Common and diet-specific metabolic pathways underlying residual feed intake in fattening Charolais yearling bulls

Optimizing rangeland use: Forage selection and grazing patterns of Nguni and Bonsmara cattle across traditional and commercial systems

This study examined the grazing dynamics of Nguni and Bonsmara cattle across traditional communal and commercial ranching systems in semi-arid South Africa. Eighty cattle (n = 20 per breed and management system) were monitored over 12 months to assess grazing behavior, forage selection, and environmental interactions. Data collection involved direct behavioral observations, GPS tracking of movement patterns, and forage quality assessments across seasons. Significant breed-specific differences were observed, with Nguni cattle exhibiting longer grazing durations (p = 0.02), higher step rates (p = 0.03), and broader dietary flexibility (p = 0.04) in communal systems, enabling efficient utilization of lower-quality forage. Conversely, Bonsmara cattle, optimized for commercial production, displayed a preference for high-quality forage and engaged in shorter, more concentrated grazing bouts (p = 0.01), leading to superior weight gain (p = 0.03) in nutrient-rich pastures. Seasonal fluctuations significantly influenced grazing behavior, with reduced forage availability during the dry season disproportionately affecting Bonsmara cattle in communal areas (p = 0.02). These findings underscore the importance of breed selection and adaptive grazing management for optimizing livestock productivity and sustainability across diverse agroecological systems.

Unraveling Ruminant Feed Efficiency Through Metabolomics: A Systematic Review

BACKGROUND

Advancements in metabolomic technologies have revolutionized our understanding of feed efficiency (FE) in livestock, offering new pathways to enhance both profitability and sustainability in ruminant production.

METHODS

This review offers a critical and systematic evaluation of the metabolomics methods used to measure and assess FE in ruminants. We conducted a comprehensive search of PubMed, Web of Science, and Scopus databases, covering publications from 1971 to 2023. This review synthesizes findings from 71 studies that applied metabolomic approaches to uncover the biological mechanisms driving interindividual variations in FE across cattle, sheep, goats, and buffaloes.

RESULTS

Most studies focused on cattle and employed targeted metabolomics to identify key biomarkers, including amino acids, fatty acids, and other metabolites linked to critical pathways such as energy metabolism, nitrogen utilization, and muscle development. Despite promising insights, challenges remain, including small sample sizes, methodological inconsistencies, and a lack of validation studies, particularly for non-cattle species.

CONCLUSIONS

By leveraging state-of-the-art metabolomic methods, this review highlights the potential of metabolomics to provide cost-effective, non-invasive molecular markers for FE evaluation, paving the way for more efficient and sustainable livestock management. Future research should prioritize larger, species-specific studies with standardized methods to validate identified biomarkers and enhance practical applications in livestock production systems.

Development and validation of a model for early prediction of residual feed intake in beef cattle using plasma biomarkers

Identification of plasma biomarkers for feed efficiency in growing beef cattle offers a promising opportunity for developing prediction models to improve precision feeding strategies. However, these models must accurately predict feed efficiency at early stages of fattening. Our study aimed to evaluate the reliability of candidate biomarkers previously identified in late-fattening cattle when analysed during early fattening stages and to develop diet-specific prediction equations for residual feed intake (RFI). From a total of 364 Charolais bulls across seven cohorts, we selected 64 animals with extreme RFI values. The animals were fed either a corn‑ or grass-silage diets. These animals were chosen from four out of the available seven cohorts. Animals from three cohorts (24 high-RFI and 24 low-RFI, having a mean RFI difference of 1.48 kg/d) were used for biomarker confirmation and prediction model training. Animals from a fourth cohort (8 high-RFI and 8 low-RFI, having a mean RFI difference of 0.98 kg/d) were used for model external validation. Blood samples were collected at the beginning of the feed efficiency test (333 ± 20 days), and plasma underwent targeted metabolomic for 630 metabolites, natural abundance of 15N (δ15N), insulin, and IGF-1 analysis. Seven previously identified plasma biomarkers for RFI in late-fattening beef cattle still kept their capability for discriminating low and high RFI animals when analysed during early fattening stages (P < 0.05). Among these confirmed biomarkers, five were common for both grass- and corn-fed animals (creatinine, β-alanine, triglyceride TG18:0_34:2, symmetric dimethyl-arginine and phosphatidylcholine PC aa C30:2) while two were diet-specific (IGF-1 for grass silage-based diet, and isoleucine for corn silage-based diet. No new plasma biomarkers of RFI were identified at early-fattening stages (false discovery rate  > 0.05). Prediction models were developed based on seven confirmed RFI biomarkers analysed during early-fattening. Two logistic regression models incorporating creatinine and either IGF-1 (for grass silage-based diet) or PC aa C30:2 (for corn silage-based diet) effectively distinguished between high- and low-RFI animals with high sensitivity and specificity (area under the curve > 0.80). The biomarkers used in the models showed moderate to high repeatability between early and late fattening stages (0.45 < r < 0.65). The models were successfully externally validated, with more than 85% of animals from the fourth cohort correctly classified. Once validated in larger cohorts and utilising cost-effective and rapid analytical methods, these models could support precision feeding and breeding programmes, aiming to reduce the cost of raising beef cattle.

Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes

Residual feed intake (RFI) is a metric that provides a more accurate measure of feed efficiency. The lower the RFI, the higher the feed efficiency. The changes in the host microbiome and metabolome contribute to the greater feed efficiency of low RFI (LRFI) animals. The aim of this study was to explore the differences in rumen microorganisms, rumen metabolites and plasma metabolites of Hu sheep with differing RFI through the microbiome and metabolome. A total of 80 Hu sheep were used. The experiment consisted of a 15-d pretrial period and a 128-d experimental period. The RFI in the experimental period was calculated for all sheep, and the sheep were screened into high RFI (HRFI, n = 8) and LRFI (n = 8) groups. The HRFI and LRFI sheep did not differ in their initial and final body weights, average daily gain and body measurements, but the dry matter intake of LRFI sheep was significantly decreased (28.4%, P < 0.001). The sheep with LRFI had higher digestibility of crude protein (P = 0.010) and ether extract (P = 0.010) compared to HRFI group. The concentrations of acetate (P = 0.036), propionate (P = 0.010), valerate (P = 0.027) and total volatile fatty acids (P = 0.048) in rumen of LRFI group were higher compared to HRFI group. The results of 16S rDNA sequencing indicated that the sheep with LRFI had higher proportions of Prevotella genus in rumen liquid (P = 0.031). The rumen metabolome and plasma metabolome results showed that the citrate cycle, pyruvate metabolism and alanine, aspartate and glutamate metabolism processes were more active for sheep in LRFI group, which provided more energy substrate such as malic acid, oxoglutaric acid and citric acid. In conclusion, sheep with LRFI can utilize feed more efficiently, and the more active energy metabolism pathway and the production of energy substances may account for the higher feed efficiency.

Effect of residual feed intake on meat quality in fattening Charolais bulls fed two contrasting diets

The selection of more efficient animals for breeding is of both economic and environmental interest to the industry. The aim of this study was to evaluate the influence of the animals' residual feed intake (RFI) ranking in interaction with the type of diet on the meat quality of Charolais beef cattle. Indeed, several biological mechanisms are associated with RFI, especially when animals are fed high starch-diets. It is therefore possible that quality parameters may show greater changes due to RFI in the context of high starch diets compared to high forage diets. An 84-day feed efficiency trial followed immediately by a second 112-day feed efficiency trial was conducted with a total of 100 animals fed either maize- or grass-diets for 196-days. At the end of the 84-day period, the 32 most divergent RFI animals (16 extreme RFI animals per diet, 8 RFI+ and 8 RFI-) were identified. They were slaughtered after 112-days of finishing. The Longissimus thoracis was characterised in terms of nutritional and sensory quality. RFI had no effect on lab colour, muscle shear force, total fat, fatty acid ratios and most of the total fatty acid content (especially n-3) irrespective of the diet. However, more efficient animals (RFI-) showed higher CLA contents compared to less efficient animals (RFI+) regardless of the diet and also a lower n6/n3 ratio only in animals fed the maize diets. Diet also had a significant effect on lipid and FA content as well as on FA composition.

