Maternal nutrient restriction in mid-to-late gestation influences fetal mRNA expression in muscle tissues in beef cattle.

BACKGROUND: Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared with 140% of total metabolizable energy requirements, fed to cows during mid-to-late gestation, influences phenotypic development of fetuses and mRNA expression of growth (Insulin-Like Growth Factor family and Insulin Receptor (INSR)), myogenic (Myogenic Differentiation 1 (MYOD1), Myogenin (MYOG), Myocyte Enhancer Factor 2A (MEF2A), Serum Response Factor (SRF)) and adipogenic (Peroxisome Proliferator Activated Receptor Gamma (PPARG)) genes in fetal longissimus dorsi (LD) and semitendinosus (ST) muscle. DNA methylation of imprinted genes, Insulin Like Growth Factor 2 (IGF2) and Insulin Like Growth Factor 2 Receptor (IGF2R), and micro RNA (miRNA) expression, were also examined as potential consequences of poor maternal nutrition, but also potential regulators of altered gene expression patterns. RESULTS: While the nutrient restriction impacted dam body weight, no differences were observed in phenotypic fetal measurements (weight, crown-rump length, or thorax circumference). Interestingly, LD and ST muscles responded differently to the differential pre-natal nutrient levels. While LD muscle of restricted fetal calves had greater mRNA abundances for Insulin Like Growth Factor 1 and its receptor (IGF1 and IGF1R), IGF2R, INSR, MYOD1, MYOG, and PPARG, no significant differences were observed for gene expression in ST muscle. Similarly, feed restriction had a greater impact on the methylation level of IGF2 Differentially Methylated Region 2 (DMR2) in LD muscle as compared to ST muscle between treatment groups. A negative correlation existed between IGF2 mRNA expression and IGF2 DMR2 methylation level in both LD and ST muscles. Differential expression of miRNAs 1 and 133a were also detected in LD muscle. CONCLUSIONS: Our data suggests that a nutrient restriction of 85% as compared to 140% of total metabolizable energy requirements during the 2nd half of gestation can alter the expression of growth, myogenic and adipogenic genes in fetal muscle without apparent differences in fetal phenotype. It also appears that the impact of feed restriction varies between muscles suggesting a priority for nutrient partitioning depending on muscle function and/or fiber composition. Differences in the methylation level in IGF2, a well-known imprinted gene, as well as differences in miRNA expression, may be functional mechanisms that precede the differences in gene expression observed, and could lead to trans-generational epigenetic programming.

Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle.

BACKGROUND: Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet management. In this study, 81 and 83 fatty acid traits were measured in subcutaneous adipose (SQ) and longissimus lumborum muscle (LL), respectively, from 1366 purebred and crossbred beef steers and heifers that were genotyped on the Illumina BovineSNP50 Beadchip. The objective was to conduct genome-wide association studies (GWAS) for the fatty acid traits and to evaluate the accuracy of genomic prediction for fatty acid composition using genomic best linear unbiased prediction (GBLUP) and Bayesian methods. RESULTS: In total, 302 and 360 significant SNPs spanning all autosomal chromosomes were identified to be associated with fatty acid composition in SQ and LL tissues, respectively. Proportions of total genetic variance explained by individual significant SNPs ranged from 0.03 to 11.06% in SQ, and from 0.005 to 24.28% in the LL muscle. Markers with relatively large effects were located near fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), and thyroid hormone responsive (THRSP) genes. For the majority of the fatty acid traits studied, the accuracy of genomic prediction was relatively low (<0.40). Relatively high accuracies (> = 0.50) were achieved for 10:0, 12:0, 14:0, 15:0, 16:0, 9c-14:1, 12c-16:1, 13c-18:1, and health index (HI) in LL, and for 12:0, 14:0, 15:0, 10 t,12c-18:2, and 11 t,13c + 11c,13 t-18:2 in SQ. The Bayesian method performed similarly as GBLUP for most of the traits but substantially better for traits that were affected by SNPs of large effects as identified by GWAS. CONCLUSIONS: Fatty acid composition in beef is influenced by a few host genes with major effects and many genes of smaller effects. With the current training population size and marker density, genomic prediction has the potential to predict the breeding values of fatty acid composition in beef cattle at a moderate to relatively high accuracy for fatty acids that have moderate to high heritability.

