High Residual Feed Intake Groups Research Articles

PSI-36 Phenotypic Relationship of Feed Efficiency and Fertility in Angus and Red Angus Bulls

Abstract Recent advances in measuring feed intake improve selection for efficient beef bulls; however, such selection must not decrease bull fertility. Objectives herein were to determine the phenotypic relationship between feed efficiency and fertility traits in growing Angus (n = 14) and Red Angus (n = 14) bulls. Two feeding trials were conducted at the CSU, Chico University Farm in 2017 (87 d) and 2018 (84 d). Each year, bulls were randomly assigned to 7 x 18 m pens equipped with GrowSafe feed intake units and allowed ad libitum access to water and feed (CP: 15.6%, TDN: 56.22%, NDF: 52%, DM basis). Performance traits included: feed conversion ratio (FCR) and residual feed intake [RFI; measured as the difference between predicted dry matter intake (PDMI) and actual dry matter intake (DMI)], start weight (SWT), end weight (EWT), metabolic mid-weight (MMWT), residual gain and average daily gain (ADG). Breeding soundness exams (BSE) were conducted at 18 mo of age and included traits: scrotal circumference (SC), motility (MT), and morphology (MP). Residual feed intake was calculated by regressing DMI on ADG and MMWT. The RFI group was categorized as low (0.5 SD above the RFI mean), marginal (± 0.5 SD about the RFI mean), and high (0.5 SD above the RFI mean) by year. Data were analyzed using ANOVA, blocking on year-pen and fitting breed and RFI group as independent factors. Tukey pairwise contrasts were run. Motility among breeds and RFI group were analyzed using chi-square. Pearson correlations were calculated between growth, feed efficiency, and BSE measures of SC and MP. There were no differences (P > 0.05) among breeds nor RFI groups for SWT, EWT, MMWT, residual gain, SC, and MT. No interaction was detected between breed and RFI group with exception of MP (P = 0.049); specifically, low RFI Red Angus bulls had poor MP compared to marginal and high RFI groups (66.94 ± 6.87 vs. 87.43 ± 3.77 and 93.74 ± 5.48 %, respectively). Angus bulls were superior to Red Angus bulls in ADG (1.23 ± 0.04 vs. 1.06 ± 0.05 kg/d; P = 0.01), FCR (7.98 ± 0.31 vs. 9.18 ± 0.38; P = 0.04), and RFI (-0.24 ± 0.09 vs. 0.09 ± 0.11 kg DMI/d; P = 0.04). High and marginal RFI groups had greater DMI compared to low RFI group (10.40 ± 0.26 and 9.64 ± 0.18 kg/d vs. 8.31 ± 0.32 kg/d; P < 0.001). There were no significant phenotypic correlations between growth and efficiency measures with SC and MP (P > 0.05). Cumulatively, results indicate that SC and MT were not affected in efficient bulls.

Comparative analyses of enteric methane emissions, dry matter intake, and milk somatic cell count in different residual feed intake categories of dairy cows

This study compared the different residual feed intake (RFI) categories of lactating Holsteins with respect to methane (CH4) emissions, dry matter intake (DMI, kg), milk somatic cell count (SCC, 103∙mL−1), and β-hydroxybutyrate (BHB, mmol∙L−1). The RFI was calculated in 131 lactating Holstein cows that were then categorized into −RFI (RFI < 0) vs. +RFI (RFI > 0) and low- [RFI < −0.5 standard deviation (SD)] vs. high-RFI (RFI > 0.5 SD) groups. Milk traits were recorded in 131 cows, whereas CH4 and carbon dioxide were measured in 83. Comparisons of −RFI vs. +RFI and low- vs. high-RFI showed 7.9% (22.3 ± 0.40 vs. 24.2 ± 0.39) and 12.8% (21.1 ± 0.40 vs. 24.2 ± 0.45) decrease (P < 0.05) in DMI of −RFI and low-RFI groups, respectively. Similarly, −RFI and low-RFI cows had lower (P < 0.05) CH4 (g∙d−1) by 9.7% (343.5 ± 11.1 vs. 380.4 ± 10.9) and 15.5% (332.5 ± 12.9 vs. 393.5 ± 12.6), respectively. Milk yield was not different (P > 0.05) in −RFI vs. +RFI and low vs. high comparisons. The −RFI and low-RFI cows had lower (P < 0.05) SCC in −RFI vs. +RFI and low-RFI vs. high-RFI comparisons. The BHB was lower (P < 0.05) in low-RFI compared with the high-RFI group. Low-RFI dairy cows consumed less feed, emitted less CH4 (g∙d−1), and had lower milk SCC and BHB without differing in milk yield.

Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle

BackgroundOptimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed.ResultsOn average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways.ConclusionThe most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.

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.

Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens.

Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.

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

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

PSII-34 Comparison of the activity level of high and low residual feed intake beef steers

Abstract Activity level may affect residual feed intake (RFI), and cattle that move more may have less energy for gain. We compared activity level in high and low RFI beef steers under different nutritional conditions. Lying time, lying duration and lying bouts were recorded at 1-minute intervals utilizing Hobo G Pendant Loggers attached to the right hind leg. To identify RFI classification, 57 Angus-cross steers were individually housed and offered ad libitum access to a TMR for 56 d. RFI was defined as the residual of the regression of DMI on mid-test BW0.75 and ADG. High and low RFI groups (14 steers each) were defined as &amp;gt; 0.5 SD above or below the mean of zero, respectively. Ad libitum feeding was followed by restricted feeding at 75% of previous ad libitum DMI/BW0.75. After 56 d ad libitum feeding, steers were moved to group pens, ad libitum fed 4 days (ADLIBFED), then fasted 4 days (ADLIBFASTED). This was followed by the 56 d individual restricted feeding, after which, steers were moved to group pens, fed 4 days of restricted DMI (RESTRICTFED), then fasted 4 days (RESTRICTFASTED). There was no difference in lying time (800 and 804 minutes/day, P = 0.85), lying bouts per day (9.8 and 11.4, P = 0.16) and lying duration (99 and 84 minutes/bout, P = 0.18) between low RFI and high RFI cattle, respectively. Fasted animals had less lying time each day (P &amp;lt; 0.05), manifested by fewer lying bouts per day (P &amp;lt; 0.05), that tended (P &amp;gt; 0.05) to be slightly longer than fed animals. Ad lib animals tended (P &amp;gt; 0.05) to have less lying time each day, with a similar number of lying bouts per day, that were slightly (P &amp;gt; 0.05) shorter than restricted animals. Although activity is not affected by RFI level, results suggest that periods of limited feed availability increases activity level.

Analysis of the basal colonic innate immune response of pigs divergent in feed efficiency and following an ex vivo lipopolysaccharide challenge.

While feed efficiency is influenced by multiple physiological processes, it is not known how efficient and inefficient pigs differ in relation to their basal immune response, and particularly their innate immune response to a microbial challenge. Hence, the objective was to examine the expression of genes encoding innate immune response markers in basal colonic tissue and colonic tissue following an ex vivo lipopolysaccharide (LPS) challenge from pigs divergent in residual feed intake (RFI). Pigs that differed in RFI were selected from two different farms of origin. Colonic tissue was harvested from high RFI (HRFI) and low (LRFI) pigs, and two experimental conditions were explored: the first was basal unchallenged tissue and the second was colonic tissue following an ex vivo LPS challenge. RNA was extracted and tested on a Nanostring panel of 72 genes coding for barrier defense proteins, transmembrane receptors, kinases, transcription regulators, cytokines, and cytokine regulators. In the basal unchallenged tissue, the LRFI pigs had increased expression of AOAH, AP1, and TRAM and the cytokines TNF, IL10, and CXCL8, compared with the HRFI pigs (P < 0.05), with a significant effect of farm of origin on 31 genes (P < 0.05). In the LPS-challenged tissues, the LRFI group had higher expression of TLR1, TLR7, TLR8, GPR43/FFAR2, JAK2, and NFAM1 compared with the HRFI group (P < 0.05). In conclusion, these data suggest that LRFI pigs have an upregulated basal colonic inflammatory state and a heightened response to an LPS challenge compared with the inefficient HRFI pigs. This immune profile potentially enhances their capacity to respond to an infectious challenge.

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs

BackgroundTo date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. The aim of this research was to use machine learning to identify genes associated with feed efficiency (FE) using transcriptomic (RNA-Seq) data from pigs that are phenotypically extreme for RFI.MethodsRFI was computed by considering within-sex regression on mean metabolic body weight, average daily gain, and average backfat gain. RNA-Seq analyses were performed on liver and duodenum tissue from 32 high and 33 low RFI pigs collected at 153 d of age. Machine-learning algorithms were used to predict RFI class based on gene expression levels in liver and duodenum after adjusting for batch effects. Genes were ranked according to their contribution to the classification using the permutation accuracy importance score in an unbiased random forest (RF) algorithm based on conditional inference. Support vector machine, RF, elastic net (ENET) and nearest shrunken centroid algorithms were tested using different subsets of the top rank genes. Nested resampling for hyperparameter tuning was implemented with tenfold cross-validation in the outer and inner loops.ResultsThe best classification was obtained with ENET using the expression of 200 genes in liver [area under the receiver operating characteristic curve (AUROC): 0.85; accuracy: 0.78] and 100 genes in duodenum (AUROC: 0.76; accuracy: 0.69). Canonical pathways and candidate genes that were previously reported as associated with FE in several species were identified. The most remarkable pathways and genes identified were NRF2-mediated oxidative stress response and aldosterone signalling in epithelial cells, the DNAJC6, DNAJC1, MAPK8, PRKD3 genes in duodenum, and melatonin degradation II, PPARα/RXRα activation, and GPCR-mediated nutrient sensing in enteroendocrine cells and SMOX, IL4I1, PRKAR2B, CLOCK and CCK genes in liver.ConclusionsML algorithms and RNA-Seq expression data were found to provide good performance for classifying pigs into high or low RFI groups. Classification was better with gene expression data from liver than from duodenum. Genes associated with FE in liver and duodenum tissue that can be used as predictive biomarkers for this trait were identified.

Relationship between residual feed intake and radiated heat loss using infrared thermography in young beef bulls

Residual feed intake (RFI) has been used to select metabolically efficient cattle in beef breeding programs, particularly for sire selection. Adoption of genetic selection using RFI has been limited due to the cost and difficulty of measuring individual feed intake. An alternative method of predicting RFI is to measure radiated heat loss using infrared thermography (IRT) as previous studies have shown promise using this technique to predict metabolic efficiency in mature cows, heifers, and growing bulls. The objective of this study was to explore use of IRT to predict RFI in growing beef bulls. Sixty bulls in each of two years were fed either a forage-based or a grain-based ration. Eye (Ey) and cheek (Ck) surface temperatures were measured using infrared images of the head collected on 16 and 14 sample days in Years 1 and 2, respectively, using a FLIR S60 camera. In Year 2, infrared images were collected continuously using a within-pen FLIR A310 camera system. Bulls were grouped into low, medium and high classes based on ± 0.5 standard deviations of backfat adjusted residual feed intake (RFIFat); RFIFat values ranged from − 2.27 to + 2.61 kg DM day−1 (mean=0.0; SD=0.61). Sample day Ey and Ck temperatures were pooled and an average temperature was calculated for individual bulls. Average Ey and Ck temperatures measured using the FLIR S60 and the within-pen camera did not differ significantly across low, medium and high RFI groups (P > 0.05). Temperature deviations associated with extremes in ambient temperature (placing animals outside their thermoneutral zone) or underlying subclinical health problems could bias results in IRT measurements and RFI ranking. Standardization of IRT data and the conditions during measurement is necessary to more accurately assess its potential use to predict RFI.

Methane production, rumen fermentation, and diet digestibility of Holstein and Jersey dairy cows being divergent in residual feed intake and fed at 2 forage-to-concentrate ratios

Improving feed efficiency of dairy cows through breeding is expected to reduce enteric methane production per unit of milk produced. This study examined the effect of 2 forage-to-concentrate ratios on methane production, rumen fermentation, and nutrient digestibility in Holstein and Jersey dairy cows divergent in residual feed intake (RFI). Before experimental onset, RFI was estimated using a random regression model on phenotypic herd data. Ten lactating Holstein and 10 lactating Jersey cows were extracted from the herd and allocated to a high or low pre-experimental RFI group of 5 animals each within breed. Cows were fed ad libitum with total mixed rations either low (LC) or high (HC) in concentrates during 3 periods in a crossover design with a back-cross and staggered approach. Forage-to-concentrate ratio was 68:32 for LC and 39:61 for HC. Cows adapted to the diets in 12 to 24 d and feces were subsequently collected on 2 d. Afterward, gas exchange was measured in respiration chambers and rumen liquid was collected once after cows exited the chambers. Pre-experimental RFI was included in the statistical analysis as a class (low and high RFI) or continuous variable. Methane per kilogram of dry matter intake (DMI) was lower for Holsteins than Jerseys and the response to increased concentrate level was more pronounced for Holsteins than Jerseys (27.2 vs.13.8%); a similar pattern was found for the acetate:propionate ratio. However, methane production per kilogram of energy-corrected milk (ECM) was unaffected by breed. Further, total-tract digestibility of neutral detergent fiber was higher for Jerseys than Holsteins. For RFI as a class variable, DMI, methane production regardless of the expression, and digestibility were unaffected by RFI. For RFI as a continuous variable, DMI was lower and methane per kilogram of DMI was higher for cows with negative (efficient) than positive (inefficient) RFI values, and neutral detergent fiber digestibility was higher for Holsteins with negative than positive RFI values, but not for Jerseys. Daily methane production and methane per kilogram of ECM were unaffected by RFI. In conclusion, methane per kilogram of DMI of Jerseys was lowered to a smaller extent in response to the HC diet than of Holsteins. When pre-experimental RFI was used as a continuous variable, higher methane per kilogram of DMI was found for cows with negative RFI than positive RFI values, but not for methane per kilogram of ECM. These findings call for validation in larger studies.

Hepatic mitochondrial function in Hereford steers with divergent residual feed intake phenotypes1

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.

Relationships between residual feed intake and feedlot performance, profitability, and carcass traits in Brahman cattle

ABSTRACT The present study aimed to evaluate the feedlot performance, profitability and carcass traits of Brahman bulls classified according to the residual feed intake (RFI). Twenty-four bulls (19-month old, 370±34kg live weight) were housed in individual pens for 54 days and had the daily feed intake (observed dry matter intake, DMIobs; DMI % live weight, LW) and average daily gain (ADG) measured. Ultrasound carcass evaluations were performed at the initial and final weighings, when measurements were taken of Longissimus dorsi area, ratio, Longissimus and Biceps femoris fat thickness. The animals were ranked and divided into high (&gt;+0.5 standard deviation; SD), medium (between ±0.5 SD from the mean), and low (&lt;-0.5 SD) RFI groups. Low-RFI animals had lower DMIobs (P&lt;0.10) and DMI % LW (P&lt;0.05). No significant differences in initial and final weight or ADG were noticed (P&gt;0.05). Low-RFI animals showed lower weight gain cost and higher daily profit (P&lt;0.05). Carcass traits were similar between groups, regardless of evaluation date (P&gt;0.05). Selection for RFI lead to animals with lower feed intake without affecting weight gain or carcass traits, thereby providing increased profitability for beef cattle farming.

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

This study was conducted to evaluate the utilisation of the residual feed intake (RFI) as a feed efficiency selection tool and its relationship with methane emissions. Eighteen Murrah buffalo (Bubalus bubalis) heifers were fed ad libitum with total mixed ration (TMR) for 120days. Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid-test metabolic body size (MBW0.75 ), heifers were assigned into low and high RFI groups. The RFI varied from -0.09 to +0.12kg DM/day with average RFI of -0.05 and 0.05kg DM/day in low and high RFI heifers respectively. Low RFI heifers ate 11.6% less DM each day, yet average daily gain (ADG) and feed utilisation were comparable among low and high RFI groups. Low RFI heifers required significantly (p<.05) less metabolizable energy for maintenance (MEm) compared to high RFI heifers. Apparent nutrient digestibility showed non-significant difference (p>.05) among low and high RFI groups. Although the nitrogen balance was similar among heifers of low and high RFI groups, nitrogen metabolism was significantly higher (p>.05) in high RFI heifers. Comparison of data from heifers exhibiting the low (n=9) and high (n=9) RFI showed that the low RFI heifers have lower enteric methane production and methane losses than high RFI heifers. In conclusion, results of this study revealed that selection of more efficient buffalo heifers has multiple benefits, such as decreased feed intake and less emission of methane.

Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake.

Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes.

Nutrient utilisation, growth performance and blood metabolites in Murrah buffalo calves (Bubalus bubalis) divergently selected for residual feed intake

ABSTRACTThe aim of this study was to evaluate differences in efficiency of feed utilisation between buffalo calves with low and high residual feed intake (RFI) by comparing feed intake, nutrient digestibility, growth traits and blood metabolites. Eighteen male Murrah buffalo calves (aged 4–6 months; 70 ± 1.0 kg body weight) were fed ad libitum with a total mixed ration for 120 d. Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid-test metabolic body size, calves were assigned into low and high RFI groups. The RFI varied from −0.33 to +0.28 kg DM/d with an average RFI of −0.14 and 0.14 kg DM/d in low and high RFI calves, respectively. Calves had a mean DMI of 1.9 and 2.4 kg/d and an ADG of 0.5 and 0.6 kg/d in low and high RFI groups, respectively. Low RFI calves ate 19.0% less DM each day and required significantly less metabolisable energy for maintenance compared with high RFI calves (12.5 vs. 16.7 MJ/d). Nutrient digestibility and nitrogen balance did not differ among low and high RFI calves. In more efficient animals (low RFI calves) higher (p < 0.05) plasma level of growth hormone, insulin-like growth factor-1 (IGF-1), triiodothyronine (T3) and lower concentration of thyroxin hormone were detected. No significant differences in levels of insulin, hydroxyproline, plasma and urine creatinine, total protein and albumin between high and low RFI groups were found. Blood metabolites showed significant (p < 0.05) differences at initial and final stages of study in both groups. At final stage of study, RFI showed negative correlations with growth hormone, IGF-1, T3, urine creatinine and albumin. Low RFI buffalo calves are more efficient in feed utilisation and the differences in blood metabolites are probably due to differences in feed intake and body metabolism.

Endocrine and hematological responses of beef heifers divergently ranked for residual feed intake following a bovine corticotropin-releasing hormone challenge.

The objective of this study was to determine if beef heifers divergently ranked on phenotypic residual feed intake (RFI) differed in their physiological stress response to an exogenous bovine corticotropin-releasing hormone (bCRH) challenge. Yearling Limousin × Friesian heifers ( = 86) were ranked by RFI. The 15 highest (mean 0.66 kg DM/d; high RFI) and 15 lowest (mean -0.72 kg DM/d; low RFI) ranking animals were used for this study. During the study period, heifers (mean age 485 ± 13 d; mean BW 408 ± 31.4 kg) were housed in a slatted-floor facility. To facilitate intensive blood collection, heifers were fitted aseptically with indwelling jugular catheters. All heifers received dexamethasone (DEX; 20 µg/kg BW i.m.) 12 h before the bCRH challenge (d 0). Heparinized blood samples were collected at -60 and 0 min before administration of DEX, and 12 h after DEX administration. Following DEX administration, cortisol and dehydroepiandrosterone (DHEA) concentrations similarly decreased ( ≥ 0.22) between high and low RFI groups. The response of the HPA axis to a standardized dose of bCRH (0.3 μg/kg BW) was examined. On d 0, serial blood samples were collected at -20, 0, 20, 40, 60, 80, 100, 120, 150, 180, 210, 240, 270, 330, and 390 min relative to the time of bCRH administration (0 min) and were analyzed for plasma cortisol and DHEA concentrations. Blood hematology variables were also determined at -20, 0, 20, 80, 150, 270, 330, and 390 min relative to bCRH administration. Neither an RFI × sampling time interaction nor a direct effect of RFI were detected ( ≥ 0.36) for plasma cortisol, DHEA concentrations, or cortisol:DHEA ratio. An effect of sample time was observed for cortisol ( < 0.001), DHEA ( = 0.04), and cortisol:DHEA ( = 0.02), with cortisol concentration peaking at 60 min post-CRH administration. The maximum concentration and rate of change in cortisol and DHEA concentrations following bCRH administration were not different ( ≥ 0.20) between the high and low RFI phenotypes. Similarly, an effect of RFI was not evident ( ≥ 0.16) for any of the hematology variables examined including neutrophil, lymphocyte, and leukocytes counts; white and red blood cell numbers; and hemoglobin concentrations. Our results suggest that responsiveness of the HPA to stress, at least at the level of the anterior pituitary gland, is not a significant contributor to variation in RFI among growing beef heifers.

The Effect of Divergence in Feed Efficiency on the Intestinal Microbiota and the Intestinal Immune Response in Both Unchallenged and Lipopolysaccharide Challenged Ileal and Colonic Explants.

Feed efficiency is an important trait in pig production, with evidence to suggest that the efficiencies of a variety of biological systems contribute to variation in this trait. Little work has been conducted on the contribution of the intestinal innate immune response to divergence in feed efficiency. Hence, the objective of this study was to examine select bacterial populations and gene expression profiles of a range of targets relating to gut health and immunity in the intestine of pigs phenotypically divergent in feed efficiency in: a) the basal state; and (b) following an ex-vivo lipopolysaccharide (LPS) challenge of ileal and colonic tissue. Male pigs (initial BW 22.4 kg (SD = 2.03)) were fed a standard finishing diet for the final 43 days prior to slaughter to evaluate feed intake and growth for the purpose of calculating residual feed intake (RFI). On day 115, 16 animals (average weight 85 kg, SEM 2.8 kg), designated high RFI (HRFI) and low RFI (LRFI) were slaughtered. The LRFI pigs had increased lactobacillus spp. in the caecum compared to HRFI pigs (P < 0.05). RFI groups did not differ in the expression of the measured genes involved in the innate immune system in the basal ileal or colonic tissues (P > 0.10). Interestingly, there was an interaction between RFI and LPS for the cytokines IL-8, IL-1, IL-6, TNF-α, Interferon-γ (IFN-γ) and SOCS3, with the LRFI group having consistently lower gene expression in the colon following the LPS challenge, compared to the HRFI group. The lower gene expression of SOCS and cytokines following an ex vivo LPS challenge supports the theory that a possible energy saving mechanism exists in the intestinal innate immune response to an immune challenge in more feed efficient pigs.

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

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

Biological mechanisms related to differences in residual feed intake in dairy cows

Residual feed intake (RFI), defined as the difference between an animal’s actual feed intake and expected feed intake over a specific period, is an inheritable character of feed conversion efficiency in dairy cows. Research has shown that a lower RFI could improve the profitability of milk production. This study explored variation in RFI by comparing the differences in body size, milk performance, feeding behavior, and serum metabolites in 29 Holstein cows in mid lactation. The cows were selected from a total of 84 animals based on their RFI following feedlot tests. Selected cows were ranked into high RFI (RFI >1 SD above the mean, n=14) and low RFI (RFI<1 SD below the mean, n=15). The low RFI cows (more efficient) consumed 1.59 kg/day less dry matter than the high RFI group (P<0.01), while they produced nearly equal 4% fat-corrected milk. The milk : feed ratio was higher for the low RFI group than for the high RFI group (P<0.05). The levels of milk protein (P<0.01), total solids (P<0.05), and nonfat solids (P<0.05) were also higher for the low RFI group, whereas milk urea nitrogen was lower (P<0.01). The daily feeding duration was shorter for the low RFI group than for the high RFI group (P<0.01). No significant differences were found in levels of glucose, β-hydroxybutyrate, prolactin, insulin, IGF-1, growth hormone or ghrelin, but the level of neuropeptide Y was higher (P<0.01) and levels of leptin and non-esterified fatty acid (P<0.05) were lower for the low RFI group than for the high RFI group. There were substantial differences between cows with different RFI, which might affect the efficiency of milk protein metabolism and fat mobilization.