Methane emissions, body composition, and rumen fermentation traits of beef heifers differing in residual feed intake

Performance, nutrient utilization and meat quality traits in Bos indicus cattle: a meta-analysis examining the effect of residual feed intake

This meta-analysis aims to investigate the effects of residual feed intake (RFI) phenotype on performance, nutrient utilization and meat quality traits in Zebu (Bos indicus) cattle. Twenty-three peer-reviewed publications with 37 treatment means were included in the dataset. Weighted mean difference analysis compared animals categorized into low RFI (more efficient) versus medium or high RFI (less efficient) groups. Data heterogeneity via meta-regression and subgroup analysis, considering variables such as animal age, sex class, experimental duration, RFI group, dietary concentrate, and estimated metabolizable energy intake were also explored. The predominant genetic group of cattle in the dataset was Nellore (89.18%), followed by Brahman (10.81%). More efficient animals (low RFI phenotype) exhibited less dry matter intake (DMI; P < 0.010) than medium or high RFI animals (-0.95 kg vs. -0.42 kg/d). Cattle dietary crude protein and fiber digestibility were consistent across RFI groups (P > 0.05), while dietary ether extract digestibility tended to decrease (P = 0.050) in low RFI animals (-13.20 g/kg DM). Low RFI animals tended to increased (P = 0.065) ribeye area (REA) compared to the high/medium RFI groups, while carcass backfat thickness (BFT) decreased (P = 0.042) compared to high/medium RFI groups. Moreover, there was an increase (P < 0.001) of 0.22 kg in Warner-Bratzler shear force (WBSF) and a reduction (P < 0.001) in the myofibrillar fragmentation index (MFI) in low RFI animals. Meat color parameters (lightness [L*] and yellowness [b*]) and visual marbling scores were consistent (P > 0.05) across RFI groups. In conclusion, Zebu cattle classified as efficient (low RFI) exhibited reduced DMI, which improves their feed efficiency. However, BFT and meat quality parameters such as tenderness (WBSF and MFI) and redness [a*] were compromised by low RFI phenotype, highlighting the challenge of enhancing feed efficiency and meat quality traits in Zebu cattle.

Rumen fermentation parameters and papillae development in Simmental growing bulls with divergent residual feed intake

Residual feed intake (RFI), a widespread index used to measure animal feed efficiency, is influenced by various individual biological factors related to inter-animal variation that need to be assessed. Herein, 30 Simmental bulls, raised under the same farm conditions, were divided on the basis of RFI values into a high efficient group (HE, RFI =  - 1.18 ± 0.33 kg DM/d, n = 15) and a low efficient group (LE, RFI = 0.92 ± 0.35 kg DM/d, n = 15). Subsequently, bulls were slaughtered at an average BW of 734 ± 39.4 kg. Their ruminal fermentation traits were analysed immediately after slaughtering and after 24 h of in vitro incubation. Furthermore, ruminal micro-biota composition and ruminal papillae morphology were examined. The LE group exhibited a higher propionate concentration as a percentage of total volatile fatty acids (17.3 vs 16.1%, P = 0.04) in the rumen fluid collected during slaughtering, which was also confirmed after in vitro fermentation (16.6 vs 15.4% respectively for LE and HE, P = 0.01). This phenomenon resulted in a significant alteration in the acetate-to-propionate ratio (A:P) with higher values for the HE group, both after slaughter (4.01 vs 3.66, P = 0.02) and after in vitro incubation (3.78 vs 3.66, P = 0.02). Methane production was similar in both groups either as absolute production (227 vs 218 mL for HE and LE, respectively) or expressed as a percentage of total gas (approximately 22%). Even if significant differences (P < 0.20) in the relative abundance of some bacterial genera were observed for the two RFI groups, no significant variations were observed in the alpha (Shannon index) and beta (Bray-Curtis index) diversity. Considering the papillae morphology, the LE subjects have shown higher length values (6.26 vs 4.90 mm, P < 0.01) while HE subjects have demonstrated higher papillae density (46.4 vs 40.5 n/cm2, P = 0.02). Histo-morphometric analysis did not reveal appreciable modifications in the total papilla thickness, boundaries or surface between the experimental groups. In conclusion, our results contribute to efforts to analyse the factors affecting feed efficiency at the ruminal level. Propionate production, papillae morphology and a few bacterial genera certainly play a role in this regard, although not a decisive one.

Residual feed intake is related to metabolic and inflammatory response during the preweaning period in Italian Simmental calves

Residual Feed Intake (RFI) is defined as the difference between measured and predicted intake. Understanding its biological regulators could benefit farm profit margins. The most-efficient animals (M-Eff) have observed intake smaller than predicted resulting in negative RFI, whereas the least-efficient (L-Eff) animals have positive RFI. Hence, this observational study aimed at retrospectively comparing the blood immunometabolic profile in calves with divergent RFI during the preweaning period. Twenty-two Italian Simmental calves were monitored from birth through 60 d of age. Calves received 3 L of colostrum from their respective dams. From 2 to 53 d of age, calves were fed a milk replacer twice daily, whereas from 54 to 60 d (i.e., weaning) calves were stepped down to only one meal in the morning. Calves had ad libitum access to concentrate and intakes were recorded daily. The measurement of BW and blood samples were performed at 0, 1, 7, 14, 21, 28, 35, 45, 54, and 60 d of age. Calves were ranked and categorized as M-Eff or L-Eff according to the median RFI value. Median RFI was -0.06 and 0.04 kg of DMI/d for M-Eff and L-Eff, respectively. No evidence for group differences was noted for colostrum and plasma IgG concentrations. Although growth rate was not different, as expected, (0.67 kg/d [95% CI = 0.57-0.76] for both L-Eff and M-Eff) throughout the entire preweaning period (0-60 d), starter intake was greater in L-Eff compared with M-Eff calves (+36%). Overall, M-Eff calves had a greater gain-to-feed ratio compared with L-Eff calves (+16%). Plasma ceruloplasmin, myeloperoxidase, and reactive oxygen metabolites concentrations were greater in L-Eff compared with M-Eff calves. Compared with L-Eff, M-Eff calves had an overall greater plasma concentration of globulin, and γ-glutamyl transferase (indicating a better colostrum uptake) and Zn at 1 d. Retinol and urea were overall greater in L-Eff. The improved efficiency in nutrient utilization observed in M-Eff was paired with a lower grade of oxidative stress and systemic inflammation. L-Eff may have had greater energy expenditure to support the activation of the immune system.

