Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers

Estimation of genetic parameters and single-step genome-wide association studies for eating time and rumination time in Holstein dairy cows

The aims of this study were to estimate genetic parameters and to identify genomic regions associated with eating time (ET) and rumination time (RUT) in Holstein dairy cows. Genetic correlations among ET, RUT, and milk yield traits were also estimated. The data were collected from 2019 to 2022 in 6 dairy herds located in the Walloon Region of Belgium. The dataset consisted of daily ET and RUT records on 284 Holstein cows, from which 41 cows had records only for the first parity (P1), 101 cows had records from both the first and second parities, and 142 cows had records only for the second parity (P2). The number of daily ET and RUT records in the P1 and P2 cows were 18,569 (on 142 cows) and 34,464 (on 243 cows), respectively. Data on 28,994 SNPs located on 29 Bos taurus autosomes (BTA) of 747 animals (435 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 20-SNP sliding window (with an average size of 1.52 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Mean (standard deviation; SD) averaged daily ET and RUT were 327.0 (85.66) and 559.4 (77.69) min/d for cows in P1 and 316.0 (82.24) and 574.2 (75.42) min/d for cows in P2, respectively. Mean (standard deviation; SD) heritability estimates for daily ET and RUT were 0.42 (0.09) and 0.45 (0.06) for cows in P1 and 0.45 (0.04) and 0.43 (0.02) for cows in P2, respectively. Mean (SD) daily genetic correlations between daily ET and RUT were 0.27 (0.07) for P1 and 0.34 (0.08) for P2. Genome-wide association analyses identified 6 genomic regions distributed over 5 chromosomes (BTA1, BTA4, BTA11, 2 regions of BTA14, and BTA17) associated with ET or RUT. The findings of this study increase our preliminary understanding of the genetic background of feeding behavior in dairy cows; however, larger datasets are needed to determine whether ET and RUT might have the potential to be used in selection programs.

Energy efficiency of grazing Hereford heifers classified by paternal residual feed intake

Residual feed intake (RFI) has become a widely spread index of feed efficiency. Although most of beef cattle systems in the world are pasture based, RFI evaluation and research is usually performed in confinement conditions. In this context, residual heat production (RHP) estimated as the difference between actual and expected heat production (HP), could allow to identify efficient animals. Thus, the aim of this work was to evaluate the relationship between paternal estimated breeding values (EBV) for RFI and beef heifer efficiency, measured as RHP, as well as its association with heifers' productive and reproductive performance on grazing conditions. Seventy-one 25 ± 0.8-mo-old and seventy-four 24 ± 0.7-mo-old Hereford heifers were managed as contemporary groups in spring 2019 and 2020, respectively. Heifers were sired by 10 RFI-evaluated bulls and classified into three groups according to the paternal EBV for RFI: five bulls of low RFI (high efficiency, pHE), two bulls of medium RFI (medium efficiency), and three bulls of high RFI (low efficiency, pLE). The experimental period lasted 70 d prior to their first insemination where HP was determined by the heart rate-O2 pulse technique. In addition, reproductive performances during the first and second breeding and calving seasons were recorded. Heifers' RHPs expressed as MJ/d and kJ/kg of body weight (BW)0.75/d were positively correlated with paternal RFI EBVs (P < 0.05; r > 0.60). Moreover, BW and average daily gain (ADG) were greater (P < 0.01) for pHE than pLE heifers while expressed as units of BW0.75/d, neither total HP nor metabolizable energy (ME) intake differed between groups, but pHE heifers had greater retained energy (RE; P < 0.01) and lower RHP (P < 0.05) than pLE ones. Gross energy efficiency (RE/ME intake) was greater (P < 0.001) for pHE than pLE heifers while the HP/ADG and RHP/ADG were reduced (P < 0.05) and feed-to-gain ratio (ADG/DM intake) tended to be greater (P = 0.07) for pHE than pLE heifers. In addition, during the first breeding and calving seasons, small but significant (P < 0.01) differences in reproductive responses between groups suggested an earlier pregnancy in pHE heifers than the pLE group, differences that disappeared during the second breeding and calving seasons. Thus, heifers sired by high-efficiency bulls measured as RFI were more efficient measured as RHP in grazing conditions, without significant differences in reproductive performance.

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.

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

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

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

BACKGROUND

Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.

RESULTS

A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.

CONCLUSIONS

A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.

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.

Blood parameters associated with residual feed intake in beef heifers

Blood chemistry may provide indicators to greater feed efficient cattle. As a side objective to previous research, 17 Angus heifers approximately two years old underwent a feed efficiency trial to determine residual feed intake (RFI) and identify variation in blood chemistry in beef cattle divergent in feed efficiency. Heifers were categorized as high- or low-RFI based ± 0.25 standard deviations around mean RFI. Blood samples were analyzed using an i-STAT handheld blood analyzer to measure sodium, potassium, glucose, blood urea nitrogen (BUN), creatinine, hematocrit, and hemoglobin. BUN was greater in high-RFI heifers (µ = 8.7 mg/dL) contrasted to low-RFI heifers (µ = 6.5 mg/dL; P = 0.01), whereas glucose was greater in low-RFI heifers (µ = 78.1 mg/dL) contrasted to high-RFI heifers (µ = 82.0 mg/dL; P = 0.05). No other blood chemistry parameters differed by RFI. The greater abundance of BUN in high-RFI heifers may indicate inefficient utilization of protein or mobilization of tissue protein for non-protein use. Greater blood glucose concentrations in low-RFI heifers may indicate greater utilization of energy precursors, such as volatile fatty acids, or metabolites. These data suggest there are readily measurable indicators of physiological variation in nutrient utilization; however, this warrants additional studies to explore.

