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

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.

Genome-Wide Association Studies for Methane Production in Dairy Cattle

Genomic selection has been proposed for the mitigation of methane (CH₄) emissions by cattle because there is considerable variability in CH₄ emissions between individuals fed on the same diet. The genome-wide association study (GWAS) represents an important tool for the detection of candidate genes, haplotypes or single nucleotide polymorphisms (SNP) markers related to characteristics of economic interest. The present study included information for 280 cows in three dairy production systems in Mexico: 1) Dual Purpose (n = 100), 2) Specialized Tropical Dairy (n = 76), 3) Familiar Production System (n = 104). Concentrations of CH₄ in a breath of individual cows at the time of milking (MEIm) were estimated through a system of infrared sensors. After quality control analyses, 21,958 SNPs were included. Associations of markers were made using a linear regression model, corrected with principal component analyses. In total, 46 SNPs were identified as significant for CH₄ production. Several SNPs associated with CH₄ production were found at regions previously described for quantitative trait loci of composition characteristics of meat, milk fatty acids and characteristics related to feed intake. It was concluded that the SNPs identified could be used in genomic selection programs in developing countries and combined with other datasets for global selection.

Age at puberty and pregnancy rate in beef heifer genotypes with contrasting nutritional intake from 8 to 13 months of age

The aim of this study was to examine the effect of plane of nutrition between 8 and 13 months of age on reproductive performance of heifers of early (EM; n = 154) or late (LM; n = 155) maturing beef breeds and with dairy (dairy-bred, n = 154) or beef (beef-bred, n = 155) dams. Heifers were fed to have an average daily gain (ADG) of 0.50 kg (MOD) or >1.00 kg (HI) for a 141- and 150-day indoor winter period. Subsequently, heifers grazed pasture, and a 12 week breeding programme was implemented. Compared to heifers fed the MOD intake diet, heifers fed the HI intake diet were younger (P < 0.001) and had greater bodyweights (P < 0.001) at puberty but did not have a greater 6- (P =  0.41) or 12- (P =  0.32) week pregnancy rate. Dairy-bred heifers were of a similar age (P = 0.55) but had a lesser bodyweight (P <  0.001) at puberty and had a greater 6- (P <  0.05) and 12- (P < 0.01) week pregnancy rate compared to beef-bred heifers. Compared to LM heifers, EM heifers were younger (P < 0.001), had a lesser bodyweight (P < 0.01) at puberty and had a greater 6-week (P < 0.01) but not 12-week (P =  0.96) pregnancy rate. Enhanced nutrition resulted in a younger age at puberty but had no effect on 12-week pregnancy rate. Dam but not sire breed affected 12-week pregnancy rate.

Associations between residual feed intake and apparent nutrient digestibility, in vitro methane-producing activity, and volatile fatty acid concentrations in growing beef cattle1

The objectives of this study were to examine the relationship between residual feed intake (RFI) and DM and nutrient digestibility, in vitro methane production, and volatile fatty acid (VFA) concentrations in growing beef cattle. Residual feed intake was measured in growing Santa Gertrudis steers (Study 1; n = 57; initial BW = 291.1 ± 33.8 kg) and Brangus heifers (Study 2; n = 468; initial BW = 271.4 ± 26.1 kg) fed a high-roughage-based diet (ME = 2.1 Mcal/kg DM) for 70 d in a Calan-gate feeding barn. Animals were ranked by RFI based on performance and feed intake measured from day 0 to 70 (Study 1) or day 56 (Study 2) of the trial, and 20 animals with the lowest and highest RFI were identified for subsequent collections of fecal and feed refusal samples for DM and nutrient digestibility analysis. In Study 2, rumen fluid and feces were collected for in vitro methane-producing activity (MPA) and VFA analysis in trials 2, 3, and 4. Residual feed intake classification did not affect BW or BW gain (P > 0.05), but low-RFI steers and heifers both consumed 19% less (P < 0.01) DMI compared with high-RFI animals. Steers with low RFI tended (P < 0.1) to have higher DM digestibility (DMD) compared with high-RFI steers (70.3 vs. 66.5 ± 1.6% DM). Heifers with low RFI had 4% higher DMD (76.3 vs. 73.3 ± 1.0% DM) and 4 to 5% higher (P < 0.01) CP, NDF, and ADF digestibility compared with heifers with high RFI. Low-RFI heifers emitted 14% less (P < 0.01) methane (% GE intake; GEI) calculated according to Blaxter and Clapperton (1965) as modified by Wilkerson et al. (1995), and tended (P = 0.09) to have a higher rumen acetate:propionate ratio than heifers with high RFI (GEI = 5.58 vs. 6.51 ± 0.08%; A:P ratio = 5.02 vs. 4.82 ± 0.14%). Stepwise regression analysis revealed that apparent nutrient digestibilities (DMD and NDF digestibility) for Study 1 and Study 2 accounted for an additional 8 and 6%, respectively, of the variation in intake unaccounted for by ADG and mid-test BW0.75. When DMD, NDF digestibility, and total ruminal VFA were added to the base model for Study 2, trials 2, 3, and 4, the R2 increased from 0.33 to 0.47, explaining an additional 15% of the variation in DMI unrelated to growth and body size. On the basis of the results of these studies, differences in observed phenotypic RFI in growing beef animals may be a result of inter-animal variation in apparent nutrient digestibility and ruminal VFA concentrations.