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies

BACKGROUND

Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.

RESULTS

The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.

CONCLUSIONS

This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.

Replacing Fertilizer with Dried Distillers' Grains in Stocker Cattle Systems on Southern Great Plains Old World Bluestem, USA

The objective was to examine the effects of dried distillers' grains supplementation and fertilization strategies on the cattle performance and resource use efficiency of stocker cattle grazing on Plains Old World bluestem. Over 4 consecutive years, heifers and steers (average n = 239) were randomly assigned to 1 of 4 treatments: (1) low input, low stocking density, and no fertilizer or distillers grains supplementation (LOW); (2) high stocking density and no fertilizer with distillers grains supplementation (DDGS); (3) high stocking density and 90 kg of nitrogen/ha with no distillers grains supplementation (NFERT); (4) high stocking density, 90 kg of nitrogen/ha, and 39 kg of phosphorus/ha with no distillers grains supplementation (NPFERT). Cattle grazed in the pastures from mid-May to mid-September each year, except for 2011, when the experiment ended in July due to lack of forage. Data were analyzed using a linear model with fixed effects of treatment, year, and treatment × year (R software). Nitrogen use efficiency (retained/inputs) was affected by a treatment × year interaction, where LOW had the greatest efficiency in all years and DDGS was greater than NFERT and NPFERT in all years except 2012, with NFERT and NPFERT being not different in all years. The estimated total carbon equivalent emissions were greater for DDGS, NFERT, and NPFERT than LOW, but the carbon footprint (kg CO2eq/kg weight gain) was lesser for LOW and DDGS, which were not different, than NFERT and NPFERT, which were also not different. Replacing nitrogen fertilizer with dried distiller's grains improved the cattle performance and the efficiency of resource use, and could be a viable economic alternative to traditional systems.

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.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems

Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH₄), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H₂ and CO₂), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH₄-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH₄ mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.

Animal board invited review: Genomic-based improvement of cattle in response to climate change

Climate change brings challenges to cattle production, such as the need to adapt to new climates and pressure to reduce greenhouse emissions (GHG). In general, the improvement of traits in current breeding goals is favourably correlated with the reduction of GHG. Current breeding goals and tools for increasing cattle production efficiency have reduced GHG. The same amount of production can be achieved by a much smaller number of animals. Genomic selection (GS) may offer a cost-effective way of using an efficient breeding approach, even in low- and middle-income countries. As climate change increases the intensity of heatwaves, adaptation to heat stress leads to lower efficiency of production and, thus, is unfavourable to the goal of reducing GHG. Furthermore, there is evidence that heat stress during cow pregnancy can have many generation-long lowering effects on milk production. Both adaptation and reduction of GHG are among the difficult-to-measure traits for which GS is more efficient and suitable than the traditional non-genomic breeding evaluation approach. Nevertheless, the commonly used within-breed selection may be insufficient to meet the new challenges; thus, cross-breeding based on selecting highly efficient and highly adaptive breeds may be needed. Genomic introgression offers an efficient approach for cross-breeding that is expected to provide high genetic progress with a low rate of inbreeding. However, well-adapted breeds may have a small number of animals, which is a source of concern from a genetic biodiversity point of view. Furthermore, low animal numbers also limit the efficiency of genomic introgression. Sustainable cattle production in countries that have already intensified production is likely to emphasise better health, reproduction, feed efficiency, heat stress and other adaptation traits instead of higher production. This may require the application of innovative technologies for phenotyping and further use of new big data techniques to extract information for breeding.

Growth performance, reproductive parameters and fertility measures in young Nellore bulls with divergent feed efficiency

The growth, sexual maturity and fertility-related parameters related of young Nellore bulls with divergent residual feed intake (RFI) raised on pasture were evaluated. After classification of 48 young males as low and high RFI (more and less efficient, respectively), the animals were evaluated for growth and reproductive parameters at 28-day intervals from 14.3 to 24.6 months of age. The semen was cryopreserved in the last sampling and fresh and post-thaw semen samples were evaluated. Low RFI bulls exhibited higher initial and final body weight (P < 0.05), but feed intake, body condition score and growth measures evaluated by carcass ultrasound were unaffected by RFI (P > 0.05). The scrotal circumference, sperm concentration, defects, and quality of fresh semen, and ultrasonographic testicular characteristics were unaffected by RFI (P > 0.05). However, velocity parameters such as average path and curvilinear velocities determined by computer-assisted sperm analysis of thawed semen submitted to the rapid thermoresistance test were improved (P < 0.05) in low RFI bulls, but this improvement in quality did not enhance in vitro sperm fertilizing ability. Our results demonstrated significant differences in metabolism and growth performance between bulls of divergent RFI. In addition, there was slight improvement in the semen quality of bulls with low RFI bulls, but this did not enhance in vitro fertilizing ability. Selection of beef bulls for RFI can be performed, which will result in economic benefits by improving the growth performance of the animals without affecting reproductive parameters.