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.

Microbial Populations in Ruminal Liquid Samples from Beefmaster Steers at Both Extremes of RFI Values

The gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster steers (n = 10) at both extremes of residual feed intake (RFI) values (5 with the lowest and 5 with the highest RFI) from two consecutive days. Samples were processed using two different DNA extraction methods. The V3 and V4 regions of the 16S rRNA gene were amplified using PCR and sequenced with a MiSeq instrument (Illumina). We analyzed 1.6 million 16S sequences from all 40 samples (10 steers, 2 time points, and 2 extraction methods). The abundance of most microbes was significantly different between DNA extraction methods but not between high-efficiency (LRFI) and low-efficiency (HRFI) animals. Exceptions include the genus Succiniclasticum (lower in LRFI, p = 0.0011), and others. Diversity measures and functional predictions were also mostly affected by DNA extraction methods, but some pathways showed significant differences between RFI levels (e.g., methylglyoxal degradation, higher in LRFI, p = 0.006). The results suggest that the abundance of some ruminal microbes is associated with feed efficiency and serves as a cautionary tale for the interpretation of results obtained with a single DNA extraction method.

Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups

The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.

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

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

Effects of Feeding and Drinking Behavior on Performance and Carcass Traits in Beef Cattle

Feed and water efficiency are important traits to improve beef cattle production’s economic and environmental sustainability. This study evaluated residual feed intake (RFI) and residual water intake (RWI) and their relationship with performance, ingestive behavior, and carcass traits in Caracu beef cattle. The data were analyzed using a generalized linear model with least squares means. The ingestive behavior, performance, and carcass traits were influenced by sex (p < 0.05). Males showed higher dry matter intake (DMI), average daily gain (ADG), mid-test metabolic weight (BW0.75), rib eye area, and rump fat thickness than females, besides spending more time drinking and eating. Low RFI animals exhibited higher DMI than high RFI animals. Low RWI animals ingested 3.89 L/d of water further than high RWI animals. The interaction between sex and RWI influenced the DMI, BW0.75, and backfat thickness. The ingestive behavior of low and high RFI animals was similar, although high RWI animals visited a smaller number of drinkers than low RWI animals. Water intake positively affects productive efficiency, and the combined use of RWI and RFI may help improve the selection of more efficient animals contributing to reducing the costs of beef cattle production and improving environmental sustainability.

Long-term divergent selection for residual feed intake in Chinese broiler chickens

This study aimed to assess the effect of inbreeding on production traits using a long-term closed-line population recorded for residual feed intake (RFI). The study first used data from a previously reported population to determine the appropriate period of divergent selection for RFI. The results showed that RFI had similar moderate heritability estimates (0.28-0.34) during the fast-growing period (7-12 wk), and RFI at 7 to 10 wk had the highest heritability (0.34). Therefore, divergent selection was performed in a Chinese broiler population for RFI at 7 to 10 wk; the total sample size from generations zero (G0) to 13 was 9050. The divergence between the 2 lines increased steadily throughout generations, resulting in G13 with average RFI values of 304.55 in high RFI (HRFI) males, -160.31 in low RFI (LRFI) males, 296.30 in HRFI females and -157.55 in LRFI females. The feed intake (FI) and feed conversion ratio were almost higher in HRFI broilers than in LRFI broilers, and the magnitude of the difference in FI increased from approximately 4% for both sexes in G1 to approximately 33% in G13. Body weight gain was irregular from G1 to G13 and higher in LRFI broilers than in HRFI broilers after G10. Indeed, the HRFI broilers consumed more food, but they were lighter than LRFI broilers. In G13, LRFI males had heavier slaughter weight, longer cecum length, more white blood cells (WBC), red blood cells (RBC) and hemoglobin (HGB), but triglycerides, lower dressed percentage, percentage of half eviscerated yield, and eviscerated yield than HRFI males. LRFI females had a higher percentage of breast muscle and gizzard yield, longer cecum length, and more WBCs, RBCs and HGB but less abdominal fat and serum total cholesterol than HRFI females. This study was the first to verify that long-term divergent selection for RFI in Chinese broiler chickens is positive and beneficial.

Residual feed intake in peripartal dairy cows is associated with differences in milk fat yield, ruminal bacteria, biopolymer hydrolyzing enzymes, and circulating biomarkers of immunometabolism

