeding behavior measures. Energy requirements for maintenance and gain were calculated according to the BR-CORTE system. Low-RFI bulls had lower DMI (P < 0.01) than high-RFI bulls, and no differences (P > 0.05) were observed between the two groups regarding WI, performance, and feeding behavior measurements. The net energy requirements for maintenance, metabolizable energy for maintenance, and efficiency of metabolizable energy utilization were 63.4, 98.6 kcal/metabolic empty body weight (EBW)0.75 daily, and 64.3%, respectively, for low-RFI bulls, and 78.1, 123.9 kcal/EBW0.75 daily, and 63.0%, respectively, for high-RFI bulls. The equations obtained for net energy for gain (NEg) were: NEg (Mcal/EBW0.75) daily = 0.0528 × EBW0.75 × EBG0.5459 for low-RFI and 0.054 × EBW0.75 × EBG0.8618 for high-RFI bulls, where EBG is the empty body gain. We did not observe any difference (P > 0.05) regarding the composition of gain in terms of protein or fat deposition between the two groups. Both groups also presented similar (P > 0.05) carcass and non-carcass traits. Therefore, our study shows that low-RFI Nellore bulls eat less, grow at a similar rate, and have lower maintenance energy requirements than high-RFI bulls. We also suggest that the lower feed intake did not compromise the carcass traits of more efficient animals, which would reduce production costs and increase the competitiveness of the Brazilian beef sector on the world market.

Association between residual feed intake, digestion, ingestive behavior, enteric methane emission and nitrogen metabolism in Nellore beef cattle

This study aimed to evaluate nutrient intake and digestibility, enteric methane emission and nitrogen utilization efficiency in Nellore cattle ranked by residual feed intake (RFI). Twenty-four Nellore bulls at 466 ± 24 days of age and with 352 ± 14.6 kg of body weight, classified as low and high RFI, were evaluated. Animals were kept in individual pens for three periods of 28 days and variables were measured. Data were analyzed as repeated measures over time, considering as fixed effects RFI class, period and RFI class x period interaction, and linear (co)variate of age. No significant differences in dry matter or nutrient intake were detected between RFI classes, but total digestible nutrients intake tended to be lower in low RFI animals, and apparent nutrient digestibility was higher in high RFI animals. Partial efficiency of growth tended to be lower in high RFI animals. RFI class did not interfere with enteric methane production or microbial protein synthesis, but fecal nitrogen output was higher in low RFI animals. The greater efficiency of low RFI animals is consequence of lower maintenance requirements, since energy from higher nutrients digestibility in high RFI animals was spent on metabolic processes other than body tissue deposition.

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed

The relationship between rumen microbiota and host feed efficiency phenotype, for genetically divergent beef cattle breeds is unclear. This is further exacerbated when different growth stages, chemically diverse diets and production systems are considered. Residual feed intake (RFI), a measure of feed efficiency, was calculated for individually fed Charolais (CH) and Holstein-Friesian (HF) steers during each of four 70-day (excluding adaptation) successive dietary phases: namely, high-concentrate, grass silage, fresh zero-grazed grass and high-concentrate again. Rumen fluid from the ten highest- (HRFI) and ten lowest-ranking (LRFI) animals for RFI, within breed, during each dietary phase was collected using a trans-oesophageal sampler and subjected to 16S rRNA amplicon sequencing and metabolic profiling. The datasets were analysed to identify microbial and rumen fermentation markers associated with RFI status. Age, dietary phase and breed were included in the statistical model. Within breed, for each dietary phase, mid-test metabolic weight and average daily gain did not differ (P > 0.05) between HRFI and LRFI steers; however, for the initial high-concentrate, grass silage, fresh grass herbage and final high-concentrate dietary phases, HRFI HF steers consumed 19, 23, 18 and 27% more (P < 0.001) than their LRFI counterparts. Corresponding percentages for CH HRFI compared to CH LRFI steers were 18, 23, 13 and 22%. Ten OTUs were associated with RFI (q < 0.05) independent of the other factors investigated. Of these Methanomassiliicoccaceae, Mogibacteriaceae and the genus p-75-a5 of Erysipelotrichaceae and were negatively associated (q < 0.05) with RFI. The results gave evidence that microbial species could potentially be an indicator of RFI in ruminants rather than broader microbiome metrics; however, further research is required to elucidate this association.