Effects of diet on feed intake, weight change, and gas emissions in beef cows

The objective of this study was to examine the effects of diet energy density on ranking for dry matter intake (DMI), residual feed intake (RFI), and greenhouse gas emissions. Forty-two mature, gestating Angus cows (600 ± 69 kg body weight [BW]; body condition score [BCS] 5.3 ± 1.1) with a wide range in DMI expected progeny difference (-1.38 to 2.91) were randomly assigned to two diet sequences; forage then concentrate (FC) or concentrate then forage (CF). The forage diet consisted of long-stem native grass hay plus protein supplement (HAY; 1.96 Mcal ME/kg DM). The concentrate diet consisted of 35% chopped grass hay and 65% concentrate feeds on a dry matter basis (MIX; 2.5 Mcal ME/kg DM). The GreenFeed Emission Monitoring system was used to determine carbon dioxide (CO2), oxygen (O2), and methane (CH4) flux. Cow performance traits, ultrasound back fat and rump fat, feed DMI, and gas flux data were analyzed in a crossover design using a mixed model including diet, period, and sequence as fixed effects and pen and cow within sequence as random effects. For all measured traits excluding DMI, there was a diet × sequence interaction (P < 0.05). The correlation between MIX and HAY DMI was 0.41 (P = 0.067) and 0.47 (P = 0.03) for FC and CF sequences, respectively. There was no relationship (P > 0.66) between HAY and MIX average daily gain (ADG), regardless of sequence. Fifty-seven percent of the variation in DMI was explained by metabolic BW, ADG, and BCS for both diets during the first period. During the second period, the same three explanatory variables accounted for 38% and 37% of the variation in DMI for MIX and HAY diets, respectively. The negative relationship between BCS and DMI was more pronounced when cows consumed the MIX diet. There was no relationship between MIX and HAY RFI, regardless of sequence (P > 0.18). During the first period, correlations for CO2, CH4, and O2 with MIX DMI were 0.69, 0.81, and 0.56 (P ≤ 0.015), respectively, and 0.76, 0.74, and 0.64 (P < 0.01) with HAY DMI. During the second period, correlations for CO2, CH4, and O2 with MIX DMI were 0.62, 0.47, and 0.56 (P ≤ 0.11), respectively. However, HAY DMI during the second period was not related to gas flux (P > 0.47). Results from this experiment indicate that feed intake of two energy-diverse diets is moderately correlated while ADG while consuming the two diets is not related. Further experimentation is necessary to determine if gas flux data can be used to predict feed intake in beef cows.

Physiological responses and adaptations to high methane production in Japanese Black cattle

In this study, using enteric methane emissions, we investigated the metabolic characteristics of Japanese Black cattle. Their methane emissions were measured at early (age 13 months), middle (20 months), and late fattening phases (28 months). Cattle with the highest and lowest methane emissions were selected based on the residual methane emission values, and their liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood β-hydroxybutyric acid and insulin levels were high, whereas blood amino acid levels were low in cattle with high methane emissions. Further, propionate and butyrate levels differed depending on the enteric methane emissions. Hepatic genes, such as SERPINI2, SLC7A5, ATP6, and RRAD, which were related to amino acid transport and glucose metabolism, were upregulated or downregulated during the late fattening phase. The above mentioned metabolites and liver transcriptomes could be used to evaluate enteric methanogenesis in Japanese Black cattle.

Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency

Despite the significant improvement of feed efficiency (FE) in pigs over the past decades, feed costs remain a major challenge for producers profitability. Improving FE is a top priority for the global swine industry. A deeper understanding of the biology underlying FE is crucial for making progress in genetic improvement of FE traits. This review comprehensively discusses the topics related to the FE in pigs including: measurements, genetics, genomics, biological pathways and the advanced technologies and methods involved in FE improvement. We first provide an update of heritability for different FE indicators and then characterize the correlations of FE traits with other economically important traits. Moreover, we present the quantitative trait loci (QTL) and possible candidate genes associated with FE in pigs and outline the most important biological pathways related to the FE traits in pigs. Finally, we present possible ways to improve FE in swine including the implementation of genomic selection, new technologies for measuring the FE traits, and the potential use of genome editing and omics technologies.

Selecting for Feed Efficient Cows Will Help to Reduce Methane Gas Emissions

In the last decade, several countries have included feed efficiency (as residual feed intake; RFI) in their breeding goal. Recent studies showed that RFI is favorably correlated with methane emissions. Thus, selecting for lower emitting animals indirectly through RFI could be a short-term strategy in order to achieve the intended reduction set by the EU Commission (-55% for 2030). The objectives were to 1) estimate genetic parameters for six methane traits, including genetic correlations between methane traits, production, and feed efficiency traits, 2) evaluate the expected correlated response of methane traits when selecting for feed efficiency with or without including methane, 3) quantify the impact of reducing methane emissions in dairy cattle using the Danish Holstein population as an example. A total of 26,664 CH4 breath records from 647 Danish Holstein cows measured over 7 years in a research farm were analyzed. Records on dry matter intake (DMI), body weight (BW), and energy corrected milk (ECM) were also available. Methane traits were methane concentration (MeC, ppm), methane production (MeP; g/d), methane yield (MeY; g CH4/kg DMI), methane intensity (MeI; g CH4/kg ECM), residual methane concentration (RMeC), residual methane production (RMeP, g/d), and two definitions of residual feed intake with or without including body weight change (RFI1, RFI2). The estimated heritability of MeC was 0.20 ± 0.05 and for MeP, it was 0.21 ± 0.05, whereas heritability estimates for MeY and MeI were 0.22 ± 0.05 and 0.18 ± 0.04, and for the RMeC and RMeP, they were 0.23 ± 0.06 and 0.16 ± 0.02, respectively. Genetic correlations between methane traits ranged from moderate to highly correlated (0.48 ± 0.16–0.98 ± 0.01). Genetic correlations between methane traits and feed efficiency were all positive, ranging from 0.05 ± 0.20 (MeI-RFI2) to 0.76 ± 0.09 (MeP-RFI2). Selection index calculations showed that selecting for feed efficiency has a positive impact on reducing methane emissions’ expected response, independently of the trait used (MeP, RMeP, or MeI). Nevertheless, adding a negative economic value for methane would accelerate the response and help to reach the reduction goal in fewer generations. Therefore, including methane in the breeding goal seems to be a faster way to achieve the desired methane emission reductions in dairy cattle.

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).

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?

Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and  their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.

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

Residual feed intake (RFI) is one of the preferred traits for feed efficiency animal breeding. However, RFI measurement is expensive and time-consuming and animal ranking may depend on the nature of the diets. We aimed to explore RFI plasma biomarkers and to unravel the underlying metabolic pathways in yearling bulls fed either a corn-silage diet rich in starch (corn diet) or a grass-silage diet rich in fiber (grass diet). Forty-eight extreme RFI animals (Low-RFI, n = 24, versus High-RFI, n = 24, balanced per diet) were selected from a population of 364 Charolais bulls and their plasma was subjected to a targeted LC-MS metabolomic approach together with classical metabolite and hormonal plasma analyses. Greater lean body mass and nitrogen use efficiency, and lower protein turnover were identified as common mechanisms underlying RFI irrespective of the diet. On the other hand, greater adiposity and plasma concentrations of branched-chain amino acids (BCAA) together with lower insulin sensitivity in High-RFI animals were only observed with corn diet. Conversely, greater plasma concentrations of BCAA and total triglycerides, but similar insulin concentrations were noted in efficient RFI cattle with grass diet. Our data suggest that there are diet-specific mechanisms explaining RFI differences in fattening Charolais yearling bulls.