The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency

Background

Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted breeding programmes. Cattle have been shown to re-rank in terms of RFI across diets and age, while also RFI varies by breed. Therefore, we used RNA-Seq technology to investigate the hepatic transcriptome of RFI-divergent Charolais (CH) and Holstein-Friesian (HF) steers across three dietary phases to identify genes and biological pathways associated with RFI regardless of diet or breed.

Results

Residual feed intake was measured during a high-concentrate phase, a zero-grazed grass phase and a final high-concentrate phase. In total, 322 and 33 differentially expressed genes (DEGs) were identified across all diets for CH and HF steers, respectively. Three genes, GADD45G, HP and MID1IP1, were differentially expressed in CH when both the high-concentrate zero-grazed grass diet were offered. Two canonical pathways were enriched across all diets for CH steers. These canonical pathways were related to immune function.

Conclusions

The absence of common differentially expressed genes across all dietary phases and breeds in this study supports previous reports of the re-ranking of animals in terms of RFI when offered differing diets over their lifetime. However, we have identified biological processes such as the immune response and lipid metabolism as potentially associated with RFI divergence emphasising the previously reported roles of these biological processes with respect to RFI.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5906-8) contains supplementary material, which is available to authorized users.

Hot topic: Selecting cattle for low residual feed intake did not affect daily methane production but increased methane yield

Reducing enteric methane (CH₄) production and improving feed conversion efficiency of dairy cows is of high importance. Residual feed intake (RFI) is one measure of feed efficiency, with low RFI animals being more efficient in feed conversion. Enteric CH₄ is an important source of digestible energy loss in ruminants and, because research in beef cattle has reported a positive relationship between RFI and daily CH₄ production, we hypothesized that low RFI dairy heifers, which are more feed efficient, would produce less CH₄/d. We measured the daily methane production (g of CH₄/d), methane yield [g of CH₄/kg of dry matter intake (DMI)], and CH₄ per kilogram of body weight (BW) gain for 56 heifers (20-22 mo old) in a 2 × 2 factorial arrangement: factors included 2 breeds (Holstein-Friesian and Jersey; n = 28/breed), with equal numbers of animals previously determined as being either high [+2.0 kg of dry matter (DM)/d] or low RFI (-2.1 kg of DM/d; n = 28/RFI category). All heifers were commingled and offered unrestricted access to the same diet of dried alfalfa cubes. Between RFI categories, heifers did not differ in BW or BW gain but low RFI heifers had 9.3 and 10.6% lower DMI and DMI/kg of BW, respectively, than high RFI heifers. Similarly, RFI category did not affect CH₄/d or CH₄/kg of BWg, but CH₄/kg of DMI was higher in low RFI heifers because of their lower DMI. These results might reflect more complete digestion of ingested feed in the more efficient, low RFI heifers, consistent with previous reports of greater apparent digestibility of organic matter. Holstein-Friesian heifers were heavier and consumed more total DM than Jersey heifers, but breed did not affect DMI/kg of BW or BWg. Jersey heifers produced less CH₄/d, but not CH₄/kg of DMI or CH₄/kg of BWg. We detected no interaction between breed and RFI category in any of the variables measured. In conclusion, differences in RFI in dairy heifers did not affect daily CH₄ production (g/d); however, low RFI heifers had a greater CH₄ yield (g/kg of DMI) on a high forage diet.

Genome-wide association identifies methane production level relation to genetic control of digestive tract development in dairy cows

The global temperatures are increasing. This increase is partly due to methane (CH4) production from ruminants, including dairy cattle. Recent studies on dairy cattle have revealed the existence of a heritable variation in CH4 production that enables mitigation strategies based on selective breeding. We have exploited the available heritable variation to study the genetic architecture of CH4 production and detected genomic regions affecting CH4 production. Although the detected regions explained only a small proportion of the heritable variance, we showed that potential QTL regions affecting CH4 production were located within QTLs related to feed efficiency, milk-related traits, body size and health status. Five candidate genes were found: CYP51A1 on BTA 4, PPP1R16B on BTA 13, and NTHL1, TSC2, and PKD1 on BTA 25. These candidate genes were involved in a number of metabolic processes that are possibly related to CH4 production. One of the most promising candidate genes (PKD1) was related to the development of the digestive tract. The results indicate that CH4 production is a highly polygenic trait.

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10^-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.

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

Background

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

Results

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

Conclusion

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

Electronic supplementary material

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

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

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

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

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

Inhibition of Rumen Methanogenesis and Ruminant Productivity: A Meta-Analysis

Methane (CH₄) formed in the rumen and released to the atmosphere constitutes an energy inefficiency to ruminant production. Redirecting energy in CH₄ to fermentation products with a nutritional value to the host animal could increase ruminant productivity and stimulate the adoption of CH₄-suppressing strategies. The hypothesis of this research was that inhibiting CH₄ formation in the rumen is associated with greater ruminant productivity. The primary objective of this meta-analysis was to evaluate how inhibiting rumen methanogenesis relates with the efficiencies of milk production and growth and fattening. A systematic review of peer-reviewed studies in which rumen methanogenesis was inhibited with chemical compounds was conducted. Experiments were clustered based on research center, year of publication, experimental design, feeding regime, type of animal, production response, inhibitor of CH₄ production, and method of CH₄ measurement. Response variables were regressed against the random experiment effect nested in its cluster, the random effect of the cluster, the linear and quadratic effects of CH₄ production, and the random interaction between CH₄ production and the experiment nested in the cluster. When applicable, responses were adjusted by intake of different nutrients included as regressors. Inhibiting rumen methanogenesis tended to associate positively with milk production efficiency, although the relationship was influenced by individual experiments. Likewise, a positive relationship between methanogenesis inhibition and growth and fattening efficiency depended on the inclusion and weighting of individual experiments. Inhibiting rumen methanogenesis negatively associated with dry matter intake. Interpretation of the effects of inhibiting methanogenesis on productivity is limited by the availability of experiments simultaneously reporting energy losses in feces, H₂, urine and heat production, as well as net energy partition. It is concluded that inhibiting rumen methanogenesis has not consistently translated into greater animal productivity, and more animal performance experiments are necessary to better characterize the relationships between animal productivity and methanogenesis inhibition in the rumen. A more complete understanding of changes in the flows of nutrients caused by inhibiting rumen methanogenesis and their effect on intake also seems necessary to effectively re-channel energy gained from CH₄ suppression toward consistent gains in productivity.

