Intake, growth and carcass traits in male progeny of sires differing in genetic merit for beef production

Validation of economic indexes under a controlled experimental environment, can aid in their acceptance and use as breeding tools to increase herd profitability. The objective of this study was to compare intake, growth and carcass traits in bull and steer progeny of high and low ranking sires, for genetic merit in an economic index. The Beef Carcass Index (BCI; expressed in euro (€) and based on weaning weight, feed intake, carcass weight, carcass conformation and fat scores) was generated by the Irish Cattle Breeding Federation as a tool to compare animals on genetic merit for the expected profitability of their progeny at slaughter. A total of 107 male suckler herd progeny, from 22 late-maturing 'continental' beef sires of high (n = 11) or low (n = 11) BCI were compared under either a bull or steer production system, and slaughtered at approximately 16 and 24 months of age, respectively. All progeny were purchased after weaning at approximately 6 to 8 months of age. Dry matter (DM) intake and live-weight gain in steer progeny offered grazed grass or grass silage alone, did not differ between the two genetic groups. Similarly, DM intake and feed efficiency did not differ between genetic groups during an ad libitum concentrate-finishing period on either production system. Carcasses of progeny of high BCI sires were 14 kg heavier (P < 0.05) than those of low BCI sires. In a series of regression analyses, increasing sire BCI resulted in increases in carcass weight (P < 0.01) and carcass conformation (P = 0.051) scores, and decreases in carcass fat (P < 0.001) scores, but had no effect on weaning weight or DM intake of the progeny. Each unit increase in sire expected progeny difference led to an increase in progeny weaning weight, DM intake, carcass weight, carcass conformation score and carcass fat score of 1.0 (s.e. = 0.53) kg, 1.1 (s.e. = 0.32) kg, 1.3 (s.e. = 0.31) kg, 0.9 (s.e. = 0.32; scale 1 to 15) and 1.0 (s.e. = 0.25; scale 1 to 15), respectively, none of which differed from the theoretical expectation of unity. The expected difference in profitability at slaughter between progeny of the high and low BCI sires was €42, whereas the observed phenotypic profit differential of the progeny was €53 in favour of the high BCI sires. Results from this study indicate that the BCI is a useful tool in the selection of genetically superior sires, and that actual progeny performance under the conditions of this study is within expectations for both bull and steer beef production systems.     

Genome-wide association analysis for feed efficiency in Angus cattle

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.     

Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.     

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.     

Identification of polymorphisms influencing feed intake and efficiency in beef cattle

Feed efficiency is an economically important trait in beef cattle. Net feed efficiency, measured as residual feed intake (RFI), is the difference between actual feed intake and the predicted feed intake required for maintenance and gain of the animal. SNPs that show associations with RFI may be useful quantitative trait nucleotides for marker-assisted selection. This study identified associations between SNPs underlying five RFI QTL on five bovine chromosomes (BTA2, 5, 10, 20 and 29) with measures of dry matter intake (DMI), RFI and feed conversion ratio (FCR) in beef cattle. Six SNPs were found to have effects on RFI (P < 0.05). The largest single SNP allele substitution effect for RFI was -0.25 kg/day located on BTA2. The combined effects of the SNPs found significant in this experiment explained 6.9% of the phenotypic variation of RFI. Not all the RFI SNPs showed associations with DMI and FCR even though these traits are highly correlated with RFI (r = 0.77 and r = 0.62 respectively). This shows that these SNPs may be affecting the underlying biological mechanisms of feed efficiency beyond feed intake control and weight gain efficiency. These SNPs can be used in marker-assisted selection but first it will be important to verify these effects in independent populations of cattle.     

Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Background

Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associated with high and low feed efficiency and their regulator genes in Danish Holstein and Jersey cows.RNA-sequencing data from Holstein and Jersey cows with high and low residual feed intake (RFI) and treated with two diets (low and high concentrate) were used. Approximately 26 million and 25 million pair reads were mapped to bovine reference genome for Jersey and Holstein breed, respectively. Subsequently, the gene count expressions data were analysed using a Weighted Gene Co-expression Network Analysis (WGCNA) approach. Functional enrichment analysis from Ingenuity® Pathway Analysis (IPA®), ClueGO application and STRING of these modules was performed to identify relevant biological pathways and regulatory genes.