Some plasma biomarkers of residual feed intake in beef cattle remain consistent regardless of intake level

This study investigated whether plasma biomarkers of residual feed intake (RFI), identified under ad libitum feeding conditions in beef cattle, remained consistent during feed restriction. Sixty Charolais crossbred young bulls were divided into two groups for a crossover study. Group A was initially fed ad libitum (first test) and then restricted (second test) on the same diet, while Group B experienced the opposite sequence. Blood samples were collected from the 12 most divergent RFI animals in each group at the end of the first test and again after the second test. 12 plasma variables consistently increased, while three consistently decreased during feed restriction (FDR < 0.05). Only two metabolites, α-aminoadipic acid for Group A and 5-aminovaleric acid for Group B, were associated with RFI independent of feed intake level (FDR < 0.05), demonstrating moderate-to-high repeatability across feeding levels (intraclass correlation coefficient ≥ 0.59). Notably, both metabolites belong to the same metabolic pathway: lysine degradation. These metabolites consistently correlated with RFI, irrespective of fluctuations in feed intake, indicating a connection to individual metabolic processes influencing feed efficiency. These findings suggest that a portion of RFI phenotypic variance is inherent to an individual's metabolic efficiency beyond variations in feed intake.

Plasma and milk metabolomics revealed changes in amino acid metabolism in Holstein dairy cows under heat stress

Our understanding of metabolic alterations triggered by heat stress is incomplete, which limits the designing of nutritional strategies to mitigate negative productive and health effects. Thus, this study aimed to explore the metabolic responses of heat-stressed dairy cows to dietary supplementation with vitamin D3/Ca and vitamin E/Se. Twelve multiparous Holstein cows were enrolled in a split-plot Latin square design with two distinct vitamin E/Se supplementation levels, either at a low (ESe-, n = 6, 11.1 IU/kg vitamin E and 0.55 mg/kg Se) or a high dose (ESe+, n = 6 223 IU/kg vitamin E and 1.8 mg/kg Se) as the main plot. Treatment subplots, arranged in a replicated 3 × 3 Latin square design, comprised heat challenge (Temperature Humidity Index, THI: 72.0-82.0) supplemented with different levels of vitamin D3/Ca: either low (HS/DCa-, 1 012 IU/kg and 0.73%, respectively) or high (HS/DCa+, 3 764 IU/kg and 0.97%, respectively), and a pair-fed control group in thermoneutrality (THI = 61.0-64.0) receiving the low dose of vitamin D3/Ca (TN). The liquid chromatography-mass spectrometry-based metabolome profile was determined in blood plasma and milk sampled at the beginning (day 0) and end (day 14) of each experimental period. The results were analyzed for the effect of (1) TN vs. HS/ESe-/DCa-, and (2) the vitamin E/Se and vitamin D3/Ca supplementation. No group or group × day effects were detected in the plasma metabolome (false discovery rate, FDR > 0.05), except for triglyceride 52:2 being higher (FDR = 0.03) on day 0 than 14. Taurine, creatinine and butyryl-carnitine showed group × day interactions in the milk metabolome (FDR ≤ 0.05) as creatinine (+22%) and butyryl-carnitine (+190%) were increased (P < 0.01) on day 14, and taurine was decreased (-65%, P < 0.01) on day 14 in the heat stress (HS) cows, compared with day 0. Most compounds were unaffected by vitamin E/Se or vitamin D3/Ca supplementation level or their interaction (FDR > 0.05) in plasma and milk, except for milk alanine which was lower (-69%, FDR = 0.03) in the E/Se+ groups, compared with E/Se-. Our results indicated that HS triggered more prominent changes in the milk than in the plasma metabolome, with consistent results in milk suggesting increased muscle catabolism, as reflected by increased creatinine, alanine and citrulline levels. Supplementing with high levels of vitamin E/Se or vitamin D3/Ca or their combination did not appear to affect the metabolic remodeling triggered by HS.

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.

Comparative analysis of signalling pathways in tissue protein metabolism in efficient and non-efficient beef cattle: acute response to an identical single meal size

Protein turnover has been associated to residual feed intake (RFI) in beef cattle. However, this relationship may be confounded by feeding level and affected by the composition of the diet being fed. Our aim was to assess postmortem the protein metabolism signalling pathways in skeletal muscle and liver of 32 Charolais young bulls with extreme RFI phenotypes. Bulls were fed two contrasting diets during the whole fattening period but were subjected to a similar and single nutritional stimulus, induced by their respective concentrate, just prior to slaughter. The key targets were protein degradation (autophagy and ubiquitin) and synthesis signalling pathways through western-blot analysis, as well as hepatic transaminase activity. To ensure a precise assessment of all animals at the same postprandial time, they were provided with a test meal (2.5 kg of either a high-starch and high-protein concentrate or high-fibre and low-protein concentrate) 3 hours prior to slaughter, irrespective of their RFI grouping. Blood and tissues were sampled at the slaughterhouse (3 h and 3 h30 postprandially, respectively). In response to an identical single meal size, efficient RFI animals showed higher (P < 0.05) postprandial plasma β-hydroxybutyrate concentrations and insulinemia (only with the high-starch concentrate) than non-efficient animals. Moreover, efficient RFI bulls had lower muscle (P = 0.04) and liver (P = 0.08) ubiquitin protein abundance (degradation pathway) and tended to have lower alanine transaminase activity in the liver (P = 0.06) compared to non-efficient bulls, regardless of diet. A positive correlation between protein degradation potential and amino acid catabolism was identified in this study (r = 0.52, P = 0.004), which was interpreted as being biologically linked to the RFI phenotype. Efficient RFI bulls also had a faster potential for protein synthesis in the muscle, as indicated by their greater ratio of phosphorylated to total form of ribosomal protein S6 kinase (P = 0.05), regardless of diet. Results on protein synthesis pathway in muscle and plasma metabolite concentrations suggested that efficient RFI cattle may have a faster nutrient absorption and insulin responsiveness after feeding than inefficient cattle. We did not find significant differences in hepatic protein synthesis pathways between the two RFI groups (P > 0.05). Our findings suggest that, in response to an identical single meal size, efficient RFI animals exhibited lower activation of tissue protein degradation pathways and faster muscle protein synthesis activation compared to their inefficient counterparts. This pattern was observed regardless of the composition of the tested meals.

In utero choline exposure alters growth, metabolism, feed efficiency, and carcass characteristics of Holstein × Angus cattle from weaning to slaughter

Feeding rumen-protected choline (RPC) to late gestation dairy cows has potential to affect growth in offspring. The objective of this study was to evaluate the effects of in utero choline exposure on the growth, feed efficiency (FE), metabolism, and carcass quality of Angus × Holstein cattle. Multiparous Holstein cows pregnant with male (N = 17) or female (N = 30) Angus-sired calves were enrolled 21 d prepartum and randomly assigned to one of four dietary treatments varying in quantity and formulation of RPC. The treatments included a control with 0 g/d supplemental RPC (CTL), supplemental RPC fed at the recommended dose (RD) of 15 g/d from either an established RPC product (RPC1RD; ReaShure; Balchem Corp.) or choline ion from a concentrated RPC prototype (RPC2RD; Balchem Corp.), or a high dose (HD) of RPC2 fed at 22 g/d (RPC2HD). From 2 to 6 mo of age, calves were group housed and offered 2.3 kg grain/hd/d (42% CP) with ad libitum grass hay, and stepped up to a complete finishing diet by 7 mo (12.0% CP; 1.34 Mcal/kg NEg). Weight and height were measured monthly. Animal FE was measured in individual pens for 35 d at 8 mo. Feed intake was measured daily, and blood was obtained on day 18 during the FE period. Afterwards, cattle were group housed and offered a free-choice finishing diet until slaughter, where carcass yield and quality characteristics were measured. Mixed models were used in PROC MIXED (SAS, 9.4) with the fixed effects of treatment, sex, time, their interactions, and the random effect of calf. Month was the repeated measure, and preplanned contrasts were used. Blood and FE data were analyzed with the fixed effect of dam choline treatment, calf sex, and the interaction. Increasing dose of RPC tended to increase weight over the entire study period. Feeding any RPC increased hip and wither height compared with CTL, and increasing RPC dose linearly increased hip and wither height. Treatment and sex interacted on DMI whereby increasing RPC intake linearly increased DMI for males but not females. Compared with control, feeding any RPC decreased plasma insulin, glucose, and an insulin sensitivity index (RQUICKI). In utero choline exposure increased kidney-pelvic-heart fat and marbling score. Mechanisms of action for intrauterine choline exposure on offspring growth, metabolism, and carcass characteristics should be explored as they have direct implications for profitability for cattle growers and feeders.