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.

Exploring Biological Impacts of Prenatal Nutrition and Selection for Residual Feed Intake on Beef Cattle Using Omics Technologies: A Review

Approximately 70% of the cost of beef production is impacted by dietary intake. Maximizing production efficiency of beef cattle requires not only genetic selection to maximize feed efficiency (i.e., residual feed intake (RFI)), but also adequate nutrition throughout all stages of growth and development to maximize efficiency of growth and reproductive capacity, even during gestation. RFI as a measure of feed efficiency in cattle has been recently accepted and used in the beef industry, but the effect of selection for RFI upon the dynamics of gestation has not been extensively studied, especially in the context of fluctuating energy supply to the dam and fetus. Nutrient restriction during gestation has been shown to negatively affect postnatal growth and development as well as fertility of beef cattle offspring. This, when combined with the genetic potential for RFI, may significantly affect energy partitioning in the offspring and subsequently important performance traits. In this review, we discuss: 1) the importance of RFI as a measure of feed efficiency and how it can affect other economic traits in beef cattle; 2) the influence of prenatal nutrition on physiological phenotypes in calves; 3) the benefits of investigating the interaction of genetic selection for RFI and prenatal nutrition; 4) how metabolomics, transcriptomics, and epigenomics have been employed to investigate the underlying biology associated with prenatal nutrition, RFI, or their interactions in beef cattle; and 5) how the integration of omics information is adding a level of deeper understanding of the genetic architecture of phenotypic traits in cattle.

Phenotypic association among performance, feed efficiency and methane emission traits in Nellore cattle

Enteric methane (CH4) emissions are a natural process in ruminants and can result in up to 12% of energy losses. Hence, decreasing enteric CH4 production constitutes an important step towards improving the feed efficiency of Brazilian cattle herds. The aim of this study was to evaluate the relationship between performance, residual feed intake (RFI), and enteric CH4 emission in growing Nellore cattle (Bos indicus). Performance, RFI and CH4 emission data were obtained from 489 animals participating in selection programs (mid-test age and body weight: 414±159 days and 356±135 kg, respectively) that were evaluated in 12 performance tests carried out in individual pens (n = 95) or collective paddocks (n = 394) equipped with electronic feed bunks. The sulfur hexafluoride tracer gas technique was used to measure daily CH4 emissions. The following variables were estimated: CH4 emission rate (g/day), residual methane emission and emission expressed per mid-test body weight, metabolic body weight, dry matter intake (CH4/DMI), average daily gain, and ingested gross energy (CH4/GE). Animals classified as negative RFI (RFI<0), i.e., more efficient animals, consumed less dry matter (P <0.0001) and emitted less g CH4/day (P = 0.0022) than positive RFI animals (RFI>0). Nonetheless, more efficient animals emitted more CH4/DMI and CH4/GE (P < 0.0001), suggesting that the difference in daily intake between animals is a determinant factor for the difference in daily enteric CH4 emissions. In addition, animals classified as negative RFI emitted less CH4 per kg mid-test weight and metabolic weight (P = 0.0096 and P = 0.0033, respectively), i.e., most efficient animals could emit less CH4 per kg of carcass. In conclusion, more efficient animals produced less methane when expressed as g/day and per kg mid-test weight than less efficient animals, suggesting lower emissions per kg of carcass produced. However, it is not possible to state that feed efficiency has a direct effect on enteric CH4 emissions since emissions per kg of consumed dry matter and the percentage of gross energy lost as CH4 are higher for more efficient animals.

Investigation of intra-day variability of gaseous measurements in sheep using portable accumulation chambers

Portable accumulation chambers (PAC) enable short-term spot measurements of gaseous emissions including methane (CH4), carbon dioxide (CO2), and oxygen (O2) consumption from small ruminants. To date the differences in morning and evening gaseous measurements in the PAC have not been investigated. The objectives of this study were to investigate: 1) the optimal measurement time in the PAC, 2) the appropriate method of accounting for the animal's size when calculating the animal's gaseous output, and 3) the intra-day variability of gaseous measurements. A total of 12 ewe lambs (c. 10 to 11 months of age) were randomly selected each day from a cohort of 48 animals over nine consecutive days. Methane emissions from the 12 lambs were measured in 12 PAC during two measurement runs daily, AM (8 to 10 h) and PM (14 to 16 h). Animals were removed from Perennial ryegrass silage for at least 1 h prior to measurements in the PAC and animals were assigned randomly to each of the 12 chambers. Methane (ppm) concentration, O2 and CO2 percentage were measured at 5 time points (T1 = 0.0 min, T2 = 12.5 min, T3 = 25.0 min, T4 = 37.5 min, and T5 = 50.0 min from entry of the first animal into the first chamber) using an Eagle 2 monitor. The correlation between time points T5-T1 (i.e., 50 min minus 0 min after entry of the animal to the chamber) and T4-T1 was 0.95, 0.92, and 0.77 for CH4, O2, and CO2, respectively (P < 0.01). The correlation between CH4 and CO2 output and O2 consumption, calculated with live-weight and with body volume was 0.99 (P < 0.001). The correlation between the PAC measurement recorded on the same animal in the AM and PM measurement runs was 0.73. Factors associated with CH4 production included: day and time of measurement, the live-weight of the animal and the hourly relative humidity. Results from this study suggest that the optimal time for measuring an animal's gaseous output in the PAC is 50 min, that live-weight should be used in the calculation of gaseous output from an animal and that the measurement of an animal's gaseous emissions in either the AM or PM does not impact on the ranking of animals when gaseous emissions are measured using the feeding and measurement protocol outlined in the present study.