Results

WGCNA identified two groups of co-expressed genes (modules) significantly associated with RFI and one module significantly associated with diet. In Holstein cows, the salmon module with module trait relationship (MTR)?=?0.7 and the top upstream regulators ATP7B were involved in cholesterol biosynthesis, steroid biosynthesis, lipid biosynthesis and fatty acid metabolism. The magenta module has been significantly associated (MTR?=?0.51) with the treatment diet involved in the triglyceride homeostasis. In Jersey cows, the lightsteelblue1 (MTR?=???0.57) module controlled by IFNG and IL10RA was involved in the positive regulation of interferon-gamma production, lymphocyte differentiation, natural killer cell-mediated cytotoxicity and primary immunodeficiency.

Conclusion

The present study provides new information on the biological functions in liver that are potentially involved in controlling feed efficiency. The hub genes and upstream regulators (ATP7b, IFNG and IL10RA) involved in these functions are potential candidate genes for the development of new biomarkers. However, the hub genes, upstream regulators and pathways involved in the co-expressed networks were different in both breeds. Hence, additional studies are required to investigate and confirm these findings prior to their use as candidate genes.

     

Crossbreeding applied to systems of beef cattle production to improve performance traits and carcass quality

Crossbreeding represents an important technique to improve growth, beef quality and adaptability in beef production systems in tropical countries. The aim of this study was to evaluate sire and dam breed effects on performance and carcass traits of crossbred cattle produced in a tropical environment. Heifers and steers were evaluated during the pre-weaning, the post-weaning (n = 173) and the finishing phase (n = 123). Animals were produced by mating Nellore (N_N), Angus × Nellore (A_N) and Caracu × Nellore (C_N) dams with Braford, Charbray and Caracu sires. After weaning, animals were raised grazing on Marandu grass for 12 months; thereafter they were housed in individual pens and finished in a feedlot, receiving a total mixed ration. Ultrasound carcass evaluations were performed to determine ribeye area (R_A), backfat thickness (B_T) and rump fat thickness (R_T). A_N progeny were heavier at birth than N_N (P < 0.05), and Braford progeny had greater birth BW than Caracu (P < 0.05). Greater weaning BW was observed in the A_N and C_N offspring compared to N_N (P < 0.01). Greater average daily gain during the post-weaning period was verified in the N_N progeny compared to C_N (P < 0.05). No dam or sire breed effects were observed for BW at the end of the post-weaning period (P > 0.05). Progeny of N_N cows had greater B_T (P < 0.05) and R_T (P < 0.01) at the end of the post-weaning period in relation to C_N. Greater R_A was observed in the Caracu progeny than in the Braford (P < 0.05), which showed greater R_T than the Charbray progeny at the end of the post-weaning period (P < 0.05). No dam or sire breed effects were verified for final BW at the feedlot or for feed efficiency traits (P > 0.05). A_N progeny were superior in final B_T compared to C_N (P < 0.01), and Braford progeny had greater R_T at the end of finishing than Charbray (P = 0.05). The use of crossbred dams allows an increase in productivity until weaning, but this is not maintained in the post-weaning and finishing periods. The use of Braford sires produces similar growth performance in the different stages of the production system to those seen with Charbray and Caracu sires but generates animals with higher fat thickness at the end of finishing, which may improve carcass quality and commercial value.     

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake

Residual feed intake (RFI), defined as the difference between observed and expected feed intake based on growth and backfat, has been used to investigate genetic variation in feed efficiency in cattle, poultry and pigs. However, little is known about the biological basis of differences in RFI in pigs. To this end, the objective of this study was to evaluate the fifth generation of a line of pigs selected for reduced RFI against a randomly selected Control line for performance, carcass and chemical carcass composition and overall efficiency. Here, emphasis was on the early grower phase. A total of 100 barrows, 50 from each line, were paired by age and weight (22.6 ± 3.9 kg) and randomly assigned to one of four feeding treatments in 11 replicates: ad libitum (Ad), 75% of Ad (Ad75), 55% of Ad (Ad55) and weight stasis (WS), which involved weekly adjustments in intake to keep body weight (BW) constant for each pig. Pigs were individually penned (group housing was used for selection) and were on treatment for 6 weeks. Initial BW did not significantly differ between the lines (P > 0.17). Under Ad feeding, the low RFI pigs consumed 8% less feed compared with Control line pigs (P < 0.06), had less carcass fat (P < 0.05), but with no significant difference in growth rate (P > 0.85). Under restricted feeding, low RFI pigs under the Ad75 treatment had a greater rate of gain while consuming the same amount of feed as Control pigs. Despite the greater gain, no significant line differences in carcass composition or carcass traits were observed. For the WS treatment, low RFI pigs had similar BW (P > 0.37) with no significant difference in feed consumption (P > 0.32). Overall, selection for reduced RFI has decreased feed intake, with limited differences in growth rate but reduced carcass fat, as seen under Ad feeding. Collectively, results indicate that the effects of selection for low RFI are evident during the early grower stage, which allows for greater savings to the producer.     

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Background

Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.

Methodology/Principal findings

Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping.

Conclusions/significance

Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.     

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.     

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

The 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.     

über den Einfluß von Diäthylstilboestrol und anderer Wirkstoffe auf den Stoffwechsel männlicher Ratten

The presented study aimed at investigating the residual feed intake (RFI) of Sahiwal calves, nutrient utilisation as affected by RFI and its relationship with methane (CH₄) emissions and some blood metabolites. Eighteen male Sahiwal calves (10–18 months of age; mean body weight 133 kg) were fed ad libitum with a total mixed ration. After calculating RFI for individual calves (?0.40 to +0.34 kg DM/d), they were divided into three groups with low, medium and high RFI, respectively. Dry matter intake (DMI) was higher (p < 0.05) in Group High RFI, whereas digestibility of all nutrients except crude protein and ether extract was significantly higher in Group Low RFI. Nitrogen balance was also significantly higher in Group Low RFI (20.2 g/d) than in Group High RFI (17.0 g/d). Average daily gain and feed conversion ratio were similar among the groups. With exception of glucose, concentrations of all measured blood metabolites were higher in Group High RFI (p < 0.05). Compared with Group High RFI, the CH₄ emission of Group Low RFI was significantly lower (on the basis g/d and g/kg DMI by 11% and 19%, respectively). Furthermore, the CH₄ emission [g/d] was significantly correlated with RFI (r = 0.77). Because higher feed efficiency and less CH₄ production were observed in Group Low RFI, it was concluded that RFI can be used as a measure of feed efficiency, which has a potential to select Sahiwal calves for lowered CH₄ emissions.     

Genetic parameters for performance,feed efficiency,and carcass traits in Senepol heifers

Improving feed efficiency is a key breeding goal in the beef cattle industry. In this study, we estimated the genetic parameters for feed efficiency and carcass traits in Senepol cattle raised in tropical regions. Various indicators of feed efficiency [gain to feed ratio (G:F), feed conversion ratio (FCR), residual weight gain (RG), residual intake and body weight gain (RIG), and residual feed intake (RFI)] as well as growth [final BW, average daily gain (ADG), and DM intake (DMI)], and carcass [rib-eye area (REA), backfat thickness (BF), intramuscular fat score, and carcass conformation score] traits were included in the study. After data editing, records from 1 393 heifers obtained between 2009 and 2018 were used for the analyses. We fitted an animal model that included contemporary group (animals from the same farm that were evaluated in the same test season) as the fixed effect, and a linear effect of animal age at the beginning of the test as a covariate; in addition to random direct additive genetic and residual effects. The (co)variance components were estimated by Bayesian inference in uni- and bivariate analyses. Our results showed that feed efficiency indicators derived from residual variables such as RG, RIG, and RFI can be improved through genetic selection (h² = 0.14 ± 0.06, 0.13 ± 0.06, and 0.20 ± 0.08, respectively). Variables calculated as ratios such as G:F and FCR were more influenced by environmental factors (h² = 0.08 ± 0.05 and 0.09 ± 0.05), and were, therefore, less suitable for use in breeding programs. The traits with the greatest and impact on genetic progress in feed efficiency were ADG, REA, and BF. The traits with the greatest and least impact on growth and carcass traits were RG and RFI, respectively. Selection for feed efficiency will result in distinct overall effects on the growth and carcass traits of Senepol heifers. Direct selection for lower RFI may reduce DMI and increase carcass fatness at the finishing stage, but it might also result in reduced growth and muscle deposition. Residual BW gain is associated with the highest weight gain and zero impact on REA and BF, however, it is linked to higher feed consumption. Thus, the most suitable feed efficiency indicator was RIG, as it promoted the greatest decrease in feed intake concomitant with faster growth, with a similar impact on carcass traits when compared to the other feed efficiency indicators.     