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle

The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds.

Beef steers with average dry matter intake and divergent average daily gain have altered gene expression in the jejunum

The objective of this study was to determine the association of differentially expressed genes (DEG) in the jejunum of steers with average DMI and high or low ADG. Feed intake and growth were measured in a cohort of 144 commercial Angus steers consuming a finishing diet containing (on a DM basis) 67.8% dry-rolled corn, 20% wet distillers grains with solubles, 8% alfalfa hay, and 4.2% vitamin/mineral supplement. From the cohort, a subset of steers with DMI within ±0.32 SD of the mean for DMI and the greatest (high) and least (low) ADG were chosen for slaughter and jejunum mucosa collection ( = 8 for each group). Dry matter intake (10.1 ± 0.05 kg/d) was not different ( = 0.41) but ADG was greater in the high-gain group (2.17 and 1.72 ± 0.02 kg/d for the high- and low-ADG groups, respectively; < 0.01). A total of 13,747 genes were found to be expressed in the jejunum, of which 64 genes were differentially expressed between the 2 groups (corrected < 0.05). Ten of the DEG were upregulated in the low-ADG group and 54 were upregulated in the high-ADG group. Gene ontology analysis determined that 24 biological process terms were overrepresented ( < 0.05), including digestion, drug and xenobiotic metabolism, and carbohydrate metabolism. Additionally, 89 molecular function terms were enriched ( < 0.05), including metallopeptidase activity, transporter activity, steroid hydrolase activity, glutathione transferase activity, and chemokine receptor binding. Metabolic pathways (28 pathways) impacted by the DEG ( < 0.05) included drug and xenobiotic metabolism by cytochrome P450, carbohydrate digestion and absorption, vitamin digestion and absorption, galactose metabolism, and linoleic acid metabolism. Results from this experiment indicate that cattle with average DMI and greater ADG likely have a greater capacity to handle foreign substances (xenobiotics). It is also possible that cattle with a greater ADG have a greater potential to digest and absorb nutrients in the small intestine.

Enteric methane emissions from low- and high-residual feed intake beef heifers measured using GreenFeed and respiration chamber techniques

The objectives of this study were to evaluate the relationship between residual feed intake (RFI; g/d) and enteric methane (CH) production (g/kg DM) and to compare CH and carbon dioxide (CO) emissions measured using respiration chambers (RC) and the GreenFeed emission monitoring (GEM) system (C-Lock Inc., Rapid City, SD). A total of 98 crossbred replacement heifers were group housed in 2 pens and fed barley silage ad libitum and their individual feed intakes were recorded by 16 automated feeding bunks (GrowSafe, Airdrie, AB, Canada) for a period of 72 d to determine their phenotypic RFI. Heifers were ranked on the basis of phenotypic RFI, and 16 heifers (8 with low RFI and 8 with high RFI) were randomly selected for enteric CH and CO emissions measurement. Enteric CH and CO emissions of individual animals were measured over two 25-d periods using RC (2 d/period) and GEM systems (all days when not in chambers). During gas measurements metabolic BW tended to be greater ( ≤ 0.09) for high-RFI heifers but ADG tended ( = 0.09) to be greater for low-RFI heifers. As expected, high-RFI heifers consumed 6.9% more feed ( = 0.03) compared to their more efficient counterparts (7.1 vs. 6.6 kg DM/d). Average CH emissions were 202 and 222 g/d ( = 0.02) with the GEM system and 156 and 164 g/d ( = 0.40) with RC for the low- and high-RFI heifers, respectively. When adjusted for feed intake, CH yield (g/kg DMI) was similar for high- and low-RFI heifers (GEM: 27.7 and 28.5, = 0.25; RC: 26.5 and 26.5, = 0.99). However, CH yield differed between the 2 measurement techniques only for the high-RFI group ( = 0.01). Estimates of CO yield (g/kg DMI) also differed between the 2 techniques ( ≤ 0.03). Our study found that high- and low-efficiency cattle produce similar CH yield but different daily CH emissions. The 2 measurement techniques differ in estimating CH and CO emissions, partially because of differences in conditions (lower feed intakes of cattle while in chambers, fewer days measured in chambers) during measurement. We conclude that when intake of animals is known, the GEM system offers a robust and accurate means of estimating CH emissions from animals under field conditions.