Residual feed intake (RFI) measures feed efficiency independent of milk production level, and is typically calculated using data past peak lactation. In the current study, we retrospectively classified multiparous Holstein cows (n = 320) from 5 of our published studies into most feed-efficient (M-eff) or least feed-efficient (L-eff) groups using performance data collected during the peripartal period. Objectives were to assess differences in profiles of plasma biomarkers of immunometabolism, relative abundance of key ruminal bacteria, and activities of digestive enzymes in ruminal digesta between M-eff and L-eff cows. Individual data from cows with ad libitum access to a total mixed ration from d -28 to d +28 relative to calving were used. A linear regression model including dry matter intake (DMI), energy-corrected milk (ECM), changes in body weight (BW), and metabolic BW was used to classify cows based on RFI divergence into L-eff (n = 158) and M-eff (n = 162). Plasma collected from the coccygeal vessel at various times around parturition (L-eff = 60 cows; M-eff = 47 cows) was used for analyses of 30 biomarkers of immunometabolism. Ruminal digesta collected via esophageal tube (L-eff = 19 cows; M-eff = 29 cows) was used for DNA extraction and assessment of relative abundance (%) of 17 major bacteria using real-time PCR, as well as activity of cellulase, amylase, xylanase, and protease. The UNIVARIATE procedure of SAS 9.4 (SAS Institute Inc.) was used for analyses of RFI coefficients. The MIXED procedure of SAS was used for repeated measures analysis of performance, milk yield and composition, plasma immunometabolic biomarkers, ruminal bacteria, and enzyme activities. The M-eff cows consumed less DMI during the peripartal period compared with L-eff cows. In the larger cohort of cows, despite greater overall BW for M-eff cows especially in the prepartum (788 vs. 764 kg), no difference in body condition score was detected due to RFI or the interaction of RFI × time. Milk fat content (4.14 vs. 3.75 ± 0.06%) and milk fat yield (1.75 vs. 1.62 ± 0.04 kg) were greater in M-eff cows. Although cumulative ECM yield did not differ due to RFI (1,138 vs. 1,091 ± 21 kg), an RFI × time interaction due to greater ECM yield was found in M-eff cows. Among plasma biomarkers studied, concentrations of nonesterified fatty acids, β-hydroxybutyrate, bilirubin, ceruloplasmin, haptoglobin, myeloperoxidase, and reactive oxygen metabolites were overall greater, and glucose, paraoxonase, and IL-6 were lower in M-eff compared with L-eff cows. Among bacteria studied, abundance of Ruminobacter amylophilus and Prevotella ruminicola were more than 2-fold greater in M-eff cows. Despite lower ruminal activity of amylase in M-eff cows in the prepartum, regardless of RFI, we observed a marked linear increase after calving in amylase, cellulase, and xylanase activities. Protease activity did not differ due to RFI, time, or RFI × time. Despite greater concentrations of biomarkers reflective of negative energy balance and inflammation, higher feed efficiency measured as RFI in peripartal dairy cows might be associated with shifts in ruminal bacteria and amylase enzyme activity. Further studies could help address such factors, including the roles of the liver and the mammary gland.

Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows

The improvement of nutrient utilization efficiency in dairy cows represents an important task in view of the current rising demand for animal products and sustainable resource usage. In this perspective, the identification of appropriate markers to identify the most efficient animals for dairy production becomes a crucial factor. Residual feed intake (RFI), which represents the difference between predicted and actual intake, is used to define the efficiency of cows. In this study, subcutaneous adipose tissue (AT) was collected from five high efficient (HEF) and five low efficient (LEF) mid-lactation Holstein dairy cows, that represented subgroups of the 20% lowest RFI values (HEF) and highest 20% RFI values (LEF), out of a cohort of 155 cows that were examined for feed efficiency at the individual dairy barn at Volcani Institute, Israel. Adipose samples were examined for proteomic analysis by nano-LC/MS–MS and gene expression by RT-PCR. A total of 101 differential proteins (P ≤ 0.05 and fold change ± 1.5) and two protein networks related to feed efficiency were found between HEF and LEF cows. Among the enriched top canonical pathways, FAT10 signaling, EIF2 signaling, Sirtuin signaling, Acute phase response signaling, Protein ubiquitination and mTOR signaling pathways were related to feed efficiency in AT. Furthermore, abundance of transferrin (TF; FC = 78.35, P = 0.02) enriched pathways, including mTOR signaling, LXR/RXR and FXR/RXR activation was found in AT of HEF cows. Relative mRNA expression of RBM39, which is involved in energy metabolism, was decreased in AT of HEF versus LEF. The relationship found between the AT proteins and/or metabolic pathways and the feed efficiency demonstrates that AT may reflect metabolic adaptations to high efficiency, and suggests that these proteins together with their metabolic mechanisms are suitable candidates as biomarkers to identify efficient cows for dairy production.

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.

Serum Biochemical Parameters, Rumen Fermentation, and Rumen Bacterial Communities Are Partly Driven by the Breed and Sex of Cattle When Fed High-Grain Diet

Hybridization in bovines is practiced with the main aim of improving production performance, which may imply the microbial variations in the rumen from the parental breed cross to their progeny. Besides, the interactions of offspring breed with sex in terms of rumen bacteria are not clear. This study aims to evaluate the variations in rumen bacterial communities in different breeds and sexes, and the correlations among fattening performance, serum biochemical parameters, and rumen fermentation. Forty-two 19.2 ± 0.67-month-old beef cattle (390 ± 95 kg of initial body weight) comprising two genetic lines (Yiling and Angus × Yiling) and two sexes (heifers and steers) were raised under the same high-grain diet for 120 d. On the last two days, blood samples were collected from each animal via the jugular vein before morning feeding for analyzing serum biochemical parameters; rumen fluid samples were obtained via esophageal intubation 2 h after morning feeding for analyzing rumen fermentation parameters and bacterial communities. The results show that both breed and sex had a certain impact on fattening performance, serum biochemical parameters, and rumen fermentation. No differences in the diversity and structure of rumen bacterial communities were observed. Significant interactions (p < 0.05) of breed and sex were observed for Succinivibrionaceae UCG-002 and Prevotellaceae UCG-001. The relative abundances of the Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Succinivibrio were different (p < 0.05) between breeds. Heifers had a higher (p = 0.008) relative abundance of the Rikenellaceae RC9 gut group than steers. Correlation analysis showed a significant relationship (p < 0.05) of rumen bacteria with serum biochemical parameters, rumen pH, and rumen fermentation patterns. Additionally, only two genera, Prevotellaceae UCG-003 and Prevotellaceae UCG-001, had positive correlations with feed efficiency. In conclusion, serum biochemical parameters, rumen fermentation, and rumen bacterial communities are partly driven by the breed and sex of cattle fed a high-grain diet.