Temperament and performance of Nellore bulls classified for residual feed intake in a feedlot system

This study aimed to evaluate the performance in feedlot and temperament of Nellore bulls classified by residual feed intake. The residual feed intake was calculated as the difference between the observed and predicted dry matter intake. Bulls classified as low residual feed intake had lower dry matter intake (kg day-1) and dry matter intake (g kg-1 d-1) of body weight, and were more efficient in feed conversion ratio than those classified as medium and high. The average daily gain didn't differ among residual feed intake classes and was 1.69 kg day-1, 1.82 kg day-1 and 1.71 kg day-1 for bulls classified as low, medium, or high, respectively. The residual feed intake was positively associated with dry matter intake, feed conversion ratio and subcutaneous fat thickness. The subcutaneous fat thickness was lower in bulls classified as low residual feed intake than in those with medium and high. No differences were observed in flight speed and reactivity score among residual feed intake classes. Overall, we concluded that bulls classified as low residual feed intake consumed less dry matter than high, with no differences in average daily gain, temperamentand had better feed efficiency, albeit their subcutaneous fat thickness was lower.

Physiological parameter values for physiologically based pharmacokinetic models in food-producing animals. Part I: Cattle and swine

Physiologically based pharmacokinetic (PBPK) models for chemicals in food animals are a useful tool in estimating chemical tissue residues and withdrawal intervals. Physiological parameters such as organ weights and blood flows are an important component of a PBPK model. The objective of this study was to compile PBPK‐related physiological parameter data in food animals, including cattle and swine. Comprehensive literature searches were performed in PubMed, Google Scholar, ScienceDirect, and ProQuest. Relevant literature was reviewed and tables of relevant parameters such as relative organ weights (% of body weight) and relative blood flows (% of cardiac output) were compiled for different production classes of cattle and swine. The mean and standard deviation of each parameter were calculated to characterize their variability and uncertainty and to allow investigators to conduct population PBPK analysis via Monte Carlo simulations. Regression equations using weight or age were created for parameters having sufficient data. These compiled data provide a comprehensive physiological parameter database for developing PBPK models of chemicals in cattle and swine to support animal‐derived food safety assessment. This work also provides a basis to compile data in other food animal species, including goats, sheep, chickens, and turkeys.

Mitochondrial abundance and function in skeletal muscle and liver from Simmental beef cattle divergent for residual feed intake

Cellular mitochondrial function has been suggested to contribute to variation in feed efficiency (FE) among animals. The objective of this study was to determine mitochondrial abundance and activities of various mitochondrial respiratory chain complexes (complex I (CI) to complex IV (CIV)) in liver and muscle tissue from beef cattle phenotypically divergent for residual feed intake (RFI), a measure of FE. Individual DM intake (DMI) and growth were measured in purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial mean BW (SD) of 372 kg (39.6) and 387 kg (50.6), respectively. All animals were offered concentrates ad libitum and 3 kg of grass silage daily, and feed intake was recorded for 70 days. Residuals of the regression of DMI on average daily gain (ADG), mid-test BW0.75 and backfat (BF), using all animals, were used to compute individual RFI coefficients. Animals were ranked within sex, by RFI into high (inefficient; top third of the population), medium (middle third of population) and low (efficient; bottom third of the population) terciles. Statistical analysis was carried out using the MIXED procedure of SAS v 9.3. Overall mean ADG (SD) and daily DMI (SD) for heifers were 1.2 (0.4) and 9.1 (0.5) kg, respectively, and for bulls were 1.8 (0.3) and 9.5 (1.02) kg, respectively. Heifers and bulls ranked as high RFI consumed 10% and 15% more (P < 0.05), respectively, than their low RFI counterparts. There was no effect of RFI on mitochondrial abundance in either liver or muscle (P > 0.05). An RFI × sex interaction was apparent for CI activity in muscle. High RFI animals had an increased activity (P < 0.05) of CIV in liver tissue compared to their low RFI counterparts; however, the relevance of that observation is not clear. Our data provide no clear evidence that cellular mitochondrial function within either skeletal muscle or hepatic tissue has an appreciable contributory role to overall variation in FE among beef cattle.

Assessment of the direct economic losses associated with hydatid disease (Echinococcus granulosus sensu stricto) in beef cattle slaughtered at an Australian abattoir

Bovine hydatid disease, characterised by fluid-filled hydatid cysts, is regularly found in the offal of beef cattle at slaughter. Organs found to be infected at slaughter are removed to preclude them from entering the human food chain. The organs are either downgraded to pet food or condemned. Previous studies have focussed on total economic losses, but have not calculated the cost of disease per animal, which would be useful information for producers when determining how best to manage hydatid disease. This study estimated the direct losses associated with hydatid disease in beef cattle slaughtered at an Australian beef abattoir both at the population (all cattle slaughtered) and individual animal level. Data on annual prevalence of hydatid disease in beef cattle were obtained from an Australian abattoir for the years 2011-2017. The direct losses resulting from the condemnation and downgrading of offal infected with hydatid cysts at the abattoir were estimated using data stratified by age, sex and feed-type. Official and literature-based sources of organ weight and price were used to estimate direct losses associated with hydatid disease in beef cattle slaughtered at the abattoir. Uncertainty and variability in input parameters were represented using uniform distributions and Monte Carlo sampling was used to model output parameter uncertainty. Out of 1,097,958 beef cattle slaughtered between January 2011 and December 2017, 97,832 (8.9%) were reported infected with hydatid disease. The median estimated direct loss to the abattoir for the duration of the study period was AU$655,560 (95% confidence interval [CI] AU$544,366-787,235). This equated to approximately AU$6.70 (95% CI AU$5.56-8.05) lost per infected animal. The annual median estimated direct losses due to hydatid disease at the abattoir were AU$93,651 (95% CI AU$77,767-112,462). Direct losses varied each year of the study and ranged from AU$38,683 in 2016 to AU$163,006 in 2014. This estimate of the direct losses associated with bovine hydatid disease most likely underestimates the true extent of the overall losses because indirect losses such as reduced carcass weights were not estimated in this study. Nevertheless, these estimates illustrate the negative economic impact of bovine hydatid disease and demonstrate that improved surveillance to enable control of hydatid disease should be considered both in Australia and globally. It would be worthwhile to estimate the losses in other beef abattoirs for the same time period to compare results, and to investigate the cost-benefit of control programs for bovine hydatid disease.