Global beef cattle methane emissions: yield prediction by cluster and meta-analyses

Methane yield values (MY; g methane/kg dry-matter intake) in beef cattle reported in the global literature (expanded MitiGate database of methane-mitigation studies) were analysed by cluster and meta-analyses. The Ward and k means cluster analyses included accounting for the categorical effects of methane measurement method, cattle breed type, country or region of study, age and sex of cattle, and proportion of grain in the diet and the standardised continuous variables of number of animals, liveweight and MY. After removal of data from outlier studies, meta-analyses were conducted on subsets of data to produce prediction equations for MY. Removing outliers with absolute studentised residual values of >1, followed by meta-analysis of data accounting for categorical effects, is recommended as a method for predicting MY. The large differences among some countries in MY values were significant but difficult to interpret. On the basis of the datasets available, a single, global MY or percentage of gross energy in feed converted to methane (Ym) value is not appropriate for use in Intergovernmental Panel on Climate Change (IPCC) greenhouse accounting methods around the world. Therefore, ideally country-specific MY values should be used in each country’s accounts (i.e. an IPCC Tier 2 or 3 approach) from data generated within that country.

Feed efficiency and enteric methane production of Nellore cattle in the feedlot and on pasture

The objective of the present study was to assess the relationship between residual feed intake (RFI) evaluated in a feedlot-performance test and on pasture, and to determine the effect of feedlot RFI classification on enteric methane (CH4) production in the feedlot and on pasture. Seventy-three animals (25 with a low RFI, 24 with a medium RFI and 24 with a high RFI) classified in a feedlot performance test were subjected to performance testing on Brachiaria brizantha cv. Marandu pasture. Enteric CH4 was measured in a sample of these animals (n = 47, with high and low RFI) by the sulfur hexafluoride tracer-gas technique after the feedlot-performance test and during the performance test on pasture. In the feedlot-performance test, dry-matter intake (DMI) of low-RFI animals was 9.4% and 19.7% lower (P < 0.05) than that of medium- and high-RFI animals respectively. However, there was no difference in DMI and, consequently, in RFI on pasture among animals classified as low, medium and high RFI. Accordingly, there is evidence of re-ranking of animals for RFI performance tested in the feedlot after weaning and, subsequently, on pasture. During the period of enteric CH4 measurement in the feedlot and on pasture, the DMI, neutral detergent-fibre intake and gross-energy intake of low-RFI animals were lower than those of high-RFI animals, and low-RFI animals exhibited greater DM and neutral detergent fibre digestibility only in the feedlot. Enteric CH4 production did not differ between low- and high-RFI animals either in the feedlot (101 and 107 g CH4/day) or on pasture (101 and 95.9 g CH4/day). A significant difference in CH4 yield (CH4/kg DMI) was observed on pasture between animals with low and high RFI (17.6 and 13.7 g CH4/kg DMI respectively). The results did not support the hypothesis that an increase in feed efficiency, evaluated in growing animals in feedlot-performance tests, decreases enteric CH4 production (g/day) proportionally to the lower DMI.

Associations of rumen parameters with feed efficiency and sampling routine in beef cattle

Characterizing ruminal parameters in the context of sampling routine and feed efficiency is fundamental to understand the efficiency of feed utilization in the bovine. Therefore, we evaluated microbial and volatile fatty acid (VFA) profiles, rumen papillae epithelial and stratum corneum thickness and rumen pH (RpH) and temperature (RT) in feedlot cattle. In all, 48 cattle (32 steers plus 16 bulls), fed a high moisture corn and haylage-based ration, underwent a productive performance test to determine residual feed intake (RFI) using feed intake, growth, BW and composition traits. Rumen fluid was collected, then RpH and RT logger were inserted 5.5±1 days before slaughter. At slaughter, the logger was recovered and rumen fluid and rumen tissue were sampled. The relative daily time spent in specific RpH and RT ranges were determined. Polynomial regression analysis was used to characterize RpH and RT circadian patterns. Animals were divided into efficient and inefficient groups based on RFI to compare productive performance and ruminal parameters. Efficient animals consumed 1.8 kg/day less dry matter than inefficient cattle (P⩽0.05) while achieving the same productive performance (P⩾0.10). Ruminal bacteria population was higher (P⩽0.05) (7.6×1011 v. 4.3×1011 copy number of 16S rRNA gene/ml rumen fluid) and methanogen population was lower (P⩽0.05) (2.3×109 v. 4.9×109 copy number of 16S rRNA gene/ml rumen fluid) in efficient compared with inefficient cattle at slaughter with no differences (P⩾0.10) between samples collected on-farm. No differences (P⩾0.10) in rumen fluid VFA were also observed between feed efficiency groups either on-farm or at slaughter. However, increased (P⩽0.05) acetate, and decreased (P⩽0.05) propionate, butyrate, valerate and caproate concentrations were observed at slaughter compared with on-farm. Efficient had increased (P⩽0.05) rumen epithelium thickness (136 v. 126 µm) compared with inefficient cattle. Efficient animals also spent 318% and 93.2% more time (P⩽0.05) in acidotic (4.14% v. 1.30%) (pH⩽5.6) and optimal (5.6<pH<6.0) (8.53% v. 4.42%) RpH range compared with inefficient cattle. The circadian patterns revealed lower (P⩽0.05) RpH and no differences (P⩾0.10) in RT pre-, during, and post-prandial periods in efficient compared with inefficient cattle. In essence, superior feed efficiency in cattle seems linked to rumen features consistent with improved efficiency of feed utilization. Microbial abundance, rumen epithelial histomorphology, and RpH, may serve as indicators for feed efficiency in cattle. The divergences of assessments made on-farm and at slaughter should be considered in the development of proxies for feed efficiency.