Genome-wide association for heifer reproduction and calf performance traits in beef cattle.

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5-7, 9, 13-16, 19-21, 24, 25, and 27-29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

Analyses of plasma metabolites using a high performance four-channel CIL LC-MS method and identification of metabolites associated with enteric methane emissions in beef cattle.

Reducing enteric methane (one greenhouse gas) emissions from beef cattle not only can be beneficial in reducing global warming, but also improve efficiency of nutrient utilization in the production system. However, direct measurement of enteric methane emissions on individual cattle is difficult and expensive. The objective of this study was to detect plasma metabolites that are associated with enteric methane emissions in beef cattle. Average enteric methane emissions (CH4) per day (AVG_DAILYCH4) for each individual cattle were measured using the GreenFeed emission monitoring (GEM) unit system, and beef cattle with divergent AVG_DAILYCH4 from Angus (n = 10 for the low CH4 group and 9 for the high CH4 group), Charolais (n = 10 for low and 10 for = high), and Kinsella Composite (n = 10 for low and 10 for high) populations were used for plasma metabolite quantification and metabolite-CH4 association analyses. Blood samples of these cattle were collected near the end of the GEM system tests and a high performance four-channel chemical isotope labeling (CIL) liquid chromatography (LC) mass spectrometer (MS) method was applied to identify and quantify concentrations of metabolites. The four-channel CIL LC-MS method detected 4235 metabolites, of which 1105 were found to be significantly associated with AVG_DAILYCH4 by a t-test, while 1305 were significantly associated with AVG_DAILYCH4 by a regression analysis at p<0.05. Both the results of the t-test and regression analysis revealed that metabolites that were associated with enteric methane emissions in beef cattle were largely breed-specific whereas 4.29% to 6.39% CH4 associated metabolites were common across the three breed populations and 11.07% to 19.08% were common between two breed populations. Pathway analyses of the CH4 associated metabolites identified top enriched molecular processes for each breed population, including arginine and proline metabolism, arginine biosynthesis, butanoate metabolism, and glutathione metabolism for Angus; beta-alanine metabolism, pyruvate metabolism, glycolysis / gluconeogenesis, and citrate cycle (TCA cycle) for Charolais; phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, and arginine and proline metabolism for Kinsella Composite. The detected CH4 associated metabolites and enriched molecular processes will help understand biological mechanisms of enteric methane emissions in beef cattle. The detected CH4 associated plasma metabolites will also provide valuable resources to further characterize the metabolites and verify their utility as biomarkers for selection of cattle with reduced methane emissions.

Breed dependent regulatory mechanisms of beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue in cattle with divergent feed efficiency.

The current study aimed to determine whether breed and feed efficiency affect the molecular mechanisms regulating beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue of beef steers. Fatty acid profiling and RNA-Seq based transcriptome analysis were performed on subcutaneous adipose tissues collected from beef steers with three divergent breeds (Angus, ANG, n = 47; Charolais, CHAR, n = 48; Kinsella Composite, KC, n = 48) and different residual feed intake (RFI, a measure of feed efficiency). The comparison of fatty acid profiles showed that KC had higher beneficial FAs compared to the other two breeds. Distinct FA profiles between H-RFIfat and L-RFIfat steers was more obvious for KC steers, where H-RFIfat steers tended to have higher proportion of healthy FAs and lower proportion of the unhealthy FAs. A higher number of differentially expressed (DE) genes were observed for KC steers, whereas ANG and CHAR steers had a lower number of DE genes between H- and L-RFIfat steers. The association analyses of the gene expressions and FA profiles showed that 10 FA metabolism-associated genes together with the one upstream regulator (SREBF1) were associated with the proportion of C18:2n-6, total n-6, PUFA and PUFA/SFA for KC steers but not the other two breeds. Subcutaneous adipose tissue FA profiles and healthy FA index differed in cattle with divergent feed efficiency and such variation was unique for the three examined cattle breeds. Key FA metabolism-associated genes together with SREBF1 which is the upstream regulator of a set of genes involved in lipid metabolism may be of importance for genetic selection of meat with higher healthy FA index in beef cattle.