Evaluation of Ingestive Behavior, Ruminal and Blood Parameters, Performance, and Thermography as a Phenotypic Divergence Markers of Residual Feed Intake in Rearing Dairy Heifers

Simple Summary

The selection of highly efficient animals will support meeting the world’s future demand for products and food of animal origin. Thus, the identification of efficient animals and an understanding of the mechanisms inherent to this efficiency is fundamental for the progress of breeding systems. In the present study, we identify highly efficient animals for residual feed intake in dairy heifers. This animal category is unexplored in relation to this index. We utilized the classical parameters evaluated in cattle of different ages to carry out the study on these animals.

Abstract

The objectives of this study were: (1) to identify and rank phenotypically divergent animals for residual feed intake (RFI) regarding their efficiency (high: HE or low: LE); (2) to evaluate their relationships with ingestive behavior, ruminal and blood parameters, performance, and infrared thermography; and (3) to determine if such measurements can be used as feed efficiency markers in rearing dairy heifers. Thirty-eight heifers, 143 d ± 4 (Mean ± SD) of age and 108.7 kg ± 17.9 of body weight were used. The animals were fed with a total mixed ration during the 91 d of the trial. A phenotypic divergence of DMI for RFI was observed between −0.358 and 0.337 kg/d for HE and LE, respectively. Dry matter intake (DMI) was lower in the HE (2.5 kg DMI/d vs. 3.1 kg DMI/d), as was the number of visits to the feed bin with consumption (59 vs. 71). Feed intake was the best predictor of said divergence. Water intake and number of visits to the feed bin were presented moderate correlations with RFI. The ruminal fermentation variables, blood metabolites, blood hormones (such as the other ingestive behavior variables), and infrared thermography were not able to accurately predict HE or LE animals.

How Divergence for Feed Efficiency Traits Affects Body Measurements and Metabolites in Blood and Ruminal Parameters on Pre-Weaning Dairy Heifers

The objectives of this study were: (1) to evaluate feed efficiency indexes and their relationships with body measurements and blood and ruminal metabolites in the pre-weaning period; (2) to determine if such measurements can be used as feed-efficiency markers during the pre-weaning period. Holstein-Gyr heifer calves (n = 36), enrolled between 4 and 12 weeks of age, were classified into two residual feed intake (RFI) and residual body weight gain (RG) groups: high efficiency (HE; RFI, n = 10; and RG, n = 9), and low efficiency (LE; RFI, n = 10; and RG, n = 8). Calves were fed whole milk (6 L/day) and solid feed ad libitum. Body developments were measured weekly and feed intake (milk and solid feed) daily during the whole period. Blood samples were collected at 12 weeks of age and analyzed for glucose, insulin and β-hydroxybutyrate (BHB). Samples of ruminal content were collected on the same day and analyzed for pH, NH₃-N, and volatile fatty acids (VFA). Among the growth characteristics, only the initial hip width differed between the RFI groups, and withers height differed between the RG groups. Concentration of BHB was greater and glucose: insulin ratios tended to be greater in LE-RG animals. Butyric acid proportions were similar among RFI groups, but tended to be greater for HE-RG than for LE-RG. Overall, correlation coefficients between RFI or RG and blood, rumen, or morphometric markers were low. Thus, it is unlikely that measurements of metabolic indicators, per se, will be useful in the early identification of more efficient animals. Understanding the underlying physiological basis for improved feed efficiency in dairy heifers requires further investigation.

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

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

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

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

Review: Markers and proxies to monitor ruminal function and feed efficiency in young ruminants

Developing the rumen's capacity to utilise recalcitrant and low-value feed resources is important for ruminant production systems. Early-life nutrition and management practices have been shown to influence development of the rumen in young animals with long-term consequences on their performance. Therefore, there has been increasing interest to understand ruminal development and function in young ruminants to improve feed efficiency, health, welfare, and performance of both young and adult ruminants. However, due to the small size, rapid morphological changes and low initial microbial populations of the rumen, it is difficult to study ruminal function in young ruminants without major invasive approaches or slaughter studies. In this review, we discuss the usefulness of a range of proxies and markers to monitor ruminal function and nitrogen use efficiency (a major part of feed efficiency) in young ruminants. Breath sulphide and methane emissions showed the greatest potential as simple markers of a developing microbiota in young ruminants. However, there is only limited evidence for robust indicators of feed efficiency at this stage. The use of nitrogen isotopic discrimination based on plasma samples appeared to be the most promising proxy for feed efficiency in young ruminants. More research is needed to explore and refine potential proxies and markers to indicate ruminal function and feed efficiency in young ruminants, particularly for neonatal ruminants.