Methane and Carbon Dioxide Emission of Beef Heifers in Relation with Growth and Feed Efficiency

Simple Summary

For sustainable meat production, beef farmers must make the best use of grass and roughage while limiting the carbon footprint of their herds. The genetic improvement in feed efficiency and enteric methane production of replacement heifers is possible if the recorded phenotypes are available. Intuitively, the relationship between the two traits should be negative, i.e., favorable, since the energy lost with the methane is not available for heifer metabolism. The measurement of feed efficiency requires several weeks of feed intake recording. The enteric methane emission rate can also be recorded over several weeks. The two traits of 326 beef heifers from two experimental farms were measured simultaneously for 8 to 12 weeks. The correlations between roughage intake, daily gain, and methane were all positive. The enteric methane emission rate was positively related to body weight, daily gain, and dry matter intake. The relationship with feed efficiency was slightly positive, i.e., unfavorable. Therefore, the two traits should be recorded simultaneously to evidence low-emitting and efficient heifers. This study also showed that replacing the feed intake recording with the carbon dioxide emission rate appeared potentially beneficial for selecting these low-emitting and efficient heifers.

Abstract

Reducing enteric methane production and improving the feed efficiency of heifers on roughage diets are important selection objectives for sustainable beef production. The objective of the current study was to assess the relationship between different methane production and feed efficiency criteria of beef heifers fed ad libitum roughage diets. A total of 326 Charolais heifers aged 22 months were controlled in two farms and fed either a grass silage (n = 252) or a natural meadow hay (n = 74) diet. Methane (CH₄) and carbon dioxide (CO₂) emission rates (g/day) were measured with GreenFeed systems. The dry matter intake (DMI), average daily gain (ADG), CH₄ and CO₂ were measured over 8 to 12 weeks. Positive correlations were observed among body weight, DMI, ADG, CH₄ and CO₂. The residual feed intake (r_wgDMI) was not related to CH₄ or residual methane (r_wiCH₄). It was negatively correlated with methane yield (CH₄/DMI): R_p = −0.87 and −0.83. Residual gain (r_wiADG) and ADG/DMI were weakly and positively related to residual methane (r_wiCH₄): R_p = 0.21 on average. The ratio ADG/CO₂ appeared to be a useful proxy of ADG/DMI (R_p = 0.64 and 0.97) and CH₄/CO₂ a proxy of methane yield (R_p = 0.24 and 0.33) for selecting low-emitting and efficient heifers.

Genetic parameters and genome-wide association study regarding feed efficiency and slaughter traits in Charolais cows

Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h2 = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.

Relationship between feed efficiency and slaughter traits of French Charolais bulls

Improving feed efficiency is of interest to French beef producers so as to increase their profitability. To enable this improvement through selection, genetic correlations with production traits need to be quantified. The objective of this study was to estimate the genetic parameters for growth, feed efficiency (FE), and slaughter performance of young beef bulls of the French Charolais breed. Three feed efficiency criteria were calculated: residual feed intake (RFI), residual gain (RG), and ratio of FE. Data on feed intake, growth, and FE were available for 4,675 Charolais bulls tested in performance test stations and fed with pelleted diet. Between 1985 and 1989, 60 among 510 of these bulls were selected to procreate one generation of 1,477 progeny bulls which received the same pelleted diet at the experimental farm in Bourges. In addition to feed intake, growth, and FE traits, these terminal bulls also had slaughter traits of carcass yield, carcass composition, and weight of visceral organs collected. Genetic parameters were estimated using linear mixed animal models. Between performance test bulls and terminal bulls, the genetic correlation of RFI was 0.80 ± 0.18; it was 0.70 ± 0.21 for RG and 0.46 ± 0.20 for FE. For carcass traits, RFI was negatively correlated with carcass yield (-0.18 ± 0.14) and muscle content (-0.47 ± 0.14) and positively with fat content (0.48 ± 0.13). Conversely, RG and FE were positively correlated with carcass yield and muscle content and negatively with fat content. For the three FE criteria, efficient animals had leaner carcass. For visceral organs (as a proportion of empty body weight), RFI was genetically correlated with the proportions of the 5th quarter (0.51 ± 0.17), internal fat (0.36 ± 0.14), abomasum (0.46 ± 0.20), intestines (0.38 ± 0.17), liver (0.36 ± 0.16), and kidneys (0.73 ± 0.11). Conversely, RG and FE were negatively associated with these traits. The high-energy expenditure associated with the high-protein turnover in visceral organs may explain this opposite relationship between FE and the proportion of visceral organs. Selection for final weight and RFI increased growth and FE in progeny, and also improved carcass yield and muscle content in the carcass. To conclude, determinations of growth and feed intake in performance test stations are effective to select bulls to improve their growth, FE, and muscle content in carcass.

Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle

Background

Feed accounts for up to 75% of costs in beef production systems, thus any improvement in feed efficiency (FE) will benefit the profitability of this enterprise. Residual feed intake (RFI) is a measure of FE that is independent of level of production. Adipose tissue (AT) is a major endocrine organ and the primary metabolic energy reservoir. It modulates a variety of processes related to FE such as lipid metabolism and glucose homeostasis and thus measures of inter-animal variation in adiposity are frequently included in the calculation of the RFI index. The aim of this study was to determine the effect of phenotypic RFI status and gender on the expression of key candidate genes related to processes involved in energy metabolism within AT. Dry matter intake (DMI) and average daily gain (ADG) were measured over a period of 70 d for 52 purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial BW±SD of 372±39.6 kg and 387±50.6 kg, respectively. Residual feed intake was calculated and animals were ranked within gender by RFI into high (inefficient; n = 9 heifers and n = 8 bulls) and low (efficient; n = 9 heifers and n = 8 bulls) groups.

Results

Average daily gain ±SD and daily DMI ±SD for heifers and bulls were 1.2±0.4 kg and 9.1±0.5 kg, and 1.8±0.3 kg and 9.5±1 kg respectively. High RFI heifers and bulls consumed 10% and 15% more (P < 0.05) than their low RFI counterparts, respectively. Heifers had a higher expression of all genes measured than bulls (P < 0.05). A gender × RFI interaction was detected for HMGCS2(P < 0.05) in which high RFI bulls tended to have lower expression of HMGCS2 than low RFI bulls (P < 0.1), whereas high RFI heifers had higher expression than low RFI heifers (P < 0.05) and high RFI bulls (P < 0.05). SLC2A4 expression was consistently higher in subcutaneous AT of low RFI animals across gender.

Conclusion

The findings of this study indicate that low RFI cattle exhibit upregulation of the molecular mechanisms governing glucose metabolism in adipose tissue, in particular, glucose clearance. The decreased expression of SLC2A4 in the inefficient cattle may result in less efficient glucose metabolism in these animals. We conclude that SLC2A4 may be a potential biomarker for RFI in cattle.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0282-9) contains supplementary material, which is available to authorized users.

Review: Biological determinants of between-animal variation in feed efficiency of growing beef cattle

Animal's feed efficiency in growing cattle (i.e. the animal ability to reach a market or adult BW with the least amount of feed intake), is a key factor in the beef cattle industry. Feeding systems have made huge progress to understand dietary factors influencing the average animal feed efficiency. However, there exists a considerable amount of animal-to-animal variation around the average feed efficiency observed in beef cattle reared in similar conditions, which is still far from being understood. This review aims to identify biological determinants and molecular pathways involved in the between-animal variation in feed efficiency with particular reference to growing beef cattle phenotyped for residual feed intake (RFI). Moreover, the review attempts to distinguish true potential determinants from those revealed through simple associations or indirectly linked to RFI through their association with feed intake. Most representative and studied biological processes which seem to be connected to feed efficiency were reviewed, such as feeding behaviour, digestion and methane production, rumen microbiome structure and functioning, energy metabolism at the whole body and cellular levels, protein turnover, hormone regulation and body composition. In addition, an overall molecular network analysis was conducted for unravelling networks and their linked functions involved in between-animal variation in feed efficiency. The results from this review suggest that feeding and digestive-related mechanisms could be associated with RFI mainly because they co-vary with feed intake. Although much more research is warranted, especially with high-forage diets, the role of feeding and digestive related mechanisms as true determinants of animal variability in feed efficiency could be minor. Concerning the metabolic-related mechanisms, despite the scarcity of studies using reference methods it seems that feed efficient animals have a significantly lower energy metabolic rate independent of the associated intake reduction. This lower heat production in feed efficient animals may result from a decreased protein turnover and a higher efficiency of ATP production in mitochondria, both mechanisms also identified in the molecular network analysis. In contrast, hormones and body composition could not be conclusively related to animal-to-animal variation in feed efficiency. The analysis of potential biological networks underlying RFI variations highlighted other significant pathways such as lipid metabolism and immunity and stress response. Finally, emerging knowledge suggests that metabolic functions underlying genetic variation in feed efficiency could be associated with other important traits in animal production. This emphasizes the relevance of understanding the biological basis of relevant animal traits to better define future balanced breeding programmes.