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

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

Genetic potential for residual feed intake and diet fed during early- to mid-gestation influences post-natal DNA methylation of imprinted genes in muscle and liver tissues in beef cattle.

Discovery of epigenetic modifications associated with feed efficiency or other economically important traits would increase our understanding of the molecular mechanisms underlying these traits. In combination with known genetic markers, this would provide opportunity to improve genomic selection accuracy in cattle breeding programs. It would also allow cattle to be managed to improve favorable gene expression. The objective of this study was to identify variation in DNA methylation between beef cattle of differential pre-natal nutrition and divergent genetic potential for residual feed intake (RFI). Purebred Angus offspring with the genetic potential for either high (HRFI) or low (LRFI) RFI were prenatally exposed to either a restricted maternal diet of 0.5 kg/d average daily gain (ADG) or a moderate maternal diet of 0.7 kg/d ADG from 30 to 150 d of gestation. We performed DNA methylation analysis of differentially methylated regions (DMR) of imprinted genes (Insulin-like growth factor 2 (IGF2) DMR2, IGF2/H19 imprinting control region (ICR) and IGF2 receptor (IGF2R) DMR2) using post-natal samples of longissimus dorsi (LD) muscle taken from male and female calves at birth and weaning, and of LD muscle, semimembranosus (SM) muscle, and liver samples collected from steers at slaughter (17 months of age). Interestingly, for all three DMR investigated in liver, LRFI steers had higher levels of methylation than HRFI steers. In LD muscle, IGF2/H19 ICR methylation differences for heifers at birth were due to pre-natal diet, while for steers at birth they were mostly the result of genetic potential for RFI with LRFI steers again having higher levels of methylation than HRFI steers. While results from repeated measures analysis of DNA methylation in steers grouped by RFI revealed few differences, in steers grouped by diet, we found higher methylation levels of IGF2 DMR2 and IGF2R DMR2 in LD muscle of restricted diet steers at weaning and slaughter than at birth, as well as increased methylation in LD muscle of restricted diet steers compared with moderate diet steers at weaning and/or slaughter. Our results suggest that differential pre-natal nutrition, and divergent genetic potential for RFI, induces tissue- and sex-specific alterations in post-natal IGF2 and IGF2R methylation patterns and that these patterns can vary with age in Angus beef cattle.

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

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

Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes.

MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.

The Bovine Metabolome.

From an animal health perspective, relatively little is known about the typical or healthy ranges of concentrations for many metabolites in bovine biofluids and tissues. Here, we describe the results of a comprehensive, quantitative metabolomic characterization of six bovine biofluids and tissues, including serum, ruminal fluid, liver, Longissimus thoracis (LT) muscle, semimembranosus (SM) muscle, and testis tissues. Using nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and inductively coupled plasma-mass spectrometry (ICP-MS), we were able to identify and quantify more than 145 metabolites in each of these biofluids/tissues. Combining these results with previous work done by our team on other bovine biofluids, as well as previously published literature values for other bovine tissues and biofluids, we were able to generate quantitative reference concentration data for 2100 unique metabolites across five different bovine biofluids and seven different tissues. These experimental data were combined with computer-aided, genome-scale metabolite inference techniques to add another 48,628 unique metabolites that are biochemically expected to be in bovine tissues or biofluids. Altogether, 51,801 unique metabolites were identified in this study. Detailed information on these 51,801 unique metabolites has been placed in a publicly available database called the Bovine Metabolome Database.

Oversupplying metabolizable protein in late gestation for beef cattle: effects on prepartum BW, ruminal fermentation, nitrogen balance, and skeletal muscle catabolism.

The objective of the study was to determine the effect of oversupplying MP during late gestation on maternal BW, ruminal fermentation, nitrogen balance, and skeletal muscle catabolism. Crossbred Hereford heifers (n = 24) were assigned to a control treatment designed to meet MP requirements (CON) or a treatment providing 133% of the MP requirement (HMP). Heifers were individually fed their treatment from day -55 ± 3 relative to parturition and DMI was summarized by week. BW was measured on day -55 ± 3, -41 ± 3, -27 ± 3, and -8 ± 3. Ruminal digesta samples were collected on day -34 ± 5 and -15 ± 4 for short-chain fatty acid and ammonia-N (NH3-N) concentration. Plasma was collected the day prior to ruminal digesta samples and analyzed for plasma urea-N. Nitrogen balance was measured over a 6-d period starting on day -34 ± 4 and -15 ± 4. Following completion of the N balance periods, muscle biopsies were collected from the longissimus dorsi and analyzed for abundance of proteins relating to skeletal muscle catabolism. Data were analyzed as a randomized complete block (date of parturition) design with repeated measures using the MIXED procedure of SAS. Heifers fed HMP increased conceptus-corrected BW by a greater magnitude than CON at day -8 relative to -55 and -41 (treatment × day, P < 0.01). DMI increased (P < 0.01) by 18% on week -2 compared to -8, but then decreased (P < 0.01) by 8.0% for week -1. N-intake, apparent N digestion, N excretion, and N retention (g/d) were all greater (P < 0.01) for HMP heifers than CON but did not differ when expressed as a proportion of N intake. Ruminal NH3-N decreased (treatment × day, P < 0.01) as parturition approached for HMP (10.1 to 8.6 mg/dL); whereas, NH3-N was not affected for CON (1.0 to 1.3 mg/dL). Consequently, plasma urea-N was greater (P < 0.01) for HMP heifers (15.0 vs. 7.5 mg/dL). Heifers fed HMP had improved (P < 0.01) DM, OM, and NDF digestibility relative to CON heifers. The abundance of calpastatin was greater (P = 0.03) and calpain tended to be greater (P = 0.085) for CON cows compared to HMP. Feeding greater quantities of MP during late gestation may improve ruminal fermentation, N balance, and improve BW gain prepartum.

Oversupplying metabolizable protein in late gestation for beef cattle: effects on postpartum ruminal fermentation, blood metabolites, skeletal muscle catabolism, colostrum composition, milk yield and composition, and calf growth performance.

The objective of the study was to determine whether oversupplying MP prepartum affects postpartum cow BW, colostrum composition, milk production and composition, protein catabolism in the dam, and calf growth. Crossbred Hereford heifers were individually fed a control treatment designed to meet MP requirements (CON; n = 10) or 133% of the MP requirement (HMP; n = 11) from day -55 ± 4 until parturition. All cows were provided a common postpartum diet. Cow BW was measured on days 7 ± 1, 14 ± 2, 28 ± 3, 57 ± 4, 82 ± 5, and 111 ± 3 relative to parturition. DMI and ruminal pH were measured daily and summarized by week until day 33. Milk yield was estimated based on a 12-h two-quarter milk yield on days 7 ± 1, 12 ± 1, 28 ± 3, 33 ± 3, 70 ± 3, and 112 ± 3. Urine samples were collected from cows over a 6-d period starting on days 7 ± 1 and 28 ± 3 and the composited samples were analyzed for 3-methylhistidine (3-MH) and creatinine. Muscle samples were collected from cows on day 13 ± 1 while calf muscle samples were collected on days 2 and 111 ± 3 of age. Muscle samples from cows were analyzed for markers of protein catabolism, and calf muscle samples were analyzed for genes regulating cell growth and differentiation. Data were analyzed as a randomized complete block design using the MIXED procedure of SAS accounting for repeated measures when necessary. Postpartum BW did not differ (P ≥ 0.30) by treatment, day, or the interaction of treatment and day (T × D), but rump fat decreased (P = 0.011) as lactation progressed. DMI decreased during weeks 2 and 3 compared to 1 and 4, whereas ruminal pH was less during weeks 2, 3, and 4 relative to week 1. Colostrum fat concentration was less (P = 0.003) for HMP than CON; but, milk production was not affected by treatment. Milk yield was greatest from days 7 to 33 and decreased thereafter (P < 0.01). Urinary 3-MH and the 3-MH:creatinine ratio did not differ by treatment, day, or the T × D (P ≥ 0.22) interaction, nor was there a difference (P ≥ 0.13) in the abundance of catabolic proteins. Calf growth was not affected by treatment, but HMP calves had greater expression (T × D, P = 0.05) of PPARG while PKM expression increased for CON calves (T × D, P = 0.04) at day 111 compared to their expression at day 2. Overfeeding MP during late gestation does not improve postpartum indicators of N balance or maternal muscle turnover but may alter colostrum composition and calf gene expression at weaning.

Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes1.

Average daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study, we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI, and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais, and KC breed population that were initially selected for a transcriptome study of RFI. At a false discovery rate <0.05 and fold change >1.5, we identified 123, 102, and 78 differentially expressed (DE) genes between high- and low-ADG animals of Angus, Charolais, and KC populations, respectively. For DMI, 108, 180, and 156 DE genes were identified between high- and low-DMI from Angus, Charolais, and KC populations, respectively, while for MWT, 80, 82, and 84 genes were differentially expressed between high- and low-MWT animals in Angus, Charolais, and KC populations, respectively. The identified DE genes were largely breed specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipids, carbohydrates, amino acids, vitamins, and minerals), small molecule biochemistry, cellular movement, cell morphology, and cell-to-cell signaling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the 3 studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and MWT of beef cattle.

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle.

BACKGROUND: The symbiotic rumen microbiota is essential for the digestion of plant fibers and contributes to the variation of production and health traits in ruminants. However, to date, the heritability of rumen microbial features and host genetic components associated with the rumen microbiota, as well as whether such genetic components are animal performance relevant, are largely unknown. RESULTS: In the present study, we assessed rumen microbiota from a cohort of 709 beef cattle and showed that multiple factors including breed, sex, and diet drove the variation of rumen microbiota among animals. The diversity indices, the relative abundance of ~ 34% of microbial taxa (59 out of 174), and the copy number of total bacteria had a heritability estimate (h2) ≥ 0.15, suggesting that they are heritable elements affected by host additive genetics. These moderately heritable rumen microbial features were also found to be associated with host feed efficiency traits and rumen metabolic measures (volatile fatty acids). Moreover, 19 single nucleotide polymorphisms (SNPs) located on 12 bovine chromosomes were found to be associated with 14 (12 of them had h2 ≥ 0.15) rumen microbial taxa, and five of these SNPs were known quantitative trait loci for feed efficiency in cattle. CONCLUSIONS: These findings suggest that some rumen microbial features are heritable and could be influenced by host genetics, highlighting a potential to manipulate and obtain a desirable and efficient rumen microbiota using genetic selection and breeding. It could be a useful strategy to further improve feed efficiency and optimize rumen fermentation through targeting both cattle and their rumen microbiota.

Level and source of fat in the diet of gestating beef cows. II. Effects on the postpartum performance of the dam and the progeny1.

A study was conducted to evaluate the effects of level and source of fat in the diet of gestating beef cows on the postpartum performance of the dam and the progeny. Each year, 75 mature pregnant (183 ± 4.8 d until calving) Angus cows with similar BW (663 ± 21.5 kg) and BCS (2.6 ± 0.12; 1 to 5 scale) were randomly assigned to 1 of 15 outdoor pens. Each pen was assigned to 1 of 3 iso-caloric and iso-nitrogenous treatments: a low-fat diet (LF; 1.4 ± 0.12% EE) and two high-fat diets (HF; 3.3 ± 0.20% EE) including a canola seed- (CAN) or a flaxseed (FLX)-based pelleted feed. Diets were formulated to meet the requirements of pregnant beef cows and fed until calving. Data were analyzed as a randomized complete block design with contrasts for the effects of level (LF vs. HF) and source (CAN vs. FLX) of fat. No differences (P ≥ 0.21) were found for BW or calving to weaning ADG of cows. The average BCS during the first 42 d of lactation was greater (P<0.01) for LF compared with HF (2.63 vs. 2.51) with no difference (P = 0.35) for CAN vs. FLX cows. Subcutaneous fat thickness over the ribs was greater (P ≤ 0.01) for LF compared with that of HF cows at calving (5.7 vs. 4.3 mm) and at weaning (4.3 vs. 3.7 mm) with no difference (P ≥ 0.11) for CAN vs. FLX cows. Over the first 42 d of lactation, no difference (P ≥ 0.23) was observed for 12-h milk yield. Milk protein concentration was greater (P = 0.03) for CAN compared with FLX (3.11 vs. 3.01%) cows, whereas no difference (P ≥ 0.28) was observed for any other milk component. Milk fat from FLX cows had greater (P < 0.01) CLA and CLnA concentrations than that of CAN cows during the first 42 d of lactation. Pregnancy rate of HF cows tended (P = 0.07) to be greater than that of LF cows with no difference (P = 0.77) for CAN vs. FLX cows. Calves from HF cows were heavier (P ≤ 0.01) at birth (42.9 vs. 40.2 kg) than those from LF cows. From calving to weaning, ADG of calves born to CAN cows was greater (P = 0.03) that that of calves born to FLX cows (1.19 vs. 1.13 kg/d) with no difference (P = 0.18) for calves born to LF vs. HF cows. At slaughter, progeny of HF cows had greater (P ≤ 0.03) shrunk BW (605 vs. 579 kg) and HCW (355 vs. 339 kg) compared with those from LF cows with no difference (P ≥ 0.16) for progeny of CAN vs. FLX cows. These results show that feeding a HF diet over gestation results in heavier calves at birth and at slaughter, and superior calf gains from birth to slaughter as well as heavier carcasses, possibly due to a developmental programming effect.