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions. Blood samples were collected after the exposure to the TN and HS conditions and the relative expression of genes was measured by qPCR. The bulls exhibited lower expression of ATP1A1 in the HS condition than in the TN condition (1.98 ± 0.27 and 2.86 ± 0.26, P = 0.02), while the relative expression of NR3C1, POMC, and LEP did not differ (P > 0.05) between climatic conditions. The breed and feed intake influenced NPY and LEP expression levels (P < 0.05). Different climate conditions associated with residual feed intake can modify the gene expression patterns of ATP1A1 and NPY. The association observed among all genes studied shows that they are involved in appetite control. Bos taurus and Bos indicus bulls exhibited similar adaptability to tropical climate conditions.

Influence of Residual Feed Intake and Cow Age on Dry Matter Intake Post-Weaning and Peak Lactation of Black Angus Cows

Simple Summary

Supplemental nutrition for cattle is the greatest operating cost for cow-calf producers, accounting for 65% of the annual expenses. In addition, residual feed intake (RFI) is being used as a selection tool for purchasing and retaining heifers, as well as selecting bulls with the goal of improving feed efficiency and/or reducing supplemental inputs. However, the use and relevance of RFI as a selection tool for the cow-calf industry needs additional research. In our studies, heifer post-weaning RFI did not influence mature cow dry matter intake and intake behavior for both lactating and non-lactating beef cows. In contrast, cow age did correspond to increases of intake and intake rates of mature cows. However, when intake was expressed as g/kg body weight⁻¹, no differences were observed with respect to cow age for lactating and non-lactating cows. Milk production was influenced by heifer post-weaning RFI in 5–6- and 8–9-year-old cows, however, did not influence 9–10-year-old cows. Therefore, our research suggests that cow age has greater impacts on dry matter intake than RFI, however, the relationship between RFI of heifers and subsequent mature cow milk production warrants further investigation.

Abstract

We evaluated heifer post-weaning residual feed intake (RFI) classification and cow age on dry matter intake (DMI) at two stages of production. Fifty-nine non-lactating, pregnant, (Study 1) and fifty-four lactating, non-pregnant (Study 2) commercial black Angus beef cows were grouped by age and RFI. Free-choice, hay pellets were fed in a GrowSafe feeding system. In Study 1, cow DMI (kg/d) and intake rate (g/min) displayed a cow age effect (p < 0.01) with an increase in DMI and intake rate with increasing cow age. In Study 2, cow DMI (kg/d) and intake rate (g/min) displayed a cow age effect (p < 0.02) with an increase in DMI and intake rate with increasing cow age. Milk production displayed a cow age × RFI interaction (p < 0.01) where both 5–6-year-old and 8–9-year-old low RFI cows produced more milk than high RFI cows. For both studies, intake and intake behavior were not influenced by RFI (p ≥ 0.16) or cow age × RFI interaction (p ≥ 0.21). In summary, heifer’s post-weaning RFI had minimal effects on beef cattle DMI or intake behavior, however, some differences were observed in milk production.

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake

The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.

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

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

Genetic mechanisms underlying feed utilization and implementation of genomic selection for improved feed efficiency in dairy cattle

The economic importance of genetically improving feed efficiency has been recognized by cattle producers worldwide. It has the potential to considerably reduce costs, minimize environmental impact, optimize land and resource use efficiency, and improve the overall cattle industry’s profitability. Feed efficiency is a genetically complex trait that can be described as units of product output (e.g., milk yield) per unit of feed input. The main objective of this review paper is to present an overview of the main genetic and physiological mechanisms underlying feed utilization in ruminants and the process towards implementation of genomic selection for feed efficiency in dairy cattle. In summary, feed efficiency can be improved via numerous metabolic pathways and biological mechanisms through genetic selection. Various studies have indicated that feed efficiency is heritable, and genomic selection can be successfully implemented in dairy cattle with a large enough training population. In this context, some organizations have worked collaboratively to do research and develop training populations for successful implementation of joint international genomic evaluations. The integration of “-omics” technologies, further investments in high-throughput phenotyping, and identification of novel indicator traits will also be paramount in maximizing the rates of genetic progress for feed efficiency in dairy cattle worldwide.

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

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

Associations of feed efficiency with circulating IGF-1 and leptin, carcass traits and meat quality of lambs

The aim of this study was to investigate the effects of feed efficiency classifications on live animal measurements, circulating IGF-1 and leptin concentrations, and carcass, non-carcass and meat quality traits of lambs. One-hundred and two lambs approximately 70 days-old with initial live weight of 24.6 ± 3.71 kg (mean ± SD) were individually fed for 56 days to determine residual feed intake (RFI) and residual feed intake and gain (RIG). Lambs were then classified as phenotypically Low-, Medium- or High-RFI and Low-, Medium- or High-RIG phenotypes. Circulating leptin and IGF-1 concentrations were higher in more efficient lambs (Low-RFI or High-RIG). Variation in RFI and RIG did not affect meat redness or tenderness, but High-RIG lambs had darker meat. These findings show that the phenotypically more efficient Low-RFI and High-RIG lambs produced carcasses with similar characteristics and meat quality as the less efficient High-RFI and Low-RIG lambs but have a strategic advantage of lower feed intake to achieve similar production outcomes.