Association between fecal methanogen species with methane production and grazed forage intake of beef heifers classified for residual feed intake under drylot conditions

Reduction in greenhouse gas emission from beef production is essential to the survival of the beef industry from environmental and social-economic perspectives. There are different systems available to measure methane from animals, but they are expensive, not easily accessible, and not suitable for large-scale methane measurements on the farm. Therefore exploring indicator traits, which are easy to measure, cost-effective, and suitable for large-scale measurement, are recommended. The objectives of this study were to examine the diversity of fecal methanogen profile among efficient and inefficient beef heifers on pasture and investigate methanogen profile as a possible proxy to predict methane emission in beef cattle consuming a forage diet. Forty pregnant (1st trimester) heifers previously classified for postweaning residual feed intake adjusted for off-test back fat (RFI_fat; 20 high and 20 low) were included in this study. To determine individual pasture grazing intake, heifers were dosed with 1 kg of C₃₂ labeled pellets once per day from Day 0 to Day 12, and fecal samples were collected twice daily from Day 8 to Day 15. Fecal samples from Days 8, 10, and 12 were analyzed for their methanogen profile. Animals were monitored individually for methane and carbon dioxide production using a GreenFeed Emissions Monitoring system. Total methanogen population and methanogenic community diversity of fecal samples were not different (P > 0.1) between low and high RFI_fat groups, as measured by quantitative PCR and α- and β-diversity indices. However, both groups had a different methanogen profile; the relative abundance of Methanobrevibacter wolinii and relatives were higher (P < 0.002), while that of Methanosphaera species ISO3-F5 was lower (P < 0.01) in low RFI_fat cattle compared to the high RFI_fat group. We also demonstrated that fecal methanogen profiles may be a useful proxy in predicting daily methane and carbon dioxide emissions with an adjusted R² of 0.53 and 0.33, respectively, for low RFI_fat heifers and 0.46 and 0.57, respectively, for the high RFI_fat group.

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.

Predicting feed intake using modelling based on feeding behaviour in finishing beef steers

Current techniques for measuring feed intake in housed cattle are both expensive and time-consuming making them unsuitable for use on commercial farms. Estimates of individual animal intake are required for assessing production efficiency. The aim of this study was to predict individual animal intake using parameters that can be easily obtained on commercial farms including feeding behaviour, liveweight and age. In total, 80 steers were used, and each steer was allocated to one of two diets (40 per diet) which consisted of (g/kg; DM) forage to concentrate ratios of either 494:506 (MIXED) or 80:920 (CONC). Individual daily fresh weight intakes (FWI; kg/day) were recorded for each animal using 32 electronic feeders over a 56-day period, and individual DM intakes (DMI; kg/day) subsequently calculated. Individual feeding behaviour variables were calculated for each day of the measurement period from the electronic feeders and included: total number of visits to the feeder, total time spent at the feeder (TOTFEEDTIME), total time where feed was consumed (TIMEWITHFEED) and average length of time during each visit to the feeder. These feeding behaviour variables were chosen due to ease of obtaining from accelerometers. Four modelling techniques to predict individual animal intake were examined, based on (i) individual animal TOTFEEDTIME relative expressed as a proportion of the dietary group (GRP) and total GRP intake, (ii) multiple linear regression (REG) (iii) random forests (RF) and (iv) support vector regressor (SVR). Each model was used to predict CONC and MIXED diets separately, giving eight prediction models, (i) GRP_CONC, (ii) GRP_MIXED, (iii) REG_CONC, (iv) REG_MIXED, (v) RF_CONC, (vi) RF_MIXED, (vii) SVR_CONC and (viii) SVR_MIXED. Each model was tested on FWI and DMI. Model performance was assessed using repeated measures correlations (R²_RM) to capture the repeated nature of daily intakes compared with standard R², RMSE and mean absolute error (MAE). REG, RF and SVR models predicted FWI with R²_RM = 0.1–0.36, RMSE = 1.51–2.96 kg and MAE = 1.19–2.49 kg, and DMI with R²_RM = 0.13–0.19, RMSE = 1.15–1.61 kg and MAE = 0.9–1.28 kg. The GRP models predicted FWI with R²_RM = 0.42–0.49, RMSE = 2.76–3.88 kg and MAE = 2.46–3.47 kg, and DMI with R²_RM = 0.32–0.44, RMSE = 0.32–0.44 kg, MAE = 1.55–2.22 kg. Whilst more simplistic GRP models showed higher R²_RM than regression and machine learning techniques, these models had larger errors, likely due to individual feeding patterns not being captured. Although regression and machine learning techniques produced lower errors associated with individual intakes, overall precision of prediction was too low for practical use.

Plasma Metabolites, Productive Performance and Rumen Volatile Fatty Acid Profiles of Northern Australian Bos indicus Steers Supplemented with Desmanthus and Lucerne

The hypothesis tested was that tropical steers supplemented with the Desmanthus legume and lucerne, a widely characterized temperate legume of high nutritive value, would elicit similar responses in plasma metabolite profiles, productive performance, nitrogen retention, and volatile fatty acids (VFA). The tannin-binding compound, polyethylene glycol-4000 (PEG), was added to the diets (160 g/kg Desmanthus dry matter) with the objective of further exploring nitrogen (N) utilization in the animals supplemented with Desmanthus relative to lucerne. From February to June 2020, sixteen yearling Brangus steers (average liveweight of 232 ± 6 kg) were fed a background diet of Rhodes grass (Chloris gayana) hay for 28 days, before introducing three Desmanthus cultivars (Desmanthus virgatus cv. JCU2, D. bicornutus cv. JCU4, D. leptophyllus cv. JCU7) and lucerne (Medicago sativa) at 30% dry matter intake (DMI). Relative to the backgrounding period, all supplemented steers exhibited similar growth performance. Steers supplemented with Desmanthus recorded a lower DMI and animal growth performance, but higher fecal N concentration than animals supplemented with lucerne. Among the three Desmanthus cultivars, there were no significant differences in N concentrations, VFA, and plasma metabolite profiles. The addition of PEG induced higher rumen iso-acid concentrations and fecal N excretion. However, feeding Desmanthus spp. to tropical Bos indicus steers could be a valuable means of increasing N utilization, which is attributable to the presence of tannins, and, consequently, improve animal productive performance. Since supplementation with lucerne resulted in higher liveweight, daily liveweight gains, and overall animal performance than supplementing with Desmanthus, the tested hypothesis that both supplements will elicit similar animal performance does not hold and must be rejected. Further in vivo investigation is needed to better understand the impact of tannins in Desmanthus on N utilization.