Buffalo heifers selected for lower residual feed intake have lower feed intake, better dietary nitrogen utilisation and reduced enteric methane production

This study was conducted to evaluate the utilisation of the residual feed intake (RFI) as a feed efficiency selection tool and its relationship with methane emissions. Eighteen Murrah buffalo (Bubalus bubalis) heifers were fed ad libitum with total mixed ration (TMR) for 120 days. Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid-test metabolic body size (MBW^0.75 ), heifers were assigned into low and high RFI groups. The RFI varied from -0.09 to +0.12 kg DM/day with average RFI of -0.05 and 0.05 kg DM/day in low and high RFI heifers respectively. Low RFI heifers ate 11.6% less DM each day, yet average daily gain (ADG) and feed utilisation were comparable among low and high RFI groups. Low RFI heifers required significantly (p < .05) less metabolizable energy for maintenance (MEm) compared to high RFI heifers. Apparent nutrient digestibility showed non-significant difference (p > .05) among low and high RFI groups. Although the nitrogen balance was similar among heifers of low and high RFI groups, nitrogen metabolism was significantly higher (p > .05) in high RFI heifers. Comparison of data from heifers exhibiting the low (n = 9) and high (n = 9) RFI showed that the low RFI heifers have lower enteric methane production and methane losses than high RFI heifers. In conclusion, results of this study revealed that selection of more efficient buffalo heifers has multiple benefits, such as decreased feed intake and less emission of methane.

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

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

Stress and immunological response of heifers divergently ranked for residual feed intake following an adrenocorticotropic hormone challenge

BACKGROUND

When an animal is exposed to a stressor, metabolic rate, energy consumption and utilisation increase primarily through activation of the hypothalamic-pituitary-adrenal (HPA) axis. Changes to partitioning of energy by an animal are likely to influence the efficiency with which it is utilised. Therefore, this study aimed to determine the physiological stress response to an exogenous adrenocorticotropic hormone (ACTH) challenge in beef heifers divergently ranked on phenotypic residual feed intake (RFI).

RESULTS

Data were collected on 34 Simmental weaning beef heifers the progeny of a well characterized and divergently bred RFI suckler beef herd. Residual feed intake was determined on each animal during the post-weaning stage over a 91-day feed intake measurement period during which they were individually offered adlibitum grass silage and 2 kg of concentrate per head once daily. The 12 highest [0.34 kg DM/d] and 12 lowest [-0.48 kg DM/d] ranking animals on RFI were selected for use in this study. For the physiological stress challenge heifers (mean age 605 ± 13 d; mean BW 518 ± 31.4 kg) were fitted aseptically with indwelling jugular catheters to facilitate intensive blood collection. The response of the adrenal cortex to a standardised dose of ACTH (1.98 IU/kg metabolic BW^0.75) was examined. Serial blood samples were analysed for plasma cortisol, ACTH and haematology variables. Heifers differing in RFI did not differ (P = 0.59) in ACTH concentrations. Concentration of ACTH peaked (P < 0.001) in both RFI groups at 20 min post-ACTH administration, following which concentration declined to baseline levels by 150 min. Similarly, cortisol systemic profile peaked at 60 min and concentrations remained continuously elevated for 150 min. A RFI × time interaction was detected for cortisol concentrations (P = 0.06) with high RFI heifers had a greater cortisol response than Low RFI from 40 min to 150 min relative to ACTH administration. Cortisol response was positively associated with RFI status (r = 0.32; P < 0.01). No effect of RFI was evident for neutrophil, lymphocytes, monocyte, eosinophils and basophil count. Plasma red blood cell number (6.07 vs. 6.23; P = 0.02) and hematocrit percentage (23.2 vs. 24.5; P = 0.02) were greater for low than high RFI animals.

CONCLUSIONS

Evidence is provided that feed efficiency is associated with HPA axis function and susceptibility to stress, and responsiveness of the HPA axis is likely to contribute to appreciable variation in the efficiency feed utilisation of cattle.

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

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

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine ruminal epithelium

Compensatory growth (CG) is utilised worldwide in beef production systems as a management approach to reduce feed costs. However the underlying biology regulating the expression of CG remains to be fully elucidated. The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced CG on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n = 60) were assigned to one of two groups: restricted feed allowance (RES; n = 30) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n = 30). At the end of each period, 15 animals from each treatment were slaughtered and rumen papillae harvested. mRNA was isolated from all papillae samples collected. cDNA libraries were then prepared and sequenced. Resultant reads were subsequently analysed bioinformatically and differentially expressed genes (DEGs) are defined as having a Benjamini-Hochberg P value of <0.05. During re-alimentation in Period 2, RES animals displayed CG, growing at 1.8 times the rate of their ADLIB contemporary animals in Period 2 (P < 0.001). At the end of Period 1, 64 DEGs were identified between RES and ADLIB, with only one DEG identified at the end of Period 2. When analysed within RES treatment (RES, Period 2 v Period 1), 411 DEGs were evident. Genes identified as differentially expressed in response to both dietary restriction and subsequent CG included those involved in processes such as cellular interactions and transport, protein folding and gene expression, as well as immune response. This study provides an insight into the molecular mechanisms underlying the expression of CG in rumen papillae of cattle; however the results suggest that the role of the ruminal epithelium in supporting overall animal CG may have declined by day 55 of re-alimentation.

