Development and validation of a model for early prediction of residual feed intake in beef cattle using plasma biomarkers

Identification of plasma biomarkers for feed efficiency in growing beef cattle offers a promising opportunity for developing prediction models to improve precision feeding strategies. However, these models must accurately predict feed efficiency at early stages of fattening. Our study aimed to evaluate the reliability of candidate biomarkers previously identified in late-fattening cattle when analysed during early fattening stages and to develop diet-specific prediction equations for residual feed intake (RFI). From a total of 364 Charolais bulls across seven cohorts, we selected 64 animals with extreme RFI values. The animals were fed either a corn‑ or grass-silage diets. These animals were chosen from four out of the available seven cohorts. Animals from three cohorts (24 high-RFI and 24 low-RFI, having a mean RFI difference of 1.48 kg/d) were used for biomarker confirmation and prediction model training. Animals from a fourth cohort (8 high-RFI and 8 low-RFI, having a mean RFI difference of 0.98 kg/d) were used for model external validation. Blood samples were collected at the beginning of the feed efficiency test (333 ± 20 days), and plasma underwent targeted metabolomic for 630 metabolites, natural abundance of 15N (δ15N), insulin, and IGF-1 analysis. Seven previously identified plasma biomarkers for RFI in late-fattening beef cattle still kept their capability for discriminating low and high RFI animals when analysed during early fattening stages (P < 0.05). Among these confirmed biomarkers, five were common for both grass- and corn-fed animals (creatinine, β-alanine, triglyceride TG18:0_34:2, symmetric dimethyl-arginine and phosphatidylcholine PC aa C30:2) while two were diet-specific (IGF-1 for grass silage-based diet, and isoleucine for corn silage-based diet. No new plasma biomarkers of RFI were identified at early-fattening stages (false discovery rate  > 0.05). Prediction models were developed based on seven confirmed RFI biomarkers analysed during early-fattening. Two logistic regression models incorporating creatinine and either IGF-1 (for grass silage-based diet) or PC aa C30:2 (for corn silage-based diet) effectively distinguished between high- and low-RFI animals with high sensitivity and specificity (area under the curve > 0.80). The biomarkers used in the models showed moderate to high repeatability between early and late fattening stages (0.45 < r < 0.65). The models were successfully externally validated, with more than 85% of animals from the fourth cohort correctly classified. Once validated in larger cohorts and utilising cost-effective and rapid analytical methods, these models could support precision feeding and breeding programmes, aiming to reduce the cost of raising beef cattle.

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.

A conceptual model of cow-calf systems functioning on native grasslands in a subtropical region

Cow-calf systems utilise grazing of native grasslands for beef cattle propagation and constitute the principal livestock activity in the Pampas and Campos areas. Cow-calf system sustainability is questioned because of their low production levels and negative environmental impact. Ecological intensification has been proposed as a way out that constitutes an alternative to dominant discourses based on increasing external-input use. There is, however, a considerable gap between the availability of scientific knowledge to promote the ecological intensification of cow-calf systems and farmers' practices. This gap between scientific knowledge availability and farmers' practices can be made explicit, and its consequences for systems performance can be explored through a conceptual model. Conceptual models are tools to build a systems view of the interactions among the production system's state variables, farm management, and resulting system performance. In this paper, we develop a conceptual model of cow-calf systems on native grasslands of the Pampas and Campos regions to support the diagnosis and redesign of farm systems towards ecological intensification. We apply the conceptual model to analyse cow-calf systems in Uruguay, drawing on a survey among 250 Uruguayan livestock farmers. Using the model, we show that in Uruguay, the level of implementation of strategic, tactical, and decision-supporting techniques is low. Consequently, most farms have poor control of the grazing intensity and timing of main events in the production cycle. This results in ample room to improve the productive and environmental performance of most cow-calf farms in Uruguay. We distinguished three broad types of cow-calf systems based on the degree of implementation of techniques, the evolution of state variables throughout the year, and productive indicators. These types imply different departure points and strategies for a sustainability transition process. The conceptual model designed in this paper may support the cow-calf systems sustainability transition in the context of co-innovation processes by aiding the interactive diagnosis and redesign of farm systems.

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.

Differential hepatic oxidative status in steers with divergent residual feed intake phenotype

Oxidative stress occurs when oxidant production exceeds the antioxidant capacity to detoxify the reactive intermediates or to repair the resulting damage. Feed efficiency has been associated with mitochondrial function due to its impact on cell energy metabolism. However, mitochondria are also recognized as a major source of oxidants. The aim of this study was to determine lipid and protein oxidative stress markers, and gene and protein expression as well as activity of antioxidant enzymes in the liver of steers of divergent residual feed intake (RFI) phenotypes. Hereford steers (n = 111) were evaluated in post-weaning 70 days standard test for RFI. Eighteen steers exhibiting the greatest (n = 9; high-RFI) and the lowest (n = 9; low-RFI) RFI values were selected for this study. After the test, steers were managed together under grazing conditions until slaughter when they reached the slaughter body weight. At slaughter, hepatic samples were obtained, were snap-frozen in liquid nitrogen and stored at -80°C until analyses. Hepatic thiobarbituric acid reactive species and protein carbonyls were greater (P = 0.05) and hepatic 4-hydroxynonenal protein adducts tended (P = 0.10) to be greater for high- than low-RFI steers. Hepatic gene expression glutathione peroxidase 4, glutamate-cysteine ligase catalytic subunit and peroxiredoxin 5 mRNA was greater (P ≤ 0.05) and glutathione peroxidase 3 mRNA tended (P = 0.10) to be greater in low- than high-RFI steers. Hepatic protein expression and enzyme activity of manganese superoxide dismutase and glutathione peroxidase enzyme activity tended (P ≤ 0.10) to be greater for low- than high-RFI steers. High-efficiency steers (low-RFI) probably had better hepatic oxidative status which was strongly associated with greater antioxidant ability near to the oxidant production site and, therefore, reduced oxidative stress of the liver. Decreased hepatic oxidative stress would reduce maintenance requirements due to a lower protein and lipid turnover and better efficiency in the use of energy.

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

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

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Background

Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired. In this study, we aimed to explore whether differences exist in the global gene expression profiles of peripheral blood of 35 to 42 day-old pigs with extremely low (more efficient) and high RFI (less efficient) values from two lines that were divergently selected for RFI during the grow-finish phase, to use such information to explore the potential molecular basis of RFI differences, and to initiate development of predictive biomarkers for RFI.

Results

We identified 1972 differentially expressed genes (DEGs) (q ≤ 0.15) between the low (n = 15) and high (n = 16) RFI groups of animals by using RNA sequencing technology. We validated 24 of 37 selected DEGs by reverse transcription-quantitative PCR (RT-qPCR) in a joint analysis of 24 (12 per line) of the 31 samples already used for RNA-seq plus 24 (12 per line) novel samples from the same contemporary group of pigs. Using an analysis of the 24 novel samples alone, only nine of the 37 selected DEGs were validated. Genes involved in small molecule biosynthetic process, antigen processing and presentation of peptide antigen via major histocompatibility complex (MHC) class I, and steroid biosynthetic process were overrepresented among DEGs that had higher expression in the low versus high RFI animals. Genes known to function in the proteasome complex or mitochondrion were also significantly enriched among genes with higher expression in the low versus high RFI animals. Alternatively, genes involved in signal transduction, bone mineralization and regulation of phosphorylation were overrepresented among DEGs with lower expression in the low versus high RFI animals. The DEGs significantly overlapped with genes associated with disease, including hyperphagia, eating disorders and mitochondrial diseases (q < 1E-05). A weighted gene co-expression network analysis (WGCNA) identified four co-expression modules that were differentially expressed between the low and high RFI groups. Genes involved in lipid metabolism, regulation of bone mineralization, cellular immunity and response to stimulus were overrepresented within the two modules that were most significantly differentially expressed between the low and high RFI groups. We also found five of the DEGs and one of the co-expression modules were significantly associated with the RFI phenotype of individual animals (q < 0.05).

Conclusions

The post-weaning blood transcriptome was clearly different between the low and high RFI groups. The identified DEGs suggested potential differences in mitochondrial and proteasomal activities, small molecule biosynthetic process, and signal transduction between the two RFI groups and provided potential new insights into the molecular basis of RFI in pigs, although the observed relationship between the post-weaning blood gene expression and RFI phenotype measured during the grow-finish phase was not strong. DEGs and representative genes in co-expression modules that were associated with RFI phenotype provide a preliminary list for developing predictive biomarkers for RFI in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2395-x) contains supplementary material, which is available to authorized users.

Effect of residual feed intake on hypothalamic gene expression and meat quality in Angus-sired cattle grown during the hot season

The relationship between heat stress, meat quality, and residual feed intake (RFI) is unknown in growing steers. To address this issue, high RFI (HRFI) and low RFI (LRFI) individuals were compared by assessing RFI in 48 Angus-sired steers during a 70-d feeding trial conducted during July through September to identify steers with calculated RFI at least 2 SD apart. The association of RFI with indices of meat quality and expression of genes within hypothalamic and adipose tissue was then determined in LRFI and HRFI steers. While on test, feed intake was recorded daily with BW and hip heights recorded every 14 d. Ultrasound measurements of rib eye area (REA) and backfat (BF) were recorded initially and before harvest. Carcass and growth data were analyzed using a mixed model with RFI level (LRFI and HRFI) as the independent variable. The least square means for RFI were -1.2 and 0.99 kg DMI/d, respectively, for the LRFI and HRFI cohorts (P < 0.0001). Dry matter intake was higher for the HRFI individuals versus the LRFI steers (P < 0.0001) while on-test gain was not different (P < 0.95). Marbling score was greater in LRFI than HRFI steers (P < 0.05). However, there were no differences in REA (P < 0.53), BF (P < 0.65), yield grade (P < 0.24), or objective Hunter color measures between LRFI and HRFI steers indicating there was no consistent relationship between RFI and indices of meat quality. Hypothalamic neuropeptide Y (NPY), agouti related protein (AGRP), relaxin-3 (RLN3), melanocortin 3 receptor, and relaxin/insulin-like family peptide receptor 1 (RXFP1) mRNA were expressed 280, 185, 202, 183, and 163% greater, respectively (P < 0.01), while proopiomelanocortin (POMC) mRNA was expressed 42% lower in LRFI than HRFI animals (P < 0.05). Hypothalamic GnRH mRNA expression was 67% lower while gonadotropin inhibiting hormone (GnIH) mRNA was 209% higher in LRFI than HRFI animals (P < 0.01). Pituitary expression of FSHβ and LHβ correlated to hypothalamic GnRH levels (P < 0.05) indicating changes in gene expression within the hypothalamus had functional consequences. Leptin mRNA expression levels were not different between adipose tissue of LRFI or HRFI steers (P < 0.84). These data indicate that animals with superior RFI evaluated during warm conditions have higher expression of orexigenic neuropeptide genes independent of the expression of adipose-derived leptin. Furthermore, the gonadotropin axis may also influence feed efficiency under these conditions.

Residual feed intake studies in Angus-sired cattle reveal a potential role for hypothalamic gene expression in regulating feed efficiency

Mechanisms underlying variation in residual feed intake (RFI), a heritable feed efficiency measure, are poorly understood while the relationship between RFI and meat quality is uncertain. To address these issues, 2 divergent cohorts consisting of High (HRFI) and Low (LRFI) RFI individuals were created by assessing RFI in 48 Angus-sired steers during a 70 d feeding trial to identify steers with divergent RFI. The association of RFI with indices of meat quality and expression of genes within hypothalamic and adipose tissue was then determined in LRFI and HRFI steers. While on test, feed intake was recorded daily with BW and hip heights recorded at 14 d intervals. Ultrasound measurements of rib eye area (REA) and backfat (BF) were recorded initially and before harvest. Carcass and growth data were analyzed using a mixed model with RFI level (LRFI, HRFI) as the independent variable. The least-square means (lsmeans) for RFI were -1.25 and 1.51 for the LRFI and HRFI cohorts (P < .0001). Dry matter intake was higher for the HRFI individuals versus the LRFI steers (P < .0001) while on test BW gain was not different between the 2 groups (P < 0.73). There were no differences detected in marbling score (P < 0.93), BF (P < 0.61), REA (P < 0.15), yield grade (P < 0.85) or objective Hunter color measures between LRFI and HRFI steers indicating that there was no relationship between RFI and meat quality. Neuropeptide-Y (NPY), relaxin-3 (RLN3), melanocortin 4 receptor (MC4R), and GnRH mRNA expression was 64%, 59%, 58%, 86% lower (P < 0.05), respectively, while gonadotropin inhibiting hormone (GnIH) and pro-opiomelanocortin (POMC) mRNA expression was 198% and 350% higher (P < 0.01) in the arcuate nucleus of LRFI steers. Expression of agouti-related protein (AGRP), relaxin/insulin-like family peptide receptor 1 (RXFP1), and melanocortin 3 receptor mRNA was similar between LRFI and HRFI animals. Pituitary expression of FSHβ (P < 0.03) and LHβ (P < 0.01) was correlated to hypothalamic GnRH levels suggesting that changes in gene expression within the arcuate nucleus had functional consequences. Leptin mRNA expression was 245% higher in the adipose tissue of LRFI steers consistent with lower levels of NPY and higher expression of POMC in their hypothalami. These data support the hypothesis that differences in hypothalamic neuropeptide gene expression underlie variation in feed efficiency in steers while the gonadotropin axis may also influence feed efficiency.