16S rRNA Sequencing Reveals Relationship Between Potent Cellulolytic Genera and Feed Efficiency in the Rumen of Bulls

The rumen microbial population dictates the host’s feed degradation capacity and subsequent nutrient supply. The rising global human population and intensifying demand for animal protein is creating environmental challenges. As a consequence, there is an increasing requirement for livestock with enhanced nutrient utilization capacity in order to more efficiently convert plant material to high quality edible muscle. In the current study, residual feed intake (RFI), a widely used and a highly accepted measure of feed efficiency in cattle, was calculated for a combination of three cohorts of Simmental bulls. All animals were managed similarly from birth and offered concentrate ad libitum in addition to 3 kg of grass silage daily during the finishing period. Solid and liquid rumen digesta samples collected at slaughter and were analyzed using amplicon sequencing targeting the 16S rRNA gene utilizing the Illumina MiSeq platform. Volatile fatty acid analysis was also conducted on the liquid digesta samples. Spearman’s correlation coefficient was utilized to determine the association between RFI and bacterial and archaeal taxa and inter-taxonomic relationships. The data indicate a tendency toward an increase in butyrate (P = 0.06), which corresponds with an increase in plasma β-hydroxybutyrate concentration in low RFI (LRFI) bulls in comparison to their high RFI (HRFI) contemporaries (P < 0.05). A decrease in propionate (P < 0.05) was also recorded in the rumen of LRFI in comparison to HRFI bulls. These results indicate alternate fermentation patterns in the rumen of LRFI bulls. The data also identified that OTUs within the phyla Tenericutes, Fibrobacteres, and Cyanobacteria may potentially influence RFI phenotype. In particular, a negative association between F. succinogenes and RFI was evident. The unique cellulolytic metabolism of F. succinogenes suggests it could contribute to host efficiency by providing substrate to the host ruminant and other microbial populations (e.g., Selenomonas ruminantium, Methanobrevibacter, and Methanomassiliicoccaceae) in the rumen. This study provides evidence that bacterial OTUs within common phyla could influence ruminant feed efficiency phenotype through their role in ruminal degradation of complex plant polysaccharides or increased capability to harvest nutrients from ingested feed.

Differences in intestinal size, structure, and function contributing to feed efficiency in broiler chickens reared at geographically distant locations

The contribution of the intestinal tract to differences in residual feed intake (RFI) has been inconclusively studied in chickens so far. It is also not clear if RFI-related differences in intestinal function are similar in chickens raised in different environments. The objective was to investigate differences in nutrient retention, visceral organ size, intestinal morphology, jejunal permeability and expression of genes related to barrier function, and innate immune response in chickens of diverging RFI raised at 2 locations (L1: Austria; L2: UK). The experimental protocol was similar, and the same dietary formulation was fed at the 2 locations. Individual BW and feed intake (FI) of chickens (Cobb 500FF) were recorded from d 7 of life. At 5 wk of life, chickens (L1, n = 157; L2 = 192) were ranked according to their RFI, and low, medium, and high RFI chickens were selected (n = 9/RFI group, sex, and location). RFI values were similar between locations within the same RFI group and increased by 446 and 464 g from low to high RFI in females and males, respectively. Location, but not RFI rank, affected growth, nutrient retention, size of the intestine, and jejunal disaccharidase activity. Chickens from L2 had lower total body weight gain and mucosal enzyme activity but higher nutrient retention and longer intestines than chickens at L1. Parameters determined only at L1 showed increased crypt depth in the duodenum and jejunum and enhanced paracellular permeability in low vs. high RFI females. Jejunal expression of IL1B was lower in low vs. high RFI females at L2, whereas that of TLR4 at L1 and MCT1 at both locations was higher in low vs. high RFI males. Correlation analysis between intestinal parameters and feed efficiency metrics indicated that feed conversion ratio was more correlated to intestinal size and function than was RFI. In conclusion, the rearing environment greatly affected intestinal size and function, thereby contributing to the variation in chicken RFI observed across locations.