Digestion and metabolism of low and high residual feed intake Nellore bulls

Understanding the reasons why animals of similar performances have different feed requirements is important to increase profits for cattle producers and to decrease the environmental footprint of beef cattle production. This study was carried out aiming to identify the associations between residual feed intake (RFI) and animal performance, nutrient digestibility, and blood metabolites related to energy balance of young Nellore bulls during the finishing period. Animals previously classified as low (n = 13) and high RFI (n = 12), with average initial body weight of 398 kg and age of 503 days were used. Cattle were fed a high energy diet and were slaughtered when rib fat thickness measured by ultrasound between the 12th and 13th ribs reached the minimum of 4 mm. A completely randomized design was adopted, being data analyzed with a mixed model that included the random effect of slaughter group, the fixed effect of RFI class, and linear effect of the covariate feedlot time. No differences were found (p > 0.10) between RFI classes for performance, dry matter, and nutrients intake. However, dry (p = 0.0911) and organic matter (p = 0.0876) digestibility tended to be lower, and digestibility of neutral detergent fiber corrected for ash and protein (p = 0.0017), and total digestible nutrients (p = 0.0657) were lower for high RFI animals, indicating lesser capacity of food utilization. Difference between low and high RFI animals was also found for blood cortisol at the end of the trial (p = 0.0044), having low RFI animals lower cortisol concentrations. Differences in the ability to digest food can affect the efficiency of transforming feed into meat by Nellore cattle.

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

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

Examination of the molecular control of ruminal epithelial function in response to dietary restriction and subsequent compensatory growth in cattle

BACKGROUND

The objective of this study was to investigate the effect of dietary restriction and subsequent compensatory growth on the relative expression of genes involved in volatile fatty acid transport, metabolism and cell proliferation in ruminal epithelial tissue of beef cattle. Sixty Holstein Friesian bulls (mean liveweight 370 ± 35 kg; mean age 479 ± 15 d) were assigned to one of two groups: (i) restricted feed allowance (RES; n = 30) for 125 d (Period 1) followed by ad libitum access to feed for 55 d (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n = 30). Target growth rate for RES was 0.6 kg/d during Period 1. At the end of each dietary period, 15 animals from each treatment group were slaughtered and ruminal epithelial tissue and liquid digesta harvested from the ventral sac of the rumen. Real-time qPCR was used to quantify mRNA transcripts of 26 genes associated with ruminal epithelial function. Volatile fatty acid analysis of rumen fluid from individual animals was conducted using gas chromatography.

RESULTS

Diet × period interactions were evident for genes involved in ketogenesis (BDH2, P = 0.017), pyruvate metabolism (LDHa, P = 0.048; PDHA1, P = 0.015) and cellular transport and structure (DSG1, P = 0.019; CACT, P = 0.027). Ruminal concentrations of propionic acid (P = 0.018) and n-valeric acid (P = 0.029) were lower in RES animals, compared with ADLIB, throughout the experiment. There was also a strong tendency (P = 0.064) toward a diet × period interaction for n-butyric with higher concentrations in RES animals, compared with ADLIB, during Period 1.

CONCLUSIONS

These data suggest that following nutrient restriction, the structural integrity of the rumen wall is compromised and there is upregulation of genes involved in the production of ketone bodies and breakdown of pyruvate for cellular energy. These results provide an insight into the potential molecular mechanisms regulating ruminal epithelial absorptive metabolism and growth following nutrient restriction and subsequent compensatory growth.

Effects of chitosan on nutrient digestibility, methane emissions, and in vitro fermentation in beef cattle

Chitosan was evaluated as a feed additive to mitigate in vivo CH4 emissions in beef cattle. Twenty-four crossbred heifers (BW = 318 ± 35 kg) were used in a randomized block design replicated in 2 periods. The design included a 2 × 3 factorial arrangement of treatments, which included diet (high concentrate [HC] or low concentrate [LC]) and 0.0, 0.5, or 1.0% of chitosan inclusion (DM basis). Diets were offered ad libitum and individual intake was recorded. An in vitro experiment to analyze chitosan’s effect on fermentation parameters and gas production kinetics was performed. A diet effect (P < 0.01) was observed for CH4 emissions expressed as grams/day, grams/kilogram of BW0.75, and grams/kilogram of DMI. Heifers consuming the LC diet produced 130 g of CH4/d vs. 45 g of CH4/d in those consuming the HC diet. Incubation fluid pH increased linearly (P < 0.05) when chitosan was included in HC substrates. In vitro CH4 production was not affected (P > 0.10) by chitosan in HC substrate; however, when incubated with the LC substrate, CH4 production increased quadratically (P < 0.01) as chitosan inclusion increased. A digestibility marker × diet interaction occurred (P < 0.05) for DM, OM, CP, NDF, and ADF digestibility. Diet × chitosan interactions (P < 0.05) occurred for DM, OM, NDF, and ADF digestibility when Cr2O3 was used. When TiO2 was used, diet × chitosan interactions (P < 0.05) were observed for NDF and ADF. However, using indigestible NDF as an internal marker, DM and OM digestibility were improved (P < 0.05) by 21 and 19%, respectively, when chitosan was included in LC diets. In conclusion, feeding up to 1% of chitosan (DM basis) to heifers consuming a LC diet increased apparent total tract digestibility of nutrients. Enteric CH4 emissions were not affected by chitosan feeding, regardless of type of diet, and heifers consuming a 36% concentrate diet produced 2.6 times more methane per day than those consuming an 85% concentrate diet.