Correlations between circulating leptin concentrations and growth performance, carcass traits, and meat quality indexes in finishing Simmental × Luxi bulls fed high-concentrate diets

Circulating leptin concentrations could potentially be used as a predictor of production traits in cattle. This study aimed to clarify the correlations between circulating leptin concentrations and growth performance, carcass traits, and meat quality indexes in finishing bulls fed high-concentrate diets (concentrate-to-forage ratio 70:30). Fifty-seven Simmental × Luxi F1 crossbred bulls were used for 112-day finishing experiment. Circulating leptin concentrations and relevant indexes of growth performance, and carcass traits and meat quality were measured during or after finishing trail. The results indicated that the leptin concentrations tended to be negatively correlated with dry matter intake (DMI) (r = -.233, p = .081), and were positively correlated with 12th-rib fat thickness (r = .330, p = .012), marbling score (r = .336, p = .011), and intramuscular fat content (r = .368, p = .021). Moreover, the leptin concentrations were negatively correlated with cholesterol content (r = -.339, p = .037) and were not correlated with sensory indexes including tenderness, juiciness, and like flavor (p > .05). In conclusion, circulating leptin concentrations may potentially be used as a predictor of carcass traits related to content of fat and beef quality traits related to content of cholesterol in finishing bulls fed high-concentrate diets.

Association between residual feed intake, digestion, ingestive behavior, enteric methane emission and nitrogen metabolism in Nellore beef cattle

This study aimed to evaluate nutrient intake and digestibility, enteric methane emission and nitrogen utilization efficiency in Nellore cattle ranked by residual feed intake (RFI). Twenty-four Nellore bulls at 466 ± 24 days of age and with 352 ± 14.6 kg of body weight, classified as low and high RFI, were evaluated. Animals were kept in individual pens for three periods of 28 days and variables were measured. Data were analyzed as repeated measures over time, considering as fixed effects RFI class, period and RFI class x period interaction, and linear (co)variate of age. No significant differences in dry matter or nutrient intake were detected between RFI classes, but total digestible nutrients intake tended to be lower in low RFI animals, and apparent nutrient digestibility was higher in high RFI animals. Partial efficiency of growth tended to be lower in high RFI animals. RFI class did not interfere with enteric methane production or microbial protein synthesis, but fecal nitrogen output was higher in low RFI animals. The greater efficiency of low RFI animals is consequence of lower maintenance requirements, since energy from higher nutrients digestibility in high RFI animals was spent on metabolic processes other than body tissue deposition.

Relationships between feed efficiency and puberty in Bos taurus and Bos indicus-influenced replacement beef heifers

The objective of this experiment was to investigate the relationship between residual feed intake (RFI) and parameters associated with reproductive efficiency in growing beef heifers. One hundred and seventy-nine replacement beef heifers (Bos taurus and Bos indicus-influenced) were enrolled in a retrospective cohort design. Heifers were assigned to a 70-d feed efficiency test, and results were utilized to retrospectively classify heifers into low (n = 51), medium (n = 66), or high (n = 62) RFI groups based on their individual RFI values. Blood samples were collected weekly throughout the feed efficiency test and breeding season, which were analyzed for plasma concentration of progesterone to determine age at puberty (PUB). By design, residual feed intake differed among RFI groups where high (1.21 ± 0.08 kg/d) had greater (P < 0.01) RFI than medium (0.00 ± 0.08 kg/d) and low RFI groups (-1.49 ± 0.09 kg/d), and medium had greater (P < 0.01) RFI than low RFI heifers. Yet, no differences were observed between breed types for RFI (P = 0.53). Average daily gain (ADG) differed between breed types where Bos taurus heifers had greater ADG (P = 0.02) than B. indicus-influenced heifers. Furthermore, ADG tended (P = 0.08) to differ among RFI groups, where medium RFI heifers tended to have reduced ADG compared with low and high RFI heifers. No differences were determined between breed types for gain-to-feed ratio (G:F; P = 0.20; however, G:F differed among RFI groups and was greater (P < 0.01) in low vs. high, and low vs. medium RFI heifers. The percentage of cycling heifers by the start of the breeding season differed (P = 0.03) by RFI group, where a greater percentage of low RFI heifers were cycling compared with high RFI heifers. A difference was determined on PUB between breed types (P = 0.03), where Bos taurus (393.40 ± 4.64 d) heifers had a reduced PUB compared with B. indicus-influenced (406.90 ± 5.07 d) heifers. In addition, PUB differed by RFI group where low (385.96 ± 6.20 d; P < 0.01) and medium (398.47 ± 5.47 d; P = 0.02) RFI heifers had a reduced PUB compared with High RFI heifers (416.03 ± 5.58 d). In conclusion, more feed efficient heifers attained PUB earlier than less feed efficient heifers. Therefore, selection of heifers for feed efficiency may positively impact reproductive performance of replacement beef heifers.

Temperament and performance of Nellore bulls classified for residual feed intake in a feedlot system

This study aimed to evaluate the performance in feedlot and temperament of Nellore bulls classified by residual feed intake. The residual feed intake was calculated as the difference between the observed and predicted dry matter intake. Bulls classified as low residual feed intake had lower dry matter intake (kg day-1) and dry matter intake (g kg-1 d-1) of body weight, and were more efficient in feed conversion ratio than those classified as medium and high. The average daily gain didn't differ among residual feed intake classes and was 1.69 kg day-1, 1.82 kg day-1 and 1.71 kg day-1 for bulls classified as low, medium, or high, respectively. The residual feed intake was positively associated with dry matter intake, feed conversion ratio and subcutaneous fat thickness. The subcutaneous fat thickness was lower in bulls classified as low residual feed intake than in those with medium and high. No differences were observed in flight speed and reactivity score among residual feed intake classes. Overall, we concluded that bulls classified as low residual feed intake consumed less dry matter than high, with no differences in average daily gain, temperamentand had better feed efficiency, albeit their subcutaneous fat thickness was lower.