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.

Methane and carbon dioxide emissions and grazed forage intake from pregnant beef heifers previously classified for residual feed intake under drylot conditions

The objectives of this study were to quantify the effect of post-weaning residual feed intake (RFI) on subsequent grazed forage intake, methane (CH4), and carbon dioxide (CO2) emissions. Beef heifers classified for RFI adjusted for off-test backfat (RFIfat; 55 high and 56 low) at 9 mo of age were monitored 7 mo later for CH4 and CO2 emissions using the GreenFeed Emissions Monitoring system. About 56 of these heifers were also monitored as high and low RFIfat groups using open-path Fourier-transform infrared spectroscopy (OP-FTIR). Heifers were dosed with 1 kg of C32-labelled pellets once daily for 15 d, with twice daily fecal sampling the last 8 d to determine individual grazed forage intake using the n-alkane method. Low RFIfat pregnant heifers consumed less forage (10.25 vs. 10.81 kg dry matter d−1; P < 0.001), and emitted less daily CH4 (238.7 vs. 250.7 g d−1; P = 0.009) and CO2 (7578 vs. 8041 g d−1; P < 0.001) compared with high RFIfat animals. Results from the OP-FTIR further confirmed that low RFIfat heifers emitted 6.3% less (g d−1; P = 0.006) CH4 compared with their high RFIfat cohorts. Thus, selection for low RFIfat will decrease daily CH4 and CO2 emissions from beef cattle.

Comparative analyses of enteric methane emissions, dry matter intake, and milk somatic cell count in different residual feed intake categories of dairy cows

This study compared the different residual feed intake (RFI) categories of lactating Holsteins with respect to methane (CH4) emissions, dry matter intake (DMI, kg), milk somatic cell count (SCC, 103∙mL−1), and β-hydroxybutyrate (BHB, mmol∙L−1). The RFI was calculated in 131 lactating Holstein cows that were then categorized into −RFI (RFI < 0) vs. +RFI (RFI > 0) and low- [RFI < −0.5 standard deviation (SD)] vs. high-RFI (RFI > 0.5 SD) groups. Milk traits were recorded in 131 cows, whereas CH4 and carbon dioxide were measured in 83. Comparisons of −RFI vs. +RFI and low- vs. high-RFI showed 7.9% (22.3 ± 0.40 vs. 24.2 ± 0.39) and 12.8% (21.1 ± 0.40 vs. 24.2 ± 0.45) decrease (P < 0.05) in DMI of −RFI and low-RFI groups, respectively. Similarly, −RFI and low-RFI cows had lower (P < 0.05) CH4 (g∙d−1) by 9.7% (343.5 ± 11.1 vs. 380.4 ± 10.9) and 15.5% (332.5 ± 12.9 vs. 393.5 ± 12.6), respectively. Milk yield was not different (P > 0.05) in −RFI vs. +RFI and low vs. high comparisons. The −RFI and low-RFI cows had lower (P < 0.05) SCC in −RFI vs. +RFI and low-RFI vs. high-RFI comparisons. The BHB was lower (P < 0.05) in low-RFI compared with the high-RFI group. Low-RFI dairy cows consumed less feed, emitted less CH4 (g∙d−1), and had lower milk SCC and BHB without differing in milk yield.

Genetic association among feeding behavior, feed efficiency, and growth traits in growing indicine cattle

This study aimed to estimate genetic parameters, including genomic data, for feeding behavior, feed efficiency, and growth traits in Nellore cattle. The following feeding behavior traits were studied (861 animals with records): time spent at the feed bunk (TF), duration of one feeding event (FD), frequency of visits to the bunk (FF), feeding rate (FR), and dry matter intake (DMI) per visit (DMIv). The feed efficiency traits (1,543 animals with records) included residual feed intake (RFI), residual weight gain (RWG), and feed conversion (FC). The growth traits studied were average daily gain (ADG, n = 1,543 animals) and selection (postweaning) weight (WSel, n = 9,549 animals). The (co)variance components were estimated by the maximum restricted likelihood method, fitting animal models that did (single-step genomic best linear unbiased prediction) or did not include (best linear unbiased prediction) genomic information in two-trait analyses. The direct responses to selection were calculated for the feed efficiency traits, ADG, and WSel, as well as the correlated responses in feed efficiency and growth by direct selection for shorter TF. The estimated heritabilities were 0.51 ± 0.06, 0.35 ± 0.06, 0.27 ± 0.07, 0.34 ± 0.06, and 0.33 ± 0.06 for TF, FD, FF, FR, and DMIv, respectively. In general, TF and FD showed positive genetic correlations with all feed efficiency traits (RFI, RWG, and FC), ADG, DMI, and WSel. Additionally, TF showed high and positive genetic and phenotypic correlations with RFI (0.71 ± 0.10 and 0.46 ± 0.02, respectively) and DMI (0.56 ± 0.09 and 0.48 ± 0.03), and medium to weak genetic correlations with growth (0.32 ± 0.11 with ADG and 0.14 ± 0.09 with WSel). The results suggest that TF is a strong indicator trait of feed efficiency, which exhibits high heritability and a weak positive genetic correlation with growth. In a context of a selection index, the inclusion of TF to select animals for shorter TF may accelerate the genetic gain in feed efficiency by reducing RFI but with zero or slightly negative genetic gain in growth traits.

Grazing diverse combinations of tanniferous and non-tanniferous legumes: Implications for beef cattle performance and environmental impact

We tested the effect of increasingly diverse combinations of tanniferous legumes (birdsfoot trefoil-BFT, sainfoin-SF) and alfalfa (ALF) on cattle performance, methane (CH₄) emissions and nitrogen (N) balance. Pairs of heifers (401 ± 49.6 kg) grazed three spatial replications of 7 treatments (n = 3/treatment): monocultures (BFT, SF, ALF) and all possible 2- and 3-way choices among strips of these legumes in a completely randomized block design of two 15-d periods during 2 consecutive years. Average daily gains (ADG) of heifers grazing the tanniferous legumes (1.05 kg/d) were 40% greater (p < 0.10) than of heifers grazing ALF (0.74 kg/d) during the first year. Heifers grazing the 3-way choice had greater intakes (10.4 vs 7.8 kg/d; p = 0.064) and ADG (1.21 vs. 0.95 kg/d, p = 0.054) than those grazing monocultures, suggesting a nutritional synergism among legumes. The average CH₄ emissions for legume monocultures vs. 2- and 3- way choices was 222 vs. 202 and 162 g/kg BW gain (p > 0.10), respectively. For heifers grazing SF and BFT compared with ALF, blood urea N was less (14.3 and 16.8 vs 20.8 mg/dL; p < 0.05) as were urinary N concentrations (3.7 and 3.5 vs 6.0 g/L; p < 0.05), but fecal N concentrations were greater (34.5 and 35.5 vs 30.5 g/kg, respectively; p < 0.05). Combining both tanniferous legumes (SF-BFT) led to the greatest declines in urinary N (2.24 g/L) and urea-N (1.71 g/L) concentration, suggesting that different types of tannins in different legumes result in associative effects that enhance N economy. In addition, heifers grazing 3-way choices partitioned less N into urine (40.7 vs 50.6%; p = 0.037) and retained more N (36.1 vs 25.2%, p = 0.046) than heifers grazing monocultures. In summary, combinations of tanniferous legumes with alfalfa improved animal performance and reduced environmental impacts relative to monocultures, resulting in a more sustainable approach to beef production in pasture-based finishing systems.

Serum Metabolite Biomarkers for Predicting Residual Feed Intake (RFI) of Young Angus Bulls

Residual feed intake (RFI) is a feed efficiency measure commonly used in the livestock industry to identify animals that efficiently/inefficiently convert feed into meat or body mass. Selection for low-residual feed intake (LRFI), or feed efficient animals, is gaining popularity among beef producers due to the fact that LRFI cattle eat less and produce less methane per unit weight gain. RFI is a difficult and time-consuming measure to perform, and therefore a simple blood test that could distinguish high-RFI (HRFI) from LRFI animals (early on) would potentially benefit beef farmers in terms of optimizing production or selecting which animals to cull or breed. Using three different metabolomics platforms (nuclear magnetic resonance (NMR) spectrometry, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and inductively coupled plasma mass spectrometry (ICP-MS)) we successfully identified serum biomarkers for RFI that could potentially be translated to an RFI blood test. One set of predictive RFI biomarkers included formate and leucine (best for NMR), and another set included C4 (butyrylcarnitine) and LysoPC(28:0) (best for LC-MS/MS). These serum biomarkers have high sensitivity and specificity (AUROC > 0.85), for distinguishing HRFI from LRFI animals. These results suggest that serum metabolites could be used to inexpensively predict and categorize bovine RFI values. Further validation using a larger, more diverse cohort of cattle is required to confirm these findings.

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.

Methane and carbon dioxide emissions from yearling beef heifers and mature cows classified for residual feed intake under drylot conditions

This study quantified methane (CH4) and carbon dioxide (CO2) production from beef heifers and cows classified for residual feed intake adjusted for off-test backfat thickness (RFIfat) and reared in drylot during cold winter temperatures. Individual performance, daily feed intake, and RFIfat were obtained for 1068 crossbred and purebred yearling heifers (eight trials) as well as 176 crossbred mature cows (six trials) during the winters of 2015–2017 at two locations. A portion of these heifers (147 high RFIfat; 167 low RFIfat) and cows (69 high RFIfat; 70 low RFIfat) was monitored for enteric CH4 and CO2 emissions using the GreenFeed Emissions Monitoring (GEM) system (C-Lock Inc., Rapid City, SD, USA). Low RFIfat cattle consumed less feed [heifers, 7.80 vs. 8.48 kg dry matter (DM) d−1; cows, 11.64 vs. 13.16 kg DM d−1] and emitted less daily CH4 (2.5% for heifers; 3.7% for cows) and CO2 (1.4% for heifers; 3.4% for cows) compared with high RFIfat cattle. However, low RFIfat heifers and cows had higher CH4 (6.2% for heifers; 9.9% for cows) and CO2 yield (7.3% for heifers; 9.8% for cows) per kilogram DM intake compared with their high RFIfat pen mates. The GEM system performed at air temperatures between +20 and −30 °C. Feed intake of heifers and mature cows was differently affected by ambient temperature reduction between +20 and −15 °C and similarly increased their feed intake at temperatures below −15 °C. In conclusion, low RFIfat animals emit less daily enteric CH4 and CO2, due mainly to lower feed consumption at equal body weight, gain, and fatness.

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency

Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = -0.53; solid, rho = -0.56) and Olsenella (solid, rho = -0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.

Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency

In this study, Bos Taurus cattle offered one high concentrate diet (92% concentrate-8% straw) during two independent trials allowed us to classify 72 animals comprising of two cattle breeds as "Low" or "High" feed efficiency groups. Digesta samples were taken from individual beef cattle at the abattoir. After metagenomic sequencing, the rumen microbiome composition and genes were determined. Applying a targeted approach based on current biological evidence, 27 genes associated with host-microbiome interaction activities were selected. Partial least square analysis enabled the identification of the most significant genes and genera of feed efficiency (VIP > 0.8) across years of the trial and breeds when comparing all potential genes or genera together. As a result, limited number of genes explained about 40% of the variability in both feed efficiency indicators. Combining information from rumen metagenome-assembled genomes and partial least square analysis results, microbial genera carrying these genes were determined and indicated that a limited number of important genera impacting on feed efficiency. In addition, potential mechanisms explaining significant difference between Low and High feed efficiency animals were analyzed considering, based on the literature, their gastrointestinal location of action. High feed efficiency animals were associated with microbial species including several Eubacterium having the genetic capacity to form biofilm or releasing metabolites like butyrate or propionate known to provide a greater contribution to cattle energy requirements compared to acetate. Populations associated with fucose sensing or hemolysin production, both mechanisms specifically described in the lower gut by activating the immune system to compete with pathogenic colonizers, were also identified to affect feed efficiency using rumen microbiome information. Microbial mechanisms associated with low feed efficiency animals involved potential pathogens within Proteobacteria and Spirochaetales, releasing less energetic substrates (e.g., acetate) or producing sialic acid to avoid the host immune system. Therefore, this study focusing on genes known to be involved in host-microbiome interaction improved the identification of rumen microbial genetic capacities and potential mechanisms significantly impacting on feed efficiency in beef cattle fed high concentrate diet.