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

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

Is there a relationship between genetic merit and enteric methane emission rate of lactating Holstein-Friesian dairy cows?

The present study was undertaken to examine the effect of cow genetic merit on enteric methane (CH4) emission rate. The study used a data set from 32 respiration calorimeter studies undertaken at this Institute between 1992 and 2010, with all studies involving lactating Holstein-Friesian dairy cows. Cow genetic merit was defined as either profit index (PIN) or profitable lifetime index (PLI), with these two United Kingdom genetic indexes expressing the expected improvement in profit associated with an individual cow, compared with the population average. While PIN is based solely on milk production, PLI includes milk production and a number of other functional traits including health, fertility and longevity. The data set had a large range in PIN (n=736 records, -£30 to +£63) and PLI (n=548 records, -£131 to +£184), days in milk (18 to 354), energy corrected milk yield (16.0 to 45.6 kg/day) and CH(4) emission (138 to 598 g/day). The effect of cow genetic merit (PIN or PLI) was evaluated using ANOVA and linear mixed modelling techniques after removing the effects of a number of animal and diet factors. The ANOVA was undertaken by dividing each data set of PIN and PLI into three sub-groups (PIN:£15, PLI:£67) with these being categorised as low, medium and high genetic merit. Within the PIN and PLI data sets there was no significant differences among the three sub-groups in terms of CH(4) emission per kg feed intake or per kg energy corrected milk yield, or CH(4) energy (CH(4)-E) output as a proportion of energy intake. Linear regression using the whole PIN and PLI data sets also demonstrated that there was no significant relationship between either PIN or PLI, and CH(4) emission per kg of feed intake or CH(4)-E output as a proportion of energy intake. These results indicate that cow genetic merit (PIN or PLI) has little effect on enteric CH(4) emissions as a proportion of feed intake. Instead enteric CH(4) production may mainly relate to total feed intake and dietary nutrient composition.

Genetic parameters for predicted methane production and laser methane detector measurements

Enteric ruminant methane is the most important greenhouse gas emitted from the pastoral agricultural systems. Genetic improvement of livestock provides a cumulative and permanent impact on performance, and using high-density SNP panels can increase the speed of improvement for most traits. In this study, a data set of 1,726 dairy cows, collected since 1990, was used to calculate a predicted methane emission (PME) trait from feed and energy intake and requirements based on milk yield, live weight, feed intake, and condition score data. Repeated measurements from laser methane detector (LMD) data were also available from 57 cows. The estimated heritabilities for PME, milk yield, DMI, live weight, condition score, and LMD data were 0.13, 0.25, 0.11, 0.92, 0.38, and 0.05, respectively. There was a high genetic correlation between DMI and PME. No SNP reached the Bonferroni significance threshold for the PME traits. One SNP was within the 3 best SNP for PME at wk 10, 20, 30, and 40. Genomic prediction accuracies between dependent variable and molecular breeding value ranged between 0.26 and 0.30. These results are encouraging; however, more work is required before a PME trait can be implemented in a breeding program.

Genetic and environmental variation in methane emissions of sheep at pasture

A total of 2,600 methane (CH4) and 1,847 CO2 measurements of sheep housed for 1 h in portable accumulation chambers (PAC) were recorded at 5 sites from the Australian Sheep CRC Information Nucleus, which was set up to test leading young industry sires for an extensive range of current and novel production traits. The final validated dataset had 2,455 methane records from 2,279 animals, which were the progeny of 187 sires and 1,653 dams with 7,690 animals in the pedigree file. The protocol involved rounding up animals from pasture into a holding paddock before the first measurement on each day and then measuring in groups of up to 16 sheep over the course of the day. Methane emissions declined linearly (with different slopes for each site) with time since the sheep were drafted into the holding area. After log transformation, estimated repeatability (rpt) and heritability (h(2)) of liveweight-adjusted CH4 emissions averaged 25% and 11.7%, respectively, for a single 1-h measurement. Sire × site interactions were small and nonsignificant. Correlations between EBV for methane emissions and Sheep Genetics Australia EBV for production traits were used as approximations to genetic correlations. Apart from small positive correlations with weaning and yearling weights (r = 0.21-0.25, P < 0.05), there were no significant relationships between production trait and methane EBV (calculated from a model adjusting for liveweight by fitting separate slopes for each site). To improve accuracy, future protocols should use the mean of 2 (rpt = 39%, h(2) = 18.6%) or 3 (rpt = 48%, h(2) = 23.2%) PAC measurements. Repeat tests under different pasture conditions and time of year should also be considered, as well as protocols measuring animals directly off pasture instead of rounding them up in the morning. Reducing the time in the PAC from 1 h to 40 min would have a relatively small effect on overall accuracy and partly offset the additional time needed for more tests per animal. Field testing in PAC has the potential to provide accurate comparisons of animal and site methane emissions, with potentially lower cost/increased accuracy compared to alternatives such as SF6 tracers or open path lasers. If similar results are obtained from tests with different protocols/seasonal conditions, use of PAC measurements in a multitrait selection index with production traits could potentially reduce methane emissions from Australian sheep for the same production level.

Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets

Background

Methane (CH₄) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility.

Results

Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P < 0.05) by diet type, with greater abundance observed while animals were offered the LF compared to the HF diet.

Conclusions

These findings suggest that differences in abundance of specific rumen methanogen species may not contribute to variation in CH₄ emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species.

