Relationships between residual feed intake and hepatic mitochondrial function in growing beef cattle

Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks

Growth-retarded yaks are of a high proportion on the Tibetan plateau and reduce the economic income of farmers. Our previous studies discovered a maldevelopment in the ruminal epithelium of growth-retarded yaks, but the molecular mechanisms are still unclear. This study aimed to reveal how the proteomic profile in the ruminal epithelium contributed to the growth retardation of yaks. The proteome of the ruminal epithelium was detected using a high-resolution mass spectrometer. There were 52 proteins significantly differently expressed between the ruminal epithelium of growth-retarded yaks and growth-normal yaks, with 32 downregulated and 20 upregulated in growth-retarded yaks. Functional analysis showed the differently expressed proteins involved in the synthesis and degradation of ketone bodies (p = 0.012), propanoate metabolism (p = 0.018), pyruvate metabolism (p = 0.020), and mineral absorption (p = 0.024). The protein expressions of SLC26A3 and FTH1, enriched in the mineral absorption, were significantly downregulated in growth-retarded yaks. The key enzymes ACAT2 and HMGCS2 enriched in ketone bodies synthesis and key enzyme PCCA enriched in propanoate metabolism had lower protein expressions in the ruminal epithelium of growth-retarded yaks. The ATP concentration and relative mitochondrial DNA copy number in the ruminal epithelium of growth-normal yaks were dramatically higher than those of growth-retarded yaks (p < 0.05). The activities of citrate synthase (CS), the α-ketoglutarate dehydrogenase complex (α-KGDHC), isocitrate dehydrogenase (ICD) in the tricarboxylic acid cycle (TCA), and the mitochondrial respiratory chain complex (MRCC) were significantly decreased in ruminal epithelium of growth-retarded yaks compared to growth-normal yaks (p < 0.05). The mRNA expressions of COQ9, COX4, and LDHA, which are the encoding genes in MRCC I, IV and anaerobic respiration, were also significantly decreased in the ruminal epithelium of growth-retarded yaks (p < 0.05). Correlation analysis revealed that the average daily gain (ADG) was significantly positively correlated to the relative mitochondrial DNA copy number (p < 0.01, r = 0.772) and ATP concentration (p < 0.01, r = 0.728) in the ruminal epithelium, respectively. The ruminal weight was positively correlated to the relative mitochondrial DNA copy number (p < 0.05, r = 0.631) and ATP concentration in ruminal epithelium (p < 0.01, r = 0.957), respectively. The ruminal papillae had a significant positive correlation with ATP concentration in ruminal epithelium (p < 0.01, r = 0.770). These results suggested that growth-retarded yaks had a lower VFA metabolism, ketone bodies synthesis, ion absorption, and ATP synthesis in the ruminal epithelium; it also indicated that the growth retardation of yaks is related to the obstruction of cellular ATP synthesis in rumen epithelial cells.

Peripheral blood mononuclear cell mitochondrial enzyme activity in calves is associated with average daily gain, reproductive outcomes, lactation performance, and survival

Mitochondria are central to metabolism and are the primary energy producers for all biosynthesis. The objective of this study was to determine if the mitochondrial enzyme activity of peripheral blood mononuclear cells in heifers was associated with average daily gain, reproductive outcomes, first-lactation milk production, and survival. Twenty-three Holstein and 23 Jersey heifer calves were enrolled, and blood and body weight data were collected at 1, 2, 8, 36, 52, and 110 wk of age. Respiratory and fecal scores were recorded daily for the first 30 d of life. Milk production data were collected from herd management software through first lactation and health events were tracked to the fourth lactation on surviving animals. Mitochondrial isolation and enzyme activities for citrate synthase, complex I, complex IV, and complex V were determined using kits from Abcam. Data were analyzed using GLM and the Logistic procedure of SAS (version 9.4, SAS Institute Inc.). Multivariate regression analyses were conducted to determine if calf mitochondrial enzymatic activity and covariate health indices (fecal and respiratory scores, number of treatments, hematology) were associated with average daily gain (8, 36, 52, and 110 wk), lactation performance (milk yield, fat yield, solids yield, energy-corrected milk, 305-d mature equivalent, and relative value), and reproduction (age at first service, age at first conception, age at first calving, and number of services). For Holsteins and Jerseys, mitochondrial enzyme activities and health indices were correlated with all average daily gain and milk production outcomes (R2 ≥ 0.63 and R2 ≥ 0.45, respectively). Reproduction outcomes were correlated with body weight gain, mitochondrial function, and red blood cell traits for Holsteins and Jerseys (R2 ≥ 0.47 and R2 ≥ 0.55, respectively). Logistic regression analyses were performed to determine if early-life enzymatic activity affected survival outcomes in the herd. Calves below the median for complex V enzyme activity at 1 wk were more likely to be removed from the herd compared with calves above the median by lactation 1, 2, 3, and 4 (odds ratio = 4.7, 7.7, 7.0, and 6.9, respectively). Calves below the median for the difference in hematocrit from 2 to 1 wk were more likely to be removed from the herd compared with calves above the median by lactation 1, 2, 3, and 4 (odds ratio = 13, 10, 5.2, and 4.7, respectively). These findings suggest that predictions of cow performance could be improved by considering the effect of early-life mitochondrial enzymatic activity and health indices.

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

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

Liver and Muscle Transcriptomes Differ in Mid-Lactation Cows Divergent in Feed Efficiency in the Presence or Absence of Supplemental Rumen-Protected Choline

Improving dairy cow feed efficiency is critical to the sustainability and profitability of dairy production, yet the underlying mechanisms that contribute to individual cow variation in feed efficiency are not fully understood. The objectives of this study were to (1) identify genes and associated pathways that are altered in cows with high- or low-residual feed intake (RFI) using RNA sequencing, and (2) determine if rumen-protected choline supplementation during mid-lactation would influence performance or feed efficiency. Mid-lactation (134 ± 20 days in milk) multiparous Holstein cows were randomly assigned to either supplementation of 0 g/d supplementation (CTL; n = 32) or 30 g/d of a rumen-protected choline product (RPC; 13.2 g choline ion; n = 32; Balchem Corp., New Hampton, NY, USA). Residual feed intake was determined as dry matter intake regressed on milk energy output, days in milk, body weight change, metabolic body weight, and dietary treatment. The 12 cows with the highest RFI (low feed efficient; LE) and 12 cows with the lowest RFI (high feed efficient; HE), balanced by dietary treatment, were selected for blood, liver, and muscle analysis. No differences in production or feed efficiency were detected with RPC supplementation, although albumin was greater and arachidonic acid tended to be greater in RPC cows. Concentrations of β-hydroxybutyrate were greater in HE cows. Between HE and LE, 268 and 315 differentially expressed genes in liver and muscle tissue, respectively, were identified through RNA sequencing. Pathway analysis indicated differences in cell cycling, oxidative stress, and immunity in liver and differences in glucose and fatty acid pathways in muscle. The current work indicates that unique differences in liver and muscle post-absorptive nutrient metabolism contribute to sources of variation in feed efficiency and that differences in amino acid and fatty acid oxidation, cell cycling, and immune function should be further examined.

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.

Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency

The regulatory axis plays a vital role in interpreting the information exchange and interactions among mammal organs. In this study on feed efficiency, it was hypothesized that a rumen-liver-muscle-fat (RLMF) regulatory axis exists and scrutinized the flow of energy along the RLMF axis employing consensus network analysis from a spatial transcriptomic standpoint. Based on enrichment analysis and protein-protein interaction analysis of the consensus network and tissue-specific genes, it was discovered that carbohydrate metabolism, energy metabolism, immune and inflammatory responses were likely to be the biological processes that contribute most to feed efficiency variation on the RLMF regulatory axis. In addition, clusters of genes related to the electron respiratory chain, including ND (2,3,4,4L,5,6), NDUF (A13, A7, S6, B3, B6), COX (1,3), CYTB, UQCR11, ATP (6,8), clusters of genes related to fatty acid metabolism including APO (A1, A2, A4, B, C3), ALB, FG (A, G), as well as clusters of the ribosomal-related gene including RPL (8,18A,18,15,13, P1), the RPS (23,27A,3A,4X), and the PSM (A1-A7, B6, C1, C3, D2-D4, D8 D9, E1) could be the primary effector genes responsible for feed efficiency variation. The findings demonstrate that high feed efficiency cattle, through the synergistic action of the regulatory axis RLMF, may improve the efficiency of biological processes (carbohydrate metabolism, protein ubiquitination, and energy metabolism). Meanwhile, high feed efficiency cattle might enhance the ability to respond to immunity and inflammation, allowing nutrients to be efficiently distributed across these organs associated with digestion and absorption, energy-producing, and energy-storing organs. Elucidating the distribution of nutrients on the RLMF regulatory axis could facilitate an understanding of feed efficiency variation and achieve the study on its molecular regulation.

Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P-value ≤0.08) to be associated with birth weight and weaning weight. There was no association (P-value >0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were -0.30 ± 0.16 with birth weight, -0.31 ± 0.16 with weaning weight, -0.15 ± 0.14 with post-weaning gain, -0.11 ± 0.19 with average daily dry-matter intake, -0.04 ± 0.22 with average daily gain, -0.29 ± 0.13 with mature cow weight, -0.11 ± 0.13 with slaughter weight, -0.14 ± 0.13 with carcass weight, -0.07 ± 0.14 with carcass backfat, 0.14 ± 0.14 with carcass marbling, and -0.06 ± 0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits.

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.

Peripheral blood mononuclear cell mitochondrial enzyme activity is associated with parity and lactation performance in early lactation Holstein dairy cows

Mitochondria are central to metabolism and are the primary energy producers for all biosynthesis, including lactation. The objectives of this study were to determine if high- and low-producing dairy cows exhibit differences in peripheral blood mononuclear cell mitochondrial enzyme activities of citrate synthase, complex I, complex IV, and complex V during early lactation and, thus, to determine whether those differences were related to differences in lactation performance in the dairy cow. Fifty-six Holstein cows were assigned to 1 of 4 groups: (1) primiparous high, (2) primiparous low, (3) multiparous high, or (4) multiparous low. Primiparous and multiparous cows were analyzed separately. Then, cows were divided into high or low production groups for each production parameter [peak milk, average milk, energy-corrected milk (ECM), fat-corrected milk (FCM), milk lactose, milk fat, milk protein, total solids (TS), solids-not-fat, feed efficiency, and somatic cell count (SCC)]. For all data analysis, production parameters are expressed as yields (kg/d) and SCC (10³ cells/mL). High and low production groups were defined by their respective mean production parameters for the 56 cows, with below average cows defined as low and above average cows defined as high. Whole blood samples were collected at one time point, approximately 70 d in milk at 0800 h, and processed for crude mitochondrial extracts from peripheral blood mononuclear cells to determine the activity rates of mitochondrial enzymes. Milk samples were collected 9 times (3 d, 3 times per d) during the week of blood collection and analyzed for major components (fat, protein, lactose, TS, and SCC). Multiparous cows had lower citrate synthase activity than primiparous cows across all production parameters. High-producing cows had greater complex I activity for peak milk, milk yield, ECM, FCM, milk fat, TS, and feed efficiency, and greater complex V activity for ECM, FCM, milk lactose, milk fat, and TS across parities. These findings imply that the most influential respiratory chain enzymes on the level of milk production are those responsible for electron transport chain initialization and ATP production.

Residual Feed Intake in Beef Cattle Is Associated With Differences in Hepatic mRNA Expression of Fatty Acid, Amino Acid, and Mitochondrial Energy Metabolism Genes

We evaluated the mRNA expression of genes involved in hepatic fatty acid, amino acid, and mitochondrial energy metabolism in crossbred beef steers with divergent low and high residual feed intake (RFI). Low-RFI beef steers (n = 8; RFI = - 1.93 kg/d) and high-RFI beef steers (n = 8; RFI = + 2.01kg/d) were selected from a group of 56 growing crossbred beef steers (average BW = 261 ± 18.5 kg) fed a high-forage total mixed ration after a 49-d performance testing period. At the end of the 49-d performance testing period, liver biopsies were collected from the low-RFI and high-RFI beef steers for RNA extraction and cDNA synthesis. The mRNA expression of 84 genes each related to fatty acid metabolism, amino acid metabolism, and mitochondrial energy metabolism were analyzed using pathway-focused PCR-based arrays. The mRNA expression of 8 genes (CRAT, SLC27A5, SLC27A2, ACSBG2, ACADL, ACADSB, ACAA1, and ACAA2) involved fatty acid transport and β-oxidation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI, compared to high-RFI steers. Among those involved in amino acid metabolism, hepatic mRNA expression of a gene encoding for aminoadipate aminotransferase, an enzyme related to lysine degradation, was downregulated (FC = -5.45, FDR = 0.01) in low-RFI steers, whereas those of methionine adenosyltransferase I and aspartate aminotransferase 2, which both link amino acid and lipid metabolism, were upregulated (FC ≥ 2.0, FDR ≤ 0.05). Two mitochondrial energy metabolism genes (UQCRC1 and ATP5G1) involved in ATP synthesis via oxidative phosphorylation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI beef steers, compared to high-RFI beef steers. The results of this study demonstrated that low-RFI beef steers exhibit upregulation of molecular mechanisms related to fatty acid transport, fatty acid β-oxidation, and mitochondrial ATP synthesis, which suggest that low-RFI beef steers have enhanced metabolic capacity to maximize capture of energy and nutrients from feeds consumed.

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging. The purpose of this study was to perform a meta-analysis of the ruminal transcriptome of two unrelated populations of animals to identify genes that are involved in feed efficiency across populations. RNA-seq data from animals with high and low residual feed intake (RFI) from a United States population of cattle (eight high and eight low RFI) and a Canadian population of cattle (nine high and nine low RFI) were analyzed for differences in gene expression. A total of 83 differentially expressed genes were identified. Some of these genes have been previously identified in other feed efficiency studies. These genes included ATP6AP1, BAG6, RHOG, and YPEL3. Differentially expressed genes involved in the Notch signaling pathway and in protein turnover were also identified. This study, combining two unrelated populations of cattle in a meta-analysis, produced several candidate genes for feed efficiency that may be more robust indicators of feed efficiency than those identified from single populations of animals.

Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers

The gastrointestinal tract (GIT) contains complex microbial communities and plays an essential role in the overall health of the host. Previous studies of beef cattle feed efficiency have primarily concentrated on the ruminal microbiota because it plays a key role in energy production and nutrient supply in the host. Although the small intestine is the important site of post-ruminal digestion and absorption of nutrients, only a few studies have explored the relationship between the microbial populations in the small intestine and feed efficiency. Moreover, variations in GIT metabolites contribute to differences in feed efficiency. The objective of this study was to investigate relationships among bacterial populations of duodenum, jejunum, ileum; microbial metabolites; and RFI phenotype of beef cattle. We carried out by using Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC–MS). In the duodenum, the relative abundances of Firmicutes ( p < 0.01), Lachnospiraceae, Ruminococcaceae, Family_XIII, Christensenellaceae, Christensenellaceae_R-7_group ( p < 0.05), and Lachnospiraceae_NK3A20_group ( p < 0.05) were higher in the low residual feed intake (LRFI) group compared with the high residual feed intake (HRFI) group, whereas the HRFI group had higher abundances of Proteobacteria and Acinetobacter ( p < 0.01). In the jejunum, the relative abundances of Lachnospiraceae and Lachnospiraceae_NK3A20_group were higher in the LRFI group ( p < 0.05). In the ileum, the relative abundances of Ruminococcaceae ( p < 0.01), Christensenellaceae, Christensenellaceae_R-7_group, and Ruminococcus_2 were also higher in the LRFI group ( p < 0.05). Moreover, the genera Lachnospiraceae_NK3A20_group, Christensenellaceae_R-7_group, and Ruminococcus_2 were negatively associated with RFI, while the genus Acinetobacter was positively associated with RFI. The metabolomics analysis revealed that the LRFI group significantly improved protein digestion and absorption, as well as glycerophospholipid metabolism in the duodenum, jejunum, ileum. The correlation between intestinal microorganisms and metabolites revealed that some microorganisms play an important role in amino acid metabolism, glycerophospholipid metabolism, nutrient digestion and absorption, and antioxidant enhancement. The present study provides a better understanding of the small intestinal microbiota and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.

Rumen Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers

Feed cost is the greatest expense during cattle production; therefore, reducing it is critical to increasing producer profits. In ruminants, the microbial population is important to nutrient digestion and absorption in the rumen. The objective of this study was to investigate the relationships among rumen bacteria, rumen metabolites, and the residual feed intake (RFI) phenotype of beef cattle. Twelve Angus heifers were selected to be sampled and divided into high RFI (HRFI; n = 6) group and low RFI (LRFI; n = 6) group according to their RFI classification determined during the feedlot-finishing period. After the ruminal liquid samples were collected at slaughter, Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC-MS) were performed to determine their bacterial composition and metabolites, respectively. At the phylum level, the relative abundance of Proteobacteria was higher in the LRFI group than in the HRFI group (P < 0.01). At the family level, the relative abundances of Rikenellaceae (P < 0.01), Ruminococcaceae, Bacteroidales_S24-7_group, and Lachnospiraceae (P < 0.05) were significantly higher in the LRFI group. At the genus level, the relative abundances of Rikenellaceae_RC9_gut_group and Ruminiclostridium_1 were higher in the LRFI group (P < 0.01), as were the relative abundances of norank_f__Bacteroidales_S24-7_group, Lachnospiraceae_ND3007_group, and Lachnospiraceae_NK3A20_group (P < 0.05). Moreover, the genera Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Christensenellaceae_R-7_group, Ruminococcaceae_UCG-010, Lachnospiraceae_ND3007_group, Ruminiclostridium_1, and Lachnospiraceae_NK3A20_group were negatively associated with the RFI; both foundational and key species are associated with feed efficiency phenotype. In addition, rumen metabolomics analysis revealed that the RFI was associated with significantly altered concentrations of rumen metabolites involved in protein digestion and absorption, Linoleic acid metabolism, Lysine degradation, and Fatty acid degradation. Correlation analysis revealed the potential relationships between the significantly differential ruminal metabolites and the genera ruminal bacteria. The present study provides a better understanding of rumen bacteria and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.

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

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

Differences in net fat oxidation, heat production, and liver mitochondrial DNA copy numbers between high and low feed-efficient dairy cows

Improving feed utilization efficiency in dairy cattle could have positive economic and environmental effects that would support the sustainability of the dairy industry. Identifying key differences in metabolism between high and low feed-efficient animals is vital to enhancing feed conversion efficiency. Therefore, our objectives were (1) to determine whether cows grouped by either high or low feed efficiency have measurable differences in net fat and carbohydrate metabolism that account for differences in heat production (HP), and if so, whether these differences also exists under conditions of feed withdrawal when the effect of feeding on HP is minimized, and (2) to determine whether the abundance of mitochondria in the liver can be related to the high or low feed-efficient groups. Ten dairy cows from a herd of 15 (parity = 2) were retrospectively grouped into either a high (H) or a low (L) feed-efficient group (n = 5 per group) based on weekly energy-corrected milk (ECM) divided by dry mater intake (DMI) from wk 4 through 30 of lactation. Livers were biopsied at wk -4, 2, and 12, and blood was sampled weekly from wk -3 to 12 relative to parturition. Blood was subset to be analyzed for the transition period (wk -3 to 3) and from wk 4 to 12. In wk 5.70 ± 0.82 (mean ± SD) postpartum (PP), cows spent 2 d in respiration chambers (RC), in which CO₂, O₂, and CH₄ gases were measured every 6 min for 24 h. Fatty acid oxidation (FOX), carbohydrate oxidation (COX), metabolic respiratory quotient (RQ), and HP were calculated from gas measurements for 23 h. Cows were fed ad libitum (AD-LIB) on d 1 and had feed withdrawn (RES, restricted diet) on d 2. Additional blood samples were taken at the end of the AD-LIB and RES feeding periods in the RC. During wk 4 to 30 PP, H had greater DMI/kg of metabolic body weight (BW^0.75), ECM per kilogram of BW^0.75 yield, and ECM/DMI ratio, compared with L, but a lower body condition score between wk 4 and 12 PP. In the RC period, we detected no differences in BW, DMI, or milk yield between groups. We also detected no significant group or group by feeding period interactions for plasma metabolites except for Revised Quantitative Insulin Sensitivity Check Index, which tended to have a group by feeding period interaction. The H group had lower HP and HP per kilogram of BW^0.75 compared with L. Additionally, H had lower FOX and FOX per kilogram of BW^0.75 compared with L during the AD-LIB period. Methane, CH₄ per kilogram of BW^0.75, and CH₄ per kilogram of milk yield were lower in H compared with L, but, when adjusted for DMI, CH₄/DMI did not differ between groups, nor did HP/DMI. Relative mitochondrial DNA copy numbers in the liver were lower in the L than in the H group. These results suggest that lower feed efficiency in dairy cows may result from fewer mitochondria per liver cell as well as a greater whole-body HP, which likely partially results from higher net fat oxidation.

Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken

Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein-protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens.

Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake

Long noncoding RNAs (LncRNAs), as key regulators, have vital functions in various biological activities. However, in sheep, little has been reported concerning the genetic mechanism of LncRNA regulation of feed efficiency. In the present study, we explored the genome-wide expression of LncRNAs and transcripts of uncertain coding potential (TUCPs) in the livers of sheep with extreme residual feed intake (RFI) using RNA sequencing. We identified 1 523 TUCPs and 1 996 LncRNAs, among which 10 LncRNAs and 16 TUCPs were identified as being differentially expressed between the High-RFI and Low-RFI groups. Co-expression and co-localization methods were used to search for LncRNA and TUCP target genes, which identified 970/1 538 and 23/27 genes, respectively. Ontology and pathways analysis revealed that the LncRNAs/TUCPs that were highly expressed in the Low-RFI group are mostly concentrated in energy metabolism pathways. For example, LNC_000890 and TUCP_000582 might regulate liver tissue metabolic efficiency. The LncRNAs/TUCPs that were highly expressed in the High-RFI group are mostly enriched in immune function pathways. For example, TUCP_000832 might regulate animal health, thereby affecting feed efficiency. Subsequently, a co-expression network was established by applying the expression information of both the differentially expressed LncRNAs and TUCPs and their target mRNAs. The network indicated that differentially expressed genes targeted by the upregulated LncRNAs and TUCPs were mainly related to energy metabolism, while those genes targeted by the downregulated LncRNAs and TUCPs were mainly related to immune response. These results provide the basis for further study of LncRNA/TUCP-mediated regulation of feed efficiency.

Effect of dietary restriction and subsequent realimentation on hepatic oxidative phosphorylation in cattle

Compensatory growth (CG) is a naturally accelerated growth which occurs upon realimentation, following a prior period of dietary restriction. The process is harnessed worldwide as a management practice to reduce feed costs in beef cattle production. The objective of this study was to assess the potential contribution of hepatic cellular mitochondrial capacity to CG through global hepatic oxidative phosphorylation gene expression analyses as well as functional mitochondrial enzyme activity assays. Holstein-Friesian bulls were separated into two groups: (i) restricted feed allowance for 125 days (Period 1) (RES; n = 30) followed by ad-libitum feeding for 55 days (Period 2) or (ii) ad-libitum access to feed throughout (Periods 1 and 2) (ADLIB; n = 30). At the end of each period, 15 animals from each treatment group were slaughtered and hepatic tissue was collected. Tissue samples were subjected to RNAseq and spectrophotometric analysis for the functional assessment of mitochondria. RES and ADLIB groups grew at 0.6 kg/day and 1.9 kg/day, respectively, during Period 1. During Period 2, the RES group underwent CG growing at 2.5 kg/day, with ADLIB animals gaining 1.4 kg/day. Oxidative phosphorylation genes were differentially expressed in response to both dietary restriction and CG. Spectrophotometric assays indicated that mitochondrial abundance was greater in animals undergoing dietary restriction at the end of Period 1 and subsequently reduced during realimentation (P < 0.02). Results indicate that mitochondrial capacity may be enhanced during dietary restriction to more effectively utilize diet-derived nutrients. However, enhanced mitochondrial capacity does not appear to be directly contributing to CG in cattle.

Gene networks for three feed efficiency criteria reveal shared and specific biological processes

Background

French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria.

Results

A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency.

Conclusions

The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.

Inferring Relationship of Blood Metabolic Changes and Average Daily Gain With Feed Conversion Efficiency in Murrah Heifers: Machine Learning Approach

Machine learning algorithms were employed for predicting the feed conversion efficiency (FCE), using the blood parameters and average daily gain (ADG) as predictor variables in buffalo heifers. It was observed that isotonic regression outperformed other machine learning algorithms used in study. Further, we also achieved the best performance evaluation metrics model with additive regression as the meta learner and isotonic regression as the base learner on 10-fold cross-validation and leaving-one-out cross-validation tests. Further, we created three separate partial least square regression (PLSR) models using all 14 parameters of blood and ADG as independent (explanatory) variables and FCE as the dependent variable, to understand the interactions of blood parameters, ADG with FCE each by inclusion of all FCE values (i), only higher FCE values (negative RFI) (ii), and inclusion of only lower FCE (positive RFI) values (iii). The PLSR model including only the higher FCE values was concluded the best, based on performance evaluation metrics as compared to PLSR models developed by inclusion of the lower FCE values and all types of FCE values. IGF1 and its interactions with the other blood parameters were found highly influential for higher FCE measures. The strength of the estimated interaction effects of the blood parameter in relation to FCE may facilitate understanding of intricate dynamics of blood parameters for growth.

Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth

Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression of CG. Forty Holstein Friesian bulls were equally assigned to one of four groups. R1 and R2 groups were subjected to restricted feed allowance for 125 days (Period 1). A1 and A2 animals had ad libitum access to feed in Period 1. Following Period 1, all animals from R1 and A1 were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum access to feed for successive 55 days (Period 2). M. longissimus dorsi samples were collected at slaughter from all animals. Proteins were isolated from samples and subjected to label-free mass spectrometry proteomic quantification. Proteins which were differentially abundant during CG (n = 39) were involved in cellular binding processes, oxidative phosphorylation and mitochondrial function. There was also evidence for up regulation of three pathways involved in nucleotide biosynthesis. Genetic variants in or regulating genes pertaining to proteins identified in this study may hold potential for use as DNA based biomarkers for genomic selection of animals with a greater ability to undergo CG.

Mitochondrial abundance and function in muscle from beef steers with divergent residual feed intakes

The objective of this study was to evaluate the relationship between muscle mitochondrial function and residual feed intake (RFI) in growing beef cattle. A 56-day feeding trial was conducted with 81 Angus × Hereford steers (initial BW = 378 ± 43 kg) from the University of California Sierra Foothills Research Station (Browns Valley, CA, USA). All steers were individually fed the same finishing ration (metabolizable energy = 3.28 Mcal/kg DM). Average daily gain (ADG), DM intake (DMI) and RFI were 1.82 ± 0.27, 8.89 ± 1.06 and 0.00 ± 0.55 kg/day, respectively. After the feeding trial, the steers were categorized into high, medium and low RFI groups. Low RFI steers consumed 13.6% less DM (P < 0.05) and had a 14.1% higher G : F ratio (P < 0.05) than the high RFI group. No differences between RFI groups were found in age, ADG or BW (P > 0.10). The most extreme individuals from the low and high RFI groups were selected to assess mitochondrial function (n = 5 low RFI and n = 6 high RFI). Mitochondrial respiration was measured using an oxygraph (Hansatech Instruments Ltd., Norfolk, UK). State 3 and State 4 respiration rates were similar between both groups (P > 0.10). Respiratory control ratios (RCRs, i.e., State 3 : State 4 oxygen uptakes) declined with animal age and were greater in low RFI steers (4.90) as compared to high RFI steers (4.26) when adjusted for age by analysis of covariance (P = 0.003). Mitochondrial complex II activity levels per gram of muscle were 42% greater in low RFI steers than in high RFI steers (P = 0.004). These data suggest that skeletal muscle mitochondria have greater reserve respiratory capacity and show greater coupling between respiration and phosphorylation in low RFI than in high RFI steers.

Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle

Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (Illumina HiSeq 2500, 100 bp, pared-end). From the 17,354 expressed genes considering all tissues, 1,335 were prioritized by five selection categories (differentially expressed, harboring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB1 were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated with FE. Moreover, we indicated potential biomarkers of FE, which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed the main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.

Hepatic mitochondrial function in Hereford steers with divergent residual feed intake phenotypes

Variations in phenotypic expression of feed efficiency could be associated with differences or inefficiencies in mitochondria function due to its impact on energy expenditure. The aim of this study was to determine hepatic mitochondrial density and function in terms of respiration, gene and protein expression, and enzyme activity of mitochondrial respiratory complex proteins, in steers of divergent residual feed intake (RFI) phenotypes. Hereford steers (n = 111 and n = 122 for year 1 and 2, respectively) were evaluated in postweaning 70 d standard test for RFI. Forty-six steers exhibiting the greatest (n = 9 and 16 for year 1 and 2; high-RFI) and the lowest (n = 9 and 12 for year 1 and 2; low-RFI) RFI values were selected for this study. After the test, steers were managed together until slaughter under grazing conditions until they reached the slaughter body weight. At slaughter, hepatic samples (biopsies) were obtained. Tissue respiration was evaluated using high-resolution respirometry methods. Data were analyzed using a mixed model that included RFI group as fixed effect and slaughter date and year as a random effect using PROC MIXED of SAS. RFI and dry matter intake were different (P < 0.001) between low and high-RFI groups of year 1 and year 2. Basal respiration and maximum respiratory rate were greater (P ≤ 0.04) for low than high-RFI steers when complex II substrates (succinate) were supplied. However, when Complex I substrates (glutamate/malate) were used maximum respiratory capacity tended to be greater (P < 0.09) for low vs. high-RFI steers. Low-RFI steers presented greater mitochondria density markers (greater (P < 0.05) citrate synthase (CS) activity and tended (P ≤ 0.08) to have greater CS mRNA and mtDNA:nDNA ratio) than high-RFI steers. Hepatic expression SDHA, UQCRC1, and CYC1 mRNA was greater (P ≤ 0.02) and expression of NDUFA4, NDUFA13, SDHD, UQCRH, and ATP5E mRNA tended (P ≤ 0.10) to be greater in low than high-RFI steers. Hepatic SDHA protein expression tended (P < 0.08) to be greater while succinate dehydrogenase activity was greater (P = 0.04) and NADH dehydrogenase activity was greater (P = 0.03) for low than high-RFI steers. High-efficiency steers (low-RFI) probably had greater efficiency in hepatic nutrient metabolism, which was strongly associated with greater hepatic mitochondrial density and functioning, mainly of mitochondrial complex II.

The effects of relative gain and age on peripheral blood mononuclear cell mitochondrial enzyme activity in preweaned Holstein and Jersey calves

Mitochondria are central to metabolism, nutrition, and health, but many factors can influence their efficiency. The objectives of this study were to determine if the mitochondrial enzyme activities of citrate synthase, complex I, complex IV, and complex V from peripheral blood mononuclear cells in Holstein and Jersey dairy calves were affected by age or relative gain as a percent of initial weight. Twenty-three Holstein and 23 Jersey heifer calves were enrolled between 3 and 6 d of age and whole blood samples were collected via jugular venipuncture at 1, 2, and 8 wk of age. Crude mitochondrial extracts were obtained from the peripheral blood mononuclear cell fraction at each time point and subsequently assayed for enzymatic activity. Age-dependent changes in activity were observed in complex V for both breeds. In Jersey calves complex IV and citrate synthase activity differed with age. Complex I activity was greater for high relative gain Jerseys and tended to be greater for high relative gain Holstein calves. Holstein calves had greater incidence of scours compared with Jersey calves, and in both breeds scouring calves exhibited greater complex V activity compared with those without scours. These data suggest that age and immune challenge in the form of scours affect mitochondrial complex V activity. Additionally, complex I activity may serve as a marker for calf growth potential because it was influenced by relative gain and not age.

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.

Associations of Blood Analysis with Feed Efficiency and Developmental Stage in Grass-Fed Beef Heifers

Simple Summary

Individual cattle of identical developmental stage vary in their efficiency of feed utilization to achieve a similar productive performance in terms of growth rate and body composition upon accounting for breed, age and gestation stage. Technical issues to measure individual feed intake on the farm limits the identification of feed-efficient cattle. This creates a demand for indirect approaches to infer feed efficiency, such as blood parameters. Our study revealed differences in blood parameters when comparing grass-fed heifers classified as either efficient or inefficient. These differences were also influenced by the developmental stage of the heifers; some blood analytes had distinct relevance to infer about feed efficiency when comparing younger non-pregnant heifers with older and pregnant heifers. In general, improved feed efficiency seems to relate to a lower oxygen carrying capacity. We also provide evidence of associations between indicators of the immune system, blood enzymes and ions and feed efficiency. Additionally, blood analysis presented metabolic differences between non-pregnant heifers with older and pregnant heifers. Blood analysis as a practical measure for feed efficiency has relevance in the nutritional management and genetic improvement of beef cattle, which will contribute to the broad sustainability of beef farming.

Abstract

Proxies for feed efficiency, such as blood-based indicators, applicable across heifers varying in genetic makeup and developmental state are needed. Assessments of blood analytes and performance were made in heifer calves and pregnant heifers. Residual feed intake, a measure of feed efficiency, was used to categorize each population of heifers as either efficient or inefficient. Efficient heifer calves had lower mean cell hemoglobin, greater lymphocyte count, and fewer segmented neutrophils at the end of the test compared to inefficient calves. Efficient pregnant heifers had greater counts of lymphocytes with fewer segmented neutrophils at the end than inefficient pregnant heifers. Efficient heifer calves exhibited higher specific immunoglobulin M than inefficient calves. Throughout the test, efficient heifer calves had elevated potassium and phosphorus, and reduced alkaline phosphatase (ALP) compared to inefficient heifers. Efficient pregnant heifers showed greater ALP, non-esterified fatty acids and creatinine, but lower cholesterol and globulin than inefficient pregnant heifers. Levels of red and white blood cells, creatine kinase, cholesterol, glucose, potassium and phosphorus were higher in heifer calves compared with pregnant heifers. There is potential for blood analytes as proxies for feed efficiency; however, it is necessary to consider the inherent associations with feed efficiency and heifers’ developmental stage.

Liver morphometrics and metabolic blood profile across divergent phenotypes for feed efficiency in the bovine

BACKGROUND

Feed costs are a major expense in the production of beef cattle. Individual variation in the efficiency of feed utilization may be evident through feed efficiency-related phenotypes such as those related to major energetic sinks. Our objectives were to assess the relationships between feed efficiency with liver morphometry and metabolic blood profile in feedlot beef cattle.

METHODS

Two populations (A = 112 and B = 45) of steers were tested for feed efficiency. Blood from the 12 most (efficient) and 12 least feed inefficient (inefficient) steers from population A was sampled hourly over the circadian period. Blood plasma samples were submitted for analysis on albumin, aspartate aminotransferase, γ-glutamyl transpeptidase urea, cholesterol, creatinine, alkaline phosphatase, creatine kinase, lipase, carbon dioxide, β-hydroxybutyrate, acetate and bile acids. Liver tissue was also harvested from 24 steers that were blood sampled from population A and the 10 steers with divergent feed efficiency in each tail of population B was sampled for microscopy at slaughter. Photomicroscopy images were taken using the portal triad and central vein as landmarks. Histological quantifications included cross-sectional hepatocyte perimeter and area, hepatocyte nuclear area and nuclei area as proportion of the hepatocyte area. The least square means comparison between efficient and inefficient steers for productive performance and liver morphometry and for blood analytes data were analyzed using general linear model and mixed model procedures of SAS, respectively.

RESULTS

No differences were observed for liver weight; however, efficient steers had larger hepatocyte (i.e. hepatocyte area at the porta triad 323.31 vs. 286.37 µm2) and nuclei dimensions at portal triad and central vein regions, compared with inefficient steers. The metabolic profile indicated efficient steers had lower albumin (36.18 vs. 37.65 g/l) and cholesterol (2.62 vs. 3.05 mmol/l) and higher creatinine (118.59 vs. 110.50 mmol/l) and carbon dioxide (24.36 vs. 23.65 mmol/l) than inefficient steers.

CONCLUSIONS

Improved feed efficiency is associated with increased metabolism by the liver (enlarged hepatocytes and no difference on organ size), muscle (higher creatinine) and whole body (higher carbon dioxide); additionally, efficient steers had reduced bloodstream pools of albumin and cholesterol. These metabolic discrepancies between feed efficient and inefficient cattle may be determinants of productive performance.

Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake

Background

Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach.

Results

The rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing. There were 122 genes differentially expressed between the rumen epithelial tissues of L- and H- RFI steers (p < 0.05) with 85 up-regulated and 37 down-regulated in L-RFI steers. Functional analysis of up-regulated genes revealed their involvement in acetylation, remodeling of adherens junctions, cytoskeletal dynamics, cell migration, and cell turnover. Additionally, a weighted gene co-expression network analysis (WGCNA) identified a significant gene module containing 764 genes that was negatively correlated with RFI (r = −0.5, p = 0.03). Functional analysis revealed significant enrichment of genes involved in modulation of intercellular adhesion through adherens junctions, protein and cell turnover, and cytoskeletal organization that suggest possible increased tissue morphogenesis in the L-RFI steers. Additionally, the L-RFI epithelium had increased expression of genes involved with the mitochondrion, acetylation, and energy generating pathways such as glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation. Further qPCR analysis of steers with different RFI (L-RFI, n = 35; M-RFI, n = 34; H-RFI, n = 35) revealed that the relative mitochondrial genome copy number per cell of the epithelium was positively correlated with RFI (r = 0.21, p = 0.03).

Conclusions

Our results suggest that the rumen epithelium of L-RFI (efficient) steers may have increased tissue morphogenesis that possibly increases paracellular permeability for the absorption of nutrients and increased energy production to support the energetic demands of increased tissue morphogenesis compared to those of H-RFI (inefficient) animals. Greater expression of mitochondrial genes and lower relative mitochondrial genome copy numbers suggest a greater rate of transcription in the rumen epithelial mitochondria of L-RFI steers. Understanding how host gene expression profiles are associated with RFI could potentially lead to identification of mechanisms behind this trait, which are vital to develop strategies for the improvement of cattle feed efficiency.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2935-4) contains supplementary material, which is available to authorized users.

Relationship between Liver Mitochondrial Respiration and Proton Leak in Low and High RFI Steers from Two Lineages of RFI Angus Bulls

The objective of this research is to evaluate liver mitochondrial oxygen consumption and proton leak kinetics in progeny from two lineages of Angus bulls with high and low residual feed intake (RFI). Two Angus bulls were selected based on results from a genetic test for RFI and were used as sires. Eight offspring at 10-11 months of age from each sire were housed in individual pens for 70–105 days following a diet adaptation period of 14 days. Progeny of the low RFI sire had 0.57 kg/d (P = 0.05) lower average RFI than progeny of the high RFI sire. There was no difference in dry matter intake between low and high RFI steers, but low RFI steers gained more body weight (P = 0.02) and tended to have higher average daily gains (P = 0.07). State 3 and State 4 respiration, RCR, and proton leak did not differ between high and low RFI steers (P = 0.96, P = 0.81, P = 0.93, and P = 0.88, resp.). Therefore, the increase in bodyweight gain which distinguished the low RFI steers from the high RFI steers may be associated with other metabolic mechanisms that are not associated with liver mitochondrial respiration and proton leak kinetics.