Exploration of Biological Markers of Feed Efficiency in Young Bulls

The efficiency with which ruminants convert feed to desirable products is difficult to measure under normal commercial settings. We explored the use of potential biological markers from easily obtainable samples, that is, blood, hair, and feces, to characterize potential causes of divergent efficiency when considered as residual feed intake (RFI) or feed conversion efficiency (FCE). A total of 54 Charolais bulls, 20 in period 1 and 34 in period 2, were examined for individual dry matter intake (DMI) and growth. Bulls were offered a diet of 70:30 wrapped grass silage to concentrate for 99 d. At the conclusion of the test period, blood samples were collected for the determination of vitamins B₂ and B₆, and plasma used for the determination of metabolites, natural isotopic ¹⁵N abundance (¹⁵N NIA, expressed as δ¹⁵N ‰) and fractionation (Δ¹⁵N_{plasma proteins-diet} and Δ¹³C_{plasma proteins-diet}) and near-infrared spectroscopy (NIRS). Feces were analyzed by NIRS. Bulls were slaughtered at 15-17 months of age and carcass characteristics determined. Bulls were ranked according to RFI with extremes (SD ± 0.5; n = 31) classified as either efficient (Neg-RFI) or inefficient (Pos-RFI). Extreme bulls were then classified for FCE (high vs low FCE), changing the groups. Pos-RFI bulls consumed 14% more feed than Neg-RFI bulls for the same level of weight gain. Low FCE bulls tended to eat more, but had lower weight gains than high FCE bulls. No differences were detected in carcass conformation, fat scores, hot carcass weight, or dressing percentage. Yet, heart and bladder weights were heavier in Pos-RFI, and rumen weight tended to be heavier in Pos-RFI bulls. RFI did not affect bulk ¹⁵N or ¹³C fractionation. A negative correlation was observed between FCE and Δ¹⁵N_{plasma proteins-diet}. Inefficient bulls (Pos-RFI) had higher δ¹⁵N in glycine compared to Neg-RFI bulls. Similarly, metabolomic analysis showed a tendency for concentrations of glycine and sarcosine to be elevated in Pos-RFI bulls, whereas aspartic acid and carnosine tended to be elevated, and serine tended to be lower in High FCE. Among vitamins, only flavin adenine dinucleotide concentration was higher in the blood of bulls with High FCE. These results suggest that the two feed efficiency metrics differ in the underlying mechanisms of metabolism, where RFI is driven by differences in the energetic requirements of visceral organs and the extent of AA catabolism.

Growth performance, rumen fermentation, bacteria composition, and gene expressions involved in intracellular pH regulation of rumen epithelium in finishing Hu lambs differing in residual feed intake phenotype

The objective of this study was to evaluate the effect of residual feed intake (RFI) on rumen function in finishing lambs. A total of 60 male Hu lambs (average initial BW = 25.2 ± 2.5kg) were used and were offered a pelleted high-concentrate diet, of which the forage to concentrate ratio was 25:75. Individual feed intake was recorded over a period of 42 d, then 10 lambs with the lowest RFI and the highest RFI were selected, respectively. The rumen fluid used for fermentation variables and relative abundance of bacteria measurement was obtained on d 10 and 20 after RFI measurement. At the end of this experiment, the selected lambs were slaughtered and rumen epithelium and liver tissues were collected for RNA extraction. Low-RFI lambs had lower ( < 0.01) DMI and greater ( < 0.05) G:F than the high-RFI ones, while the RFI groups did not differ in ADG and BW ( > 0.05). Additionally, RFI was positively ( = 0.57; < 0.01) correlated with DMI and negatively ( = -0.53; < 0.05) correlated with G:F. Total VFA and individual VFA decreased ( < 0.05) over time. The concentrations of total VFA, acetate, valerate, isobutyrate, isovalerate, and rumen pH ( > 0.05) were not affected by RFI classification. Nonetheless, low-RFI group lambs had a greater ( < 0.05) concentration of propionate, a lower ( < 0.05) concentration of butyrate, and a lower ( < 0.05) acetate to propionate ratio compared with the high-RFI group. There was a significant ( < 0.05) effect of RFI on the relative abundance of and . The relative abundance of , , and decreased ( < 0.05) over time in high-RFI group. And the relative abundance of in high-RFI group was greater ( < 0.05) than its low-RFI counterpart. Furthermore, RFI had no effect ( > 0.05) on gene expression associated with intracellular pH regulation (, , , , , , , and ) in rumen epithelium and β-hydroxybutyrate metabolism () in both rumen epithelium and liver tissues. In conclusion, even though low-RFI lambs had lower DMI, however, the number of was lower. Additionally, there was no difference in gene expressions level associated with intracellular pH regulation in rumen epithelium between RFI groups.

Enhanced expression of proteins involved in energy production and transfer in breast muscle of pedigree male broilers exhibiting high feed efficiency

In cells with fluctuating energy demand (e.g., skeletal muscle), a transfer system of proteins across the inner and outer mitochondrial membranes links mitochondrial oxidative phosphorylation to cytosolic phosphorylated creatine (PCr) that serves as a phosphate reservoir for rapid repletion of cytosolic adenosine triphosphate (ATP). Crucial proteins of this energy transfer system include several creatine kinase (CK) isoforms found in the cytosol and mitochondria. In a recent proteomic study (Kong et al., 2016), several components of this system were up-regulated in high feed efficiency (FE) compared to low FE breast muscle; notably adenine nucleotide translocase (ANT), voltage dependent activated channel (VDAC), the brain isoform of creatine kinase (CK-B), and several proteins of the electron transport chain. Reexamination of the original proteomic dataset revealed that the expression of two mitochondrial CK isoforms (CKMT1A and CKMT2) had been detected but were not recognized by the bioinformatics program used by Kong et al. (2016a). The CKMT1A isoform was up-regulated (7.8-fold, P = 0.05) in the high FE phenotype but there was no difference in CKMT2 expression (1.1-fold, P = 0.59). From these findings, we hypothesize that enhanced expression of the energy production and transfer system in breast muscle of the high FE pedigree broiler male could be fundamentally important in the phenotypic expression of feed efficiency.

Influence of fumaric acid on ruminal parameters and organ weights of growing bulls fed with grass or maize silage

The influence of the potential methane reducer, fumaric acid (FA), on ruminal parameters, the rumen wall and organ weights was investigated in a long-term study with growing bulls. In all, 20 bulls were fed with maize or grass silage as roughage, and with concentrate with or without 300 g FA per animal and day during the whole fattening period. After slaughtering, the organs were weighed and blood serum was analysed for glucose, β-hydroxybutyric acid (BHB) and non-esterified fatty acid concentration. The ruminal fluid was analysed for short-chain fatty acids, ammonia-N and the microbial community via single strand conformation polymorphism analysis. The rumen wall was examined histopathologically and results were graded as 'no visible lesions', 'few inflammatory infiltrates', 'some inflammatory infiltrates' or 'several inflammatory infiltrates'. In addition, the dimensions of the rumen villi were measured. The FA supplementation decreased the serum BHB concentration and the butyric acid concentration in the ruminal fluid. The microbial community in the ruminal fluid was not influenced by FA. An interaction between FA and silage type was observed for the inflammation centres counted in the villous area of rumen papillae. This interaction was also observed in the length and surface of the rumen villi. Rumen villi results show that the influence of FA depends on the roughage used in the diet.

Finishing pigs that are divergent in feed efficiency show small differences in intestinal functionality and structure

Controversial information is available regarding the feed efficiency-related variation in intestinal size, structure and functionality in pigs. The present objective was therefore to investigate the differences in visceral organ size, intestinal morphology, mucosal enzyme activity, intestinal integrity and related gene expression in low and high RFI pigs which were reared at three different geographical locations (Austria, AT; Northern Ireland, NI; Republic of Ireland, ROI) using similar protocols. Pigs (n = 369) were ranked for their RFI between days 42 and 91 postweaning and low and high RFI pigs (n = 16 from AT, n = 24 from NI, and n = 60 from ROI) were selected. Pigs were sacrificed and sampled on ~day 110 of life. In general, RFI-related variation in intestinal size, structure and function was small. Some energy saving mechanisms and enhanced digestive and absorptive capacity were indicated in low versus high RFI pigs by shorter crypts, higher duodenal lactase and maltase activity and greater mucosal permeability (P < 0.05), but differences were mainly seen in pigs from AT and to a lesser degree in pigs from ROI. Additionally, low RFI pigs from AT had more goblet cells in duodenum but fewer in jejunum compared to high RFI pigs (P < 0.05). Together with the lower expression of TLR4 and TNFA in low versus high RFI pigs from AT and ROI (P < 0.05), these results might indicate differences in the innate immune response between low and high RFI pigs. Results demonstrated that the variation in the size of visceral organs and intestinal structure and functionality was greater between geographic location (local environmental factors) than between RFI ranks of pigs. In conclusion, present results support previous findings that the intestinal size, structure and functionality do not significantly contribute to variation in RFI of pigs.

Effect of divergence in phenotypic residual feed intake on methane emissions, ruminal fermentation, and apparent whole-tract digestibility of beef heifers across three contrasting diets