Phenotypic and genetic relationships between growth and feed intake curves and feed efficiency and amino acid requirements in the growing pig

Improvement of feed efficiency in pigs has been achieved essentially by increasing lean growth rate, which resulted in lower feed intake (FI). The objective was to evaluate the impact of strategies for improving feed efficiency on the dynamics of FI and growth in growing pigs to revisit nutrient recommendations and strategies for feed efficiency improvement. In 2010, three BWs, at 35±2, 63±9 and 107±7 kg, and daily FI during this period were recorded in three French test stations on 379 Large White and 327 French Landrace from maternal pig populations and 215 Large White from a sire population. Individual growth and FI model parameters were obtained with the InraPorc^R software and individual nutrient requirements were computed. The model parameters were explored according to feed efficiency as measured by residual feed intake (RFI) or feed conversion ratio (FCR). Animals were separated in groups of better feed efficiency (RFI⁻ or FCR⁻), medium feed efficiency and poor feed efficiency. Second, genetic relationships between feed efficiency and model parameters were estimated. Despite similar average daily gains (ADG) during the test for all RFI groups, RFI⁻ pigs had a lower initial growth rate and a higher final growth rate compared with other pigs. The same initial growth rate was found for all FCR groups, but FCR⁻ pigs had significantly higher final growth rates than other pigs, resulting in significantly different ADG. Dynamic of FI also differed between RFI or FCR groups. The calculated digestible lysine requirements, expressed in g/MJ net energy (NE), showed the same trends for RFI or FCR groups: the average requirements for the 25% most efficient animals were 13% higher than that of the 25% least efficient animals during the whole test, reaching 0.90 to 0.95 g/MJ NE at the beginning of the test, which is slightly greater than usual feed recommendations for growing pigs. Model parameters were moderately heritable (0.30±0.13 to 0.56±0.13), except for the precocity of growth (0.06±0.08). The parameter representing the quantity of feed at 50 kg BW showed a relatively high genetic correlation with RFI (0.49±0.14), and average protein deposition between 35 and 110 kg had the highest correlation with FCR (−0.76±0.08). Thus, growth and FI dynamics may be envisaged as breeding tools to improve feed efficiency. Furthermore, improvement of feed efficiency should be envisaged jointly with new feeding strategies.     

Relationship of high density lipoprotein cholesterol to cholesterol metabolism in the baboon (Papio sp.)

Genetic effects on serum high density lipoprotein (HDL) cholesterol concentration and several parameters of a two-pool model of cholesterol metabolism were investigated in 79 baboons, the progeny of 6 sires. Significant differences (P less than 0.05) were observed among the sire progeny groups for HDL cholesterol (HDL-C), cholesterol production rate, cholesterol mass of pool A, and the rate constants KA and KAB. Rank correlations (rs) revealed that the sire progeny group means for HDL-C are closely correlated with those for the cholesterol mass of pool A (rs = 0.89), KA (rs = -0.78), and KAB (rs = -0.94). These strong correlations suggest that pool A, KA, and KAB are influenced to a large degree by the same genes that regulate HDL-C concentration. The strong inverse relationship (rs = -0.78) between HDL-C and KA suggests that the differences among these sire progeny groups for HDL-C are due chiefly to those metabolic processes which regulate cholesterol excretion from pool A. This conclusion is consistent with reports that HDL-C is a preferred precursor for bile acid synthesis.     

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.     

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.