Level and source of fat in the diet of gestating beef cows: I. Effects on the prepartum performance of the dam and birth weight of the progeny1.

A 2-yr study was conducted to evaluate the effects of level and source of fat in the diet of gestating beef cows on their prepartum performance and birth weight of progeny. Each year, 75 multiparous (≥3 calving) pregnant Angus cows were stratified by BW (663 ± 21.5 kg) and BCS (2.6 ± 0.12; 1 to 5 scale) and randomly assigned to 1 of 15 outdoor pens. Subsequently, each pen was randomly assigned to 1 of 3 (n = 5) treatments: a low-fat diet (LF; 1.4 ± 0.12% EE) consisting of grass-legume hay, barley straw, and barley grain, or 1 of 2 high-fat diets (HF; 3.3 ± 0.20% EE) that included either a canola seed (CAN) or a flaxseed (FLX) based pelleted feed. Diets were formulated to meet the requirements of pregnant beef cows during the last 2 trimesters of gestation (0.183 ± 4.8 d), adjusted for changes in environmental conditions, and offered such that each pen on average received similar daily amounts of DE (31.2 ± 2.8 Mcal/cow), CP (1.36 ± 0.13 kg/cow), and DM (12.9 ± 1.0 kg/cow). Data were analyzed as a randomized complete block design with contrasts to separate the effects of level (LF vs. HF) and source (CAN vs. FLX) of fat. After 160 d on trial, conceptus corrected-BW (CC-BW) of LF cows (708 kg) and the proportion of overconditioned cows (13.2%) were greater (P ≤ 0.04) than those of HF, with no difference (P ≥ 0.84) between CAN and FLX for CC-BW (697 kg) and proportion of overconditioned cows (3.6% vs. 2.9%). Feeding FLX diet during gestation resulted in cows with a greater (P ≤ 0.01) concentration of conjugated linolenic acid (0.12% vs. 0.05%) and n-3 (0.58% vs. 0.37%) fatty acids, and a tendency (P = 0.09) for conjugated linoleic acid concentration (1.05% vs. 0.88%) to be greater in subcutaneous adipose tissue (SCAT) when compared with cows fed the CAN diet. By the end of gestation, serum NEFA concentration of LF cows (592 µEq/L) was lower (P < 0.01) than that of HF cows, and FLX cows had greater (P < 0.01) serum NEFA concentration than CAN cows (636 vs. 961 µEq/L). Cows receiving the LF diet during gestation gave birth to lighter (P < 0.01) calves compared with those receiving the HF diets (40.2 vs. 42.9 kg), with no difference (P = 0.24) between calves born to CAN (42.4 kg) and FLX (43.3 kg) cows. In conclusion, these results suggest a partitioning of the ME in pregnant beef cows that is dependent on the type of dietary energy, resulting in heavier calves at birth for cows fed high-fat diets. Also, the type of fatty acid in the diet of gestating beef cows affected the fatty acid profile in SCAT and serum NEFA concentration.

Level and source of fat in the diet of gestating beef cows: II. Effects on the postpartum performance of the dam and the progeny.