Effects of phenotypic residual feed intake on response to a glucose tolerance test and gene expression in the insulin signaling pathway in longissimus dorsi in beef cattle

The objectives of this study were to determine the insulinogenic response to an intravenous glucose tolerance test (GTT) and examine gene expression profiles in the insulin signaling pathway (ISP) in beef animals of differing phenotypic residual feed intake (RFI). Two experiments were conducted. In Exp. 1, a total of 39 Simmental heifers, over 2 yr (yr 1, n = 22, and yr 2, n = 17; mean initial BW = 472 kg [SD = 52.4 kg]), were offered grass silage ad libitum for 104 d. Heifers were subjected to a GTT on d 8 and 65 of the RFI measurement period in yr 1 and 2, respectively. Concentrations of plasma glucose and insulin were measured at -45, -30, -15, 0, 5, 10, 15, 20, 30, 45, 60, 90, 120, 150, and 180 min relative to glucose infusion (0 min). In Exp. 2, a total of 67 Simmental bulls, over 3 yr (yr 1, n = 20; yr 2, n = 33; and yr 3, n = 14; mean initial BW = 431 kg [SD = 63.7 kg]), were offered concentrates ad libitum for 105 d. Biopsies of LM were harvested during the RFI measurement period (yr 1, d 49 and 91; yr 2, d 52 and 92; and yr 3, d 50 and 92). The residuals of the regression of DMI on ADG, midtest metabolic BW (BW(0.75)), and the fixed effect of year, using all animals, were used to compute individual RFI coefficients. Animals were ranked on RFI and assigned to high (inefficient), medium, or low groupings by dividing them into terciles, resulting in 13 heifers and 22, 23, and 22 bulls in their respective RFI groups. In Exp. 1, data from 13 heifers from each of the high- and low-RFI groups, and in Exp. 2, data from the 15 highest and 15 lowest ranking bulls on RFI are reported. In Exp. 1, glucose and insulin response and area under the response curve for glucose and insulin were similar (P > 0.05) between high- and low-RFI heifers. In Exp. 2, no differences (P > 0.05) were found for mRNA expression of 22 genes of the ISP in muscle tissue; however, expression of the transcription factor SREBP1c tended to be positively correlated (r = 0.25, P = 0.07) with RFI. Expression of GLUT4, INPPL1, and SHC increased (P < 0.05) over time, while there was no effect of sample time for any other genes measured. Collectively, these results suggest that insulin response, sensitivity, and associated expression of genes in the ISP within muscle tissue are not contributory factors to variation in RFI. However, further examination of target genes of SREBP1c, which is involved in lipogenesis, may explain some of the biochemical processes underlying variation in phenotypic RFI.

Feeding behavior, ruminal fermentation, and performance of pregnant beef cows differing in phenotypic residual feed intake offered grass silage

This study examined the relationship of residual feed intake (RFI) and performance with feeding behavior and ruminal fermentation variables in pregnant beef cows offered a grass silage diet. Individual grass silage DMI (dry matter digestibility = 666 g/kg) was recorded on 47 gestating (mean gestation d 166, SD = 26 d) Simmental and Simmental × Holstein-Friesian beef cows for a period of 80 d. Cow BW, BCS, skeletal measurements, ultrasonically scanned muscle and fat depth, visual muscular score, ruminal fermentation, blood metabolites, and feeding behavior were measured. Phenotypic RFI was calculated as actual DMI minus expected DMI. Expected DMI was computed for each animal by regressing DMI on conceptus-adjusted mean BW(0.75) and ADG over an 80-d period. Within breed, cows were ranked by RFI into low (efficient), medium, or high groups. Overall mean (SD) values for DMI (kg/d), RFI, initial conceptus-adjusted BW, and conceptus-adjusted ADG were 8.41 (1.09) kg/d, 0.01 (0.13) kg/d, 646 (70) kg, and -0.07 (0.32) kg, respectively. High-RFI cows ate 25% and 8% more than low- and medium-RFI cows, respectively. Live weight and ADG were not correlated (P > 0.05), and DMI was positively correlated (r = 0.80; P < 0.001) with RFI. The low- and high-RFI groups had similar (P > 0.05) BW, ADG, BCS, visual muscular scores, skeletal measurements, blood metabolites, calf birth weight, and calving difficulty scores. All ultrasonic fat and muscle depth measurements were similar (P > 0.05) for low- and high-RFI cows except for back fat thickness change, where low-RFI cows gained less fat (P < 0.05) than high-RFI cows. Low-RFI cows had greater pH and lower ammonia concentrations in ruminal fluid compared to their high-RFI contemporaries. Low-RFI cows had fewer (P < 0.001) daily feeding events, but these were of longer (P < 0.001) duration (min·feed event(-1)·d(-1)). Despite this, total daily duration of feeding was shorter (P < 0.001; min/d) for low- compared to high-RFI cows. High-RFI cows had more and a longer total duration of nonfeeding events (P < 0.001) than low-RFI cows. This study showed that compared to cows with high RFI, those with low RFI consumed less feed for similar levels of productivity, spent less time engaged in feeding-behavior-related activities, and differed in ruminal fermentation parameters. Feeding events are a significant (17%) contributory factor to variation in RFI in pregnant beef cows offered grass silage.

Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type

Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that Methanobrevibacter spp. are the dominant methanogens in the rumen, with Methanobrevibacter smithii being the most abundant species. Differences in the abundance of Methanobrevibacter smithii and Methanosphaera stadtmanae genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of Methanobrevibacter smithii genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals.