The relationship between feed efficiency and the circadian profile of blood plasma analytes measured in beef heifers at different physiological stages

An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle

BACKGROUND

Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network.

RESULTS

Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts.

CONCLUSIONS

Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.

Diet supplemented with olive cake as a model of circular economy: Metabolic and endocrine responses of beef cattle

Introduction

Integrating by-products into livestock diet represents a great opportunity for implementing the concept of circular economy while reducing feed costs. Olive cake (OC) is considered an agro-industrial waste, but the high content of valuable metabolites makes it a promising feed integration. Therefore, this study investigated the effect of OC integration in beef cattle diet on different blood parameters.

Methods

Forty-eight young growing fattening Limousines-−24 bulls (body weight 350 ± 15 kg) and 24 heifers (280 ± 10 kg)—, aged 240 ± 20 days, were randomly allocated to 1 of 3 dietary treatments: concentrate at 0% (Control group: CTR), 10% (Low-olive cake group: L-OC), or 15% (High-olive cake group: H-OC) of OC inclusion. Blood samples and body weights were collected before administrating the supplemented diet (0 d), at the end of the stocker growing phase (56 d), and at the end of the fattening (147 d). After being slaughtered, animal carcasses were weighted. A linear regression model was fitted for each blood parameter with the 0 d as covariate and diet, time, sex, diet × time, and diet × sex as fixed effects.

Results

In males, body weight was highest in CTR, but carcass weight was similar in all the groups. All the blood parameters were within physiological ranges, independently from the animal diet. CTR group showed the highest alanine aminotransferase (ALT, P = 0.0027) and creatine kinase (P = 0.0119), whereas total bilirubin (P = 0.0023) was higher in H-OC than in CTR. Moreover, ALT was highest in CTR at 56 d, becoming similar in all the groups at 147 d (P = 0.0280). Instead, the increase observed in total cholesterol from 56 to 147 d was lower in H-OC compared with CTR and L-OC (P = 0.0451). A significant effect of diet × sex interaction was observed on triglycerides, urea, liver enzymes, and insulin. These data support the OC inclusion of up to 15% of the concentrate with no detrimental effect on beef cattle metabolic status.

Discussion

In conclusion, OC can be considered as a component in beef diet giving an opportunity to improve agriculture sustainability.

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

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

Plasma Carboxyl-Metabolome Is Associated with Average Daily Gain Divergence in Beef Steers

We applied an untargeted metabolomics technique to analyze the plasma carboxyl-metabolome of beef steers with divergent average daily gain (ADG). Forty-eight newly weaned Angus crossbred beef steers were fed the same total mixed ration ad libitum for 42 days. On day 42, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8), and blood samples were obtained from the two groups for plasma preparation. Relative quantification of carboxylic-acid-containing metabolites in the plasma samples was determined using a metabolomics technique based on chemical isotope labeling liquid chromatography mass spectrometry. Metabolites that differed (fold change (FC) ≥ 1.2 or ≤ 0.83 and FDR ≤ 0.05) between LF and HF were identified using a volcano plot. Metabolite set enrichment analysis (MSEA) of the differential metabolites was done to determine the metabolic pathways or enzymes that were potentially altered. In total, 328 metabolites were identified. Volcano plot analysis revealed 43 differentially abundant metabolites; several short chain fatty acids and ketone bodies had greater abundance in HF steers. Conversely, several long chain fatty acids were greater in LF steers. Five enzymatic pathways, such as fatty acyl CoA elongation and fatty-acid CoA ligase were altered based on MSEA. This study demonstrated that beef steers with divergent ADG had altered plasma carboxyl-metabolome, which is possibly caused by altered abundances and/or activities of enzymes involved in fatty acid oxidation and biosynthesis in the liver.

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.

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.

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.

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.

Exploration of Biological Markers of Feed Efficiency in Young Bulls

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

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.

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.

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.