Untargeted metabolomics confirms the association between plasma branched chain amino acids and residual feed intake in beef heifers

This study explored plasma biomarkers and metabolic pathways underlying feed efficiency measured as residual feed intake (RFI) in Charolais heifers. A total of 48 RFI extreme individuals (High-RFI, n = 24; Low-RFI, n = 24) were selected from a population of 142 heifers for classical plasma metabolite and hormone quantification and plasma metabolomic profiling through untargeted LC-MS. Most efficient heifers (Low-RFI) had greater (P = 0.03) plasma concentrations of IGF-1 and tended to have (P = 0.06) a lower back fat depth compared to least efficient heifers. However, no changes were noted (P ≥ 0.10) for plasma concentrations of glucose, insulin, non-esterified fatty acids, β-hydroxybutyrate and urea. The plasma metabolomic dataset comprised 3,457 ions with none significantly differing between RFI classes after false discovery rate correction (FDR > 0.10). Among the 101 ions having a raw P < 0.05 for the RFI effect, 13 were putatively annotated by using internal databases and 6 compounds were further confirmed with standards. Metabolic pathway analysis from these 6 confirmed compounds revealed that the branched chain amino acid metabolism was significantly (FDR < 0.05) impacted by the RFI classes. Our results confirmed for the first time in beef heifers previous findings obtained in male beef cattle and pointing to changes in branched-chain amino acids metabolism along with that of body composition as biological mechanisms related to RFI. Further studies are warranted to ascertain whether there is a cause-and-effect relationship between these mechanisms and RFI.

Effects of residual feed intake divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks

Feed efficiency (FE) is a major economic trait of meat duck. This study aimed to evaluate the effects of residual feed intake (RFI) divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks. A total of 500 healthy 21-day-old male ducks were housed in individual cages until slaughter at 63 d of age. The growth performance was determined for all the ducks. The carcass yield, meat quality, and blood biochemical parameters were determined for the selected 30 high-RFI (HRFI) and 30 low-RFI (LRFI) ducks. In terms of growth performance, the RFI, feed conversion ratio (FCR), and average daily feed intake (ADFI) were found to be significantly lower in the LRFI group (P < 0.01), whereas no differences were observed in the BW and body weight gain (P > 0.05). For slaughter performance, no differences were observed in the carcass traits between the LRFI and HRFI groups (P > 0.05). For meat quality, the shear force of breast muscle was significantly lower in the LRFI group (P < 0.05), while the other meat quality traits of breast and thigh muscles demonstrated no differences (P > 0.05). For blood biochemical parameters, the serum concentrations of triglycerides (TG) and glucose (GLU) were significantly lower in the LRFI group (P < 0.05), while the other parameters showed no differences (P > 0.05). The correlation analysis demonstrated a high positive correlation between RFI, FCR, and ADFI (P < 0.01). The RFI demonstrated a negative effect on the breast muscle and lean meat yields, but a positive effect on the shear force of breast muscle (P < 0.05). Further, the RFI demonstrated a positive effect on the TG and GLU levels (P < 0.05). These results indicate that the selection for low RFI could improve the FE of small-sized meat ducks without affecting the production performance. This study provides valuable insight into the biological processes underlying the variations in FE in small-sized meat ducks.