This study aimed to examine the effect of divergent phenotypic ranking for residual feed intake (RFI) on ruminal CH emissions, diet digestibility, and indices of ruminal fermentation in heifers across 3 commercially relevant diets. Twenty-eight Limousin × Friesian heifers were used and were ranked on the basis of phenotypic RFI: 14 low-RFI and 14 high-RFI animals. Ruminal CH emissions were estimated over 5 d using the SF tracer gas technique on 3 successive occasions: 1) at the end of a 6-wk period (Period 1) on grass silage (GS), 2) at the end of an 8-wk period (Period 2) at pasture, and 3) at the end of a 5-wk period (Period 3) on a 30:70 corn silage:concentrate total mixed ration (TMR). Animals were allowed ad libitum access to feed and water at all times. Individual DMI was estimated during CH measurement and rumen samples were taken at the end of each CH measurement period. Diet type affected all feed intake and CH traits measured ( < 0.01) but was unavoidably confounded with animal age/size and experimental period. Correlation coefficients between RFI and DMI were significant ( < 0.05) only when animals were fed the TMR. Daily CH correlated with DMI ( = 0.42, < 0.05) only when animals grazed pasture. Daily DMI was lower in low-RFI animals ( = 0.047) but only when expressed as grams per kilogram metabolic BW. Absolute CH emissions did not differ between RFI groups ( > 0.05), but CH yield was greatest in low-RFI heifers ( = 0.03) as a proportion of both DMI and GE intake. Interactions between the main effects were observed ( < 0.05) for CP digestibility (CPD), DM digestibility (DMD), ruminal propionate, and the acetate:propionate ratio. Low-RFI animals had greater ( < 0.05) CPD and DMD than their high-RFI contemporaries when offered GS but not the other 2 diets. Low-RFI heifers also had greater OM digestibility ( = 0.027). Additionally, low-RFI heifers had a lower concentration of propionate ( < 0.05) compared with high-RFI heifers when fed GS, resulting in a greater ( < 0.05) acetate:propionate ratio. However, these differences were not evident for the other 2 diets. Energetically efficient animals do not have a lower ruminal methanogenic potential compared with their more inefficient counterparts and, indeed, some evidence to the contrary was found, which may reflect the greater nutrient digestive potential observed in low-RFI cattle.

Utilization of macrominerals and trace elements in pregnant heifers with distinct feed efficiencies

The objective of the study was to evaluate utilization of dietary minerals and trace elements in pregnant heifers with distinct residual feed intakes (RFI). Feed intake, body weight (BW), and body composition traits were recorded in 36 crossbred heifers over a period of 37 wk, starting shortly after weaning at 8.3 (0.10; standard deviation) mo of age with an average BW of 276 (7.8) kg. Both BW and body composition were monitored regularly throughout the study, whereas individual feed intake was assessed during the last 84 d of the trial. Data recorded were used to calculate RFI for each heifer. Heifers were ranked based on RFI and assigned to high (n=14) or low (n=10) RFI groups. After the RFI study, 24 selected heifers [age 18.2 (0.14) mo; 87.5 (4.74) d in gestation; 497 (8.5) kg of BW] were used in an indirect digestibility trial (lignin as internal marker). Heifers were fed a ration containing corn silage, haylage, and a mineral premix in which Ca, P, K, Na, Mg, S, Cu, Fe, Mn, Mo, Se, Zn, and Co were provided in the diet according to National Research Council requirements of pregnant replacement heifers. The digestibility trial lasted 1 wk, during which samples of feces were gathered twice daily, and blood and liver biopsy samples were collected on the last day. We noted no significant differences between low- and high-RFI heifers in dry matter digestibility. Apparent absorption of Cu, Zn, and Mn was increased in heifers with low RFI, and apparent absorption of Co tended to be greater for these animals. Concentrations of macrominerals and trace elements in serum of pregnant heifers were similar for both groups except for Se, which was increased in the serum of low-RFI heifers. Liver concentrations of Cu, Fe, Mn, Mo, Se, and Zn did not differ between low- and high-RFI heifers. In conclusion, whereas improved absorption of some trace elements (Cu, Zn, Mn, and Co) and increased Se serum concentration appear to be associated with superior feed efficiency in pregnant heifers, further studies are needed to investigate the causality of such relationships.

Effects of feed intake and genetics on tissue nitrogen-15 enrichment and feed conversion efficiency in sheep

This study investigated the effects of sheep genetics and feed intake on nitrogen isotopic fractionation (ΔN) and feed conversion efficiency (FCE; live weight gain/DMI), using a 2 × 2 factorial design, with 2 levels of genetic merit for growth (high vs. low) and 2 levels of feed intake (110 vs. 170% of ME for maintenance [MEm]). No effect of genetic merit was detected for live weight gain ( = 0.64), FCE ( = 0.46), plasma urea nitrogen ( = 0.52), plasma glucose ( = 0.78), and ΔN of wool ( = 0.45), blood ( = 0.09), and plasma ( = 0.51). Sheep receiving 170% of MEm had 175% higher live weight gain ( < 0.001) and 77% higher FCE ( < 0.001) than sheep receiving 110% of MEm. There was no difference among treatments at the beginning of the study for either blood or plasma ∆N, but the treatment groups started to diverge in blood and plasma ∆N at 21 and 7 d, respectively. Blood, plasma, and wool samples were enriched in N compared with feed. There was a higher blood, plasma, and wool ∆N for the low feed intake group than the high feed intake group ( < 0.001 in all cases). Across the 4 treatment groups, higher FCE in sheep was associated with lower ∆N for plasma, blood, and wool. Overall, the results are consistent with the potential of ∆N as a rapid, low-cost biomarker of FCE in sheep, despite there being no effects of genetic treatment on FCE and ∆N.