Grouping crossbred Holstein x Gyr heifers according to different feed efficiency indexes and its effects on energy and nitrogen partitioning, blood metabolic variables and gas exchanges

The objectives of this study were: i) to classify animals into groups of high and low feed efficiency (FE) using three FE indexes (Residual feed intake (RFI), Residual weight gain (RG) and Feed conversion efficiency (FCE)), and ii) to evaluate whether crossbreed Holstein x Gyr heifers divergent for FE indexes exhibit differences in nutrient intake and digestibility, energy partitioning, heat production, methane emissions, nitrogen partitioning and blood parameters. Thirty-five heifers were housed in a tie-stall, received ad libitum TMR (75:25, corn silage: concentrate) and were ranked and classified into high (HE) or low efficiency (LE) for RFI, RG and FCE. The number of animals for each HE group were 13 (< 0.5 standard deviation (SD) for RFI, 11 for RG and 11 for FCE (> 0.5 SD) and for the LE were 10 (> 0.5 SD) for RFI, 11 for RG and 12 for FCE (< 0.5 SD). Gas exchanges (O₂ consumption, CO₂ and CH₄ production) in open-circuit respiratory chambers and whole tract digestibility trial was performed. A completely randomized experimental design was used and the data were analyzed by ANOVA and correlation study. High efficiency animals for RFI produced less CO_2, consumed less O₂ and had lower heat production (HP). Methane production was positively correlated with RFI. High efficiency RG had higher O₂ consumption and CO₂ production in relation to LE-RG. High efficiency FCE had greater NFC digestibility, higher positive energy balance (EB) and excreted (11.4 g/d) less nitrogen in urine. High efficiency RG and FCE groups emitted less CH₄ per kg of weight gain than LE animals. Animals HE for RFI and FCE had lower β-hydroxybutyrate and higher glucose concentrations, respectively. The differences in intake, digestibility, energy and nitrogen partition, CH₄ emission, blood metabolic variables and heat production between the HE and LE groups varied according to the efficiency indexes adopted. The HP (kcal/d/BW^0.75) was lower for HE animals for RFI and FCE indexes.

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

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

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Relationship between feed efficiency indexes and thermography, blood, and ruminal parameters in pre-weaning dairy heifers

The objective of this study was to evaluate whether pre-weaning heifer calves divergent for residual feed intake (RFI) or residual feed intake and body weight gain (RIG) exhibit differences in thermography, blood, and ruminal parameters. Thirty-two Gyr heifer calves were enrolled in a 63-d trial and classified into 2 feed efficiency (FE) groups based on RFI and RIG (mean ± 0.5 SD). The groups were classified as high efficiency (HE) RFI (HE RFI, n = 9), HE RIG (HE RIG, n = 10), low efficiency (LE) RFI (LE RFI, n = 10), and LE RIG (LE RIG, n = 11). The amount of whole milk provided for each calf was calculated based on their metabolic weight at birth (42% x BW^0.75). The liquid diet was divided into two meals at 0700 and 1400 h. The total solid diet (TSD) was composed of 92% concentrate and 8% of Tifton 85 hay chopped in 5-cm lengths, as fed. Intake was measured daily. Blood concentrations of insulin, beta hydroxybutyrate, urea, and glucose, and ruminal pH, N-NH₃, and volatile fatty acids (VFA) were evaluated at 14, 28, 42, 56, and 70 days of age. Thermal images of the calves were taken with an infrared camera (FLIR T420, FLIR Systems Inc., Wilsonville, OR) on d 56 (±3) at 0600 h, before the morning feeding. Total VFA concentration and propionate as % of total VFA were 24.2% and 22.2% lower in HE RFI compared to LE RFI calves, respectively. On the other hand, acetate as % of total VFA was 10.6% greater in HE RFI than LE RFI calves. Blood urea concentration tended to be greater in LE RFI than HE RFI calves. High efficiency HE RIG tended to have 6.8% greater acetate and 15.4% lower propionate as % of total VFA than LE RIG. Blood insulin concentration was greater and blood glucose tended to be greater for LE RIG than HE RIG group. Low efficiency RIG group had greater left rib, left flank, and anus surface temperature measured by infrared thermography than the HE RIG group. Differences in ruminal fermentation do not seem to be associated with pre-weaning calves efficiency, while differences in protein metabolism seem to affect RFI during this phase. Infrared thermography appears to be correlated to RIG in pre-weaning heifer calves.