Ceramide metabolism associated with chronic dietary nutrient surplus and diminished insulin sensitivity in the liver, muscle, and adipose tissue of cattle

High dietary energy and protein supply is common practice in livestock nutrition, aiming to maximize growth and production performance. However, a chronic nutritional surplus induces obesity, promotes insulin insensitivity, and triggers low-grade inflammation. Thirty Holstein bulls were randomly assigned to two groups, low energy and protein (LEP), and high energy and protein (HEP) intake, provided from the 13th to the 20th month of life. Body weight, carcass composition, laminitis score, and circulating insulin and glucose concentrations were assessed. The expression and extent of phosphorylation of insulin signaling proteins were measured in the liver, muscle, and adipose tissue. The sphingolipid metabolome was quantified by a targeted liquid chromatography-mass spectrometry based metabolomics approach. The HEP bulls were obese, had hyperinsulinemia with euglycemia, and expressed clinical signs of chronic laminitis. In the liver, protein kinase B (PKB) phosphorylation was decreased and this was associated with a higher tissue concentration of ceramide 16:0, a sphingolipid that diminishes insulin action by dephosphorylating PKB. In the adipose tissue, insulin receptor expression was lower in HEP bulls, associated with higher concentration of hexosylceramide, which reduces the abundance of functional insulin receptors. Our findings confirm that diet-induced metabolic inflammation triggers ceramide accumulation and disturbs insulin signaling. As insulin insensitivity exacerbates metabolic inflammation, this self-reinforcing cycle could explain the deterioration of metabolic health apparent as chronic laminitis. By demonstrating molecular relationships between insulin signaling and sphingolipid metabolism in three major tissues, our data extend our mechanistic understanding of the role of ceramides in diet-induced metabolic inflammation.

Protein metabolism, body composition and oxygen consumption in young bulls divergent in residual feed intake offered two contrasting forage-based diets

Protein metabolism and body composition have been identified as major determinants of residual feed intake (RFI) in beef cattle fed high-starch fattening diets. This study aimed to evaluate if these two identified RFI determinants in beef cattle are the same across two contrasting silage-based diets. During two consecutive years, an 84-day feed efficiency test (Test A) immediately followed by a second 112-day feed efficiency test (Test B) was carried out using a total of 100 animals offered either one of two diets (either corn silage- or grass silage-based) over 196 days. At the end of Test A, the 32 animals most divergent for RFI (16 extreme RFI animals per diet, eight low RFI and eight high RFI) were identified and evaluated during Test B for their i) N use efficiency (NUE; N retention/N intake) calculated either from a 10-d nitrogen balance trial or from estimations based on body composition changes occurring during the whole experiment (Test A and Test B; 196 days), ii) carcass and whole-body protein turnover rates analysed through the 3-methyl-histidine urinary excretion and the N isotopic turnover rates of urine, respectively, and iii) body composition measured at the slaughterhouse at the end of Test B. Oxygen consumption was measured during Test B for the 100 animals by two GreenFeed systems. Irrespective of the diet, efficient RFI animals tended (P = 0.08) to improve their NUE when N retention was estimated for 196 days or when considering their lower urinary urea-N to total N ratio (P = 0.03). In contrast, NUE calculated during the 10-d N balance showed no differences (P = 0.65) across RFI groups suggesting that this method may not be suitable to capture small NUE differences. Efficient RFI individuals presented higher dressing percentage and muscle deposition in the carcass (P = 0.003) but lighter rumen (P = 0.001), and a trend for lower oxygen consumption (P = 0.08) than inefficient RFI animals irrespective of the diet. Lower protein degradation rates of skeletal muscle and lower protein synthesis rates of plasma proteins were found in efficient RFI cattle but only with the corn silage-based diet (RFI × Diet; P = 0.02). The higher insulinaemia associated with the corn silage-based diet (P = 0.001) seemed to be a key metabolic feature explaining the positive association between protein turnover and RFI only in this diet. Feed N was more efficiently used for growth by efficient RFI animals regardless of the diet but lower protein turnover rates in efficient RFI animals were only observed with corn silage-based diets.

Applications of Omics Technology for Livestock Selection and Improvement

Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals' actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.