Methane production and estimation from livestock husbandry: A mechanistic understanding and emerging mitigation options

Globally, livestock is an important contributor to methane (CH₄) emissions. This paper reviewed the various CH₄ measurement and estimation techniques and mitigation approaches for the livestock sector. Two approaches for enteric livestock CH₄ emission estimation are the top-down and bottom-up. The combination of both could further improve our understanding of enteric CH₄ emission and possible mitigation measures. We discuss three mitigation approaches: reducing emissions, avoiding emissions, and enhancing the removal of emissions from livestock. Dietary management, livestock management, and breeding management are viable reducing emissions pathways. Dietary manipulation is easily applicable and can bring an immediate response. Economic incentive policies can help the livestock farmers to opt for diet, breeding, and livestock management mitigation approaches. Carbon pricing creates a better option to achieve reduction targets in a given period. A combination of carbon pricing, feeding management, breeding management, and livestock management is more feasible and sustainable CH₄ emissions mitigation strategy rather than a single approach.

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.

Meat and sensory quality of major muscles from Angus, Charolais, and Angus crossbred steers with high and low residual feed intake

Effects of residual feed intake (RFI) and genetic group on growth, carcass, and meat quality characteristics of bovine longissimus lumborum (LL), triceps brachii (TB), semimembranosus (SM), and gluteus medius (GM) muscles were investigated using 72 purebred Angus, purebred Charolais, and Angus crossbred steers (n = 24 per genetic group) classified as either high (inefficient) or low (efficient) RFI (n = 12 high and low RFI steers within genetic group). There was no RFI effect (P > 0.05) on growth, carcass, and meat quality measurements except high RFI steers had the highest dry matter intake (P < 0.05), and low RFI TB was rated as having reduced beef flavour intensity and sustained juiciness (P < 0.05). Purebred Angus and Charolais LL and GM had lower shear force values (P < 0.05) than Angus crossbreds and ageing reduced mean shear force values except in TB. For TB, SM, and GM, Angus crossbred steers had the highest mean beef flavour intensity scores, and Charolais SM and TB were less tender than those of Angus crossbred (P < 0.05). Overall, RFI did not influence most meat quality traits; therefore, low RFI animals may contribute to reducing feed costs or environmental impact without compromising meat quality and palatability.

Precision feed restriction improves feed and milk efficiencies and reduces methane emissions of less efficient lactating Holstein cows without impairing their performance

A possible driver of feed inefficiency in dairy cows is overconsumption. The objective was therefore to test precision feed restriction as a lever to improve feed efficiency of the least efficient lactating dairy cows. An initial cohort of 68 Holstein lactating cows was monitored from calving to end of ad libitum feeding at 196 ± 16 d in milk, with the last 70 d being used to estimate feed efficiency. For a given expected dry matter (DM) intake (DMI) during ad libitum feeding, offered DMI during restriction was set to observed DMI of the 10% most efficient cows during ad libitum feeding for similar performance. Feed restriction lasted during 92 d, with only the last 70 d being used for data analyses. A single diet was fed during ad libitum and restriction periods, and was based on 64.9% of corn silage and 35.1% of concentrates on a DM basis. Individual DMI, body weight, milk production, milk composition, and body condition score were recorded, as well as methane emissions. Feed efficiency was defined as the repeatable part of the random effect of cow on the intercept in a mixed model predicting DMI with net energy in milk, maintenance and body weight gain and loss within parity, feeding level, and time. Milk energy efficiency was estimated in the same way, predicting net energy in milk instead of DMI. The 15 least efficient cows ate 2.6 kg of DM/d more than the 15 most efficient cows during ad libitum feeding with 2 g/kg of DMI lower methane yield, but similar daily methane emissions. Feed restriction decreased DMI by 2.6 kg of DMI/d for the least efficient cows, which was 1.8 kg of DMI/d more than the most efficient cows, and decreased daily methane emissions by 49.2 g/d for the least efficient cows, which was 22.4 g/d more than the most efficient cows. Feed restriction had no significant effect on milk, body weight, or body weight change. Feed restriction reduced the variability of both milk energy and feed efficiencies, as shown by a decrease of their standard deviation from 0.87 to 0.69 kg of DM/d for feed efficiency and from 1.14 to 0.65 UFL/d for milk energy efficiency. Despite narrow efficiency differences, the most efficient cows during ad libitum feeding remained more efficient during feed restriction (r = 0.46 for feed efficiency and 0.49 for milk energy efficiency). The 2 efficiency groups no longer differed in feed efficiency during precision feed restriction. Precision feed restriction seemed to bring the least efficient cows closer to the most efficient cows and to reduce their methane emissions without impairing their performance.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

BACKGROUND

Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle.

RESULTS

The DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi-squared distribution to a greater extent. With a threshold of P-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3'UTR, 5'UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant. Instead 3'UTR and synonymous variants explained a greater amount of genetic variance per DNA variant for all the traits examined while missense, 5'UTR and other regulatory region variants accounted for relatively more additive genetic variance per sequence variant for RFI and ADG, respectively. In total, 25 to 27 enriched cellular and molecular functions were identified with lipid metabolism and carbohydrate metabolism being the most significant for the feed efficiency traits.

CONCLUSIONS

RFI is controlled by many DNA variants with relatively small effects whereas DMI, ADG, and MWT are influenced by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory region and synonymous functional classes play a more important role per sequence variant in determining variation of the feed efficiency traits. The genetic architecture as revealed by the GWAS of the imputed 7,853,211 DNA variants will improve our understanding on the genetic control of feed efficiency traits in beef cattle.

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.