Characterization of feeding behavior traits in steers with divergent residual feed intake consuming a high-concentrate diet

The objective of this study was to examine the differences in feeding behavior patterns of steers with divergent phenotypes for residual feed intake (RFI). Three trials were conducted with 508 Angus-based composite crossbred steers (body weight [BW] = 309 ± 57 kg) fed a high-concentrate diet in pens equipped with electronic feed bunks (GrowSafe System). Initial and final carcass ultrasound measurements (intra-muscular fat, backfat depth, and rib-eye area) were collected on days 0 and 70, and BW measured at 14-d intervals. Individual dry matter intake (DMI) and feeding behavior traits were collected for 70 d, and RFI calculated as the residual from the regression of DMI on average daily gain (ADG) and mid-test BW0.75. Steers were ranked by RFI and assigned to low-, medium-, and high-RFI classes based on ± 0.5 SD from the mean RFI within the trial. The feeding behavior traits evaluated in this study included frequency and duration of bunk visit (BV) and meal events, head-down (HD) duration, mean meal length, time-to-bunk interval, the maximum nonfeeding interval, and the day-to-day variation of these traits, defined as the root mean squared error (RMSE) from linear regression of each trait on the day of trial. Additionally, three ratio traits were evaluated: BV events per meal, HD duration per BV event, and HD duration per meal event. Low-RFI (feed-efficient) steers consumed 16% less (P < 0.01) DMI, while BW and ADG were not different compared with high-RFI steers. Low-RFI steers had 18% fewer and 21% shorter (P < 0.01) BV events, and 11% fewer and 13% shorter (P < 0.01) meal events per day compared with high-RFI steers. Furthermore, low-RFI steers exhibited less (P < 0.05) day-to-day variance in DMI, as well as in frequency and duration of BV and meal events and HD duration compared with high-RFI steers. Differences in feeding behavior traits due to RFI were minimally affected by covariate adjustment for DMI, indicating that steers with divergent RFI have distinct feeding behavior patterns that are largely independent of differences in DMI. These results suggest that feeding behavior traits may be useful biomarkers for the prediction of feed efficiency in beef cattle.

The repeatability of feed intake and feed efficiency in beef cattle offered high-concentrate, grass silage and pasture-based diets

Breeding values for feed intake and feed efficiency in beef cattle are generally derived indoors on high-concentrate (HC) diets. Within temperate regions of north-western Europe, however, the majority of a growing beef animal's lifetime dietary intake comes from grazed grass and grass silage. Using 97 growing beef cattle, the objective of the current study was to assess the repeatability of both feed intake and feed efficiency across 3 successive dietary test periods comprising grass silage plus concentrates (S+C), grazed grass (GRZ) and a HC diet. Individual DM intake (DMI), DMI/kg BW and feed efficiency-related parameters, residual feed intake (RFI) and gain to feed ratio (G : F) were assessed. There was a significant correlation for DMI between the S+C and GRZ periods (r = 0.32; P < 0.01) as well as between the S+C and HC periods (r = 0.41; P < 0.001), whereas there was no association for DMI between the GRZ and HC periods. There was a significant correlation for DMI/kg BW between the S+C and GRZ periods (r = 0.33; P < 0.01) and between the S+C and HC periods (r = 0.40; P < 0.001), but there was no association for the trait between the GRZ and HC periods. There was a significant correlation for RFI between the S+C and GRZ periods (r = 0.25; P < 0.05) as well as between S+C and HC periods (r = 0.25; P < 0.05), whereas there was no association for RFI between the GRZ and HC periods. Gain to feed ratio was not correlated between any of the test periods. A secondary aspect of the study demonstrated that traits recorded in the GRZ period relating to grazing bite rate, the number of daily grazing bouts and ruminating bouts were associated with DMI (r = 0.28 to 0.42; P < 0.05 - 0.001), DMI/kg BW (r = 0.36 to 0.45; P < 0.01 - 0.001) and RFI (r = 0.31 to 0.42; P < 0.05 - 0.001). Additionally, the number of ruminating boli produced per day and per ruminating bout were associated with G : F (r = 0.28 and 0.26, respectively; P < 0.05). Results from this study demonstrate that evaluating animals for both feed intake and feed efficiency indoors on HC diets may not reflect their phenotypic performance when consuming conserved forage-based diets indoors or when grazing pasture.

Selection response and genetic parameter estimation of feeding behavior traits in Pekin ducks

Body weight-related traits and feeding behavior traits are important in poultry breeding and production. To investigate the heritability of feeding behavior and their genetic correlation with body weight-related traits in Pekin ducks, 5,594 Pekin ducks were selected. The information about body weight-related traits and feeding behavior from 3 to 6 wk of age were recorded by automatic electronic feeders. The heritability estimates for body weight, residual feed intake, and feeding behavior traits are relatively high (ranging from 0.29 to 0.65). We observed that total feed intake, meal feed intake, body weight at the age of 3 wk, and daily body weight gain had strong positive genetic correlations with body weight at the age of 6 wk. Moreover, body weight at the age of 3 wk also showed a positive genetic correlation with the feed conversion ratio (0.33). Total feeding time, daily feed intake, and feeding rate had significant positive phenotypic correlations with feed efficiency. However, the average interval between meals, the number of daily visits, and the number of meals all had a low genetic or phenotypic relationship with body weight and feed efficiency. In conclusion, our study revealed that body weight, residual feed intake, and feeding behavior traits were all highly heritable traits, and the selection for certain feeding behaviors could improve feed efficiency in Pekin ducks. This study is the first report about genetic parameter estimates about feeding behaviors in ducks based on large datasets and provides solid data for genetic study in ducks.

Genetic parameters and genome-wide association study regarding feed efficiency and slaughter traits in Charolais cows

Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h2 = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.

Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake

Background

Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals.

Results

A greater abundance of 14–3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14–3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14–3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression.

Conclusion

Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5890-z) contains supplementary material, which is available to authorized users.