A study was conducted to evaluate the effects of level and source of fat in the diet of gestating beef cows on the postpartum performance of the dam and the progeny. Each year, 75 mature pregnant (183±4.8 d until calving) Angus cows with similar BW (663±21.5 kg) and BCS (2.6±0.12; 1 to 5 scale) were randomly assigned to one of 15 outdoor pens. Each pen was assigned to one of three iso-caloric and iso-nitrogenous treatments: a low-fat diet (LF; 1.4±0.12% EE), and two high-fat diets (HF; 3.3±0.20% EE) including a canola seed (CAN) or a flaxseed (FLX) based pelleted feed. Diets were formulated to meet the requirements of pregnant beef cows and fed until calving. Data were analyzed as a randomized complete block design with contrasts for the effects of level (LF vs. HF) and source (CAN vs. FLX) of fat. No differences (P≥0.21) were found for BW or calving to weaning ADG of cows. The average BCS during the first 42 d of lactation was greater (P<0.01) for LF compared to HF (2.63 vs. 2.51) with no difference (P=0.35) for CAN vs. FLX cows. Subcutaneous fat thickness over the ribs was greater (P≤0.01) for LF compared to that of HF cows at calving (5.7 vs. 4.3 mm) and at weaning (4.3 vs. 3.7 mm) with no difference (P≥0.11) for CAN vs. FLX cows. Over the first 42 d of lactation, no difference (P≥0.23) was observed for 12-h milk yield. Milk protein concentration was greater (P=0.03) for CAN compared to FLX (3.11 vs. 3.01%) cows while no difference (P≥0.28) was observed for any other milk component. Milk fat from FLX cows had greater (P < 0.01) CLA and CLnA concentrations than that of CAN cows during the first 42 d of lactation. Pregnancy rate of HF cows tended (P=0.07) to be greater than that of LF cows with no difference (P=0.77) for CAN vs. FLX cows. Calves from HF cows were heavier (P≤0.01) at birth (42.9 vs. 40.2 kg) than those from LF cows. From calving to weaning, ADG of calves born to CAN cows was greater (P=0.03) that that of calves born to FLX cows (1.19 vs. 1.13 kg/d) with no difference (P=0.18) for calves born to LF vs. HF cows. At slaughter, progeny of HF cows had greater (P≤0.03) shrunk BW (605 vs. 579 kg) and HCW (355 vs. 339 kg) compared to those from LF cows with no difference (P≥0.16) for progeny of CAN vs. FLX cows. These results show that feeding a HF diet over gestation results in heavier calves at birth and at slaughter, and superior calf gains from birth to slaughter as well as heavier carcasses, possibly due to a developmental programming effect.

Evaluation of a genomic-enhanced sorting system for feeder cattle1.

This study evaluated the use of molecular breeding values (MBVs) for carcass traits to sort steers into quality grid and lean meat yield (LMY) groups. A discovery set of 2,609 animals with genotypes and carcass phenotypes was used to predict MBVs for LMY and marbling score (MBS) for 299 Angus, 181 Charolais, and 638 Kinsella Composite steers using genomic best linear unbiased prediction. Steers were sorted in silico into four MBV groups namely Quality (with MBVs greater than the mean for LMY and MBS), Lean (with MBVs greater than the mean for LMY but less than or equal to the mean for MBS), Marbling (with MBVs greater than the mean for MBS but less than or equal to the mean for LMY), and Other (with MBVs lower than the mean for LMY and MBS). Carcass phenotypes on the steers were then collected at slaughter and evaluated for consistency with the assigned MBV groups using descriptive statistics and least square analysis. Accuracy of MBV predictions was assessed by Pearson's correlation between predicted MBV and adjusted phenotype divided by the square root of trait heritability. Genomic breed compositions were predicted for all steers to correct for possible population stratification and breed effects in the test model. The number of steers that met the expected carcass outcome was counted to produce actual percentages for each MBV group. Results showed that on average, Quality and Marbling groups had greater back-fat and more marbling across the three populations while Lean group had leaner carcasses. Carcass weights were similar across MBV groups. Within MBV groups, decreases in variability were observed for most traits suggesting improvement in carcass uniformity. Greater than 70% of the steers in Quality, Lean, and Marbling groups met the Quality Grid and Y1-LMY target for Angus and Charolais but not for Kinsella composite. The accuracy of MBV prediction ranged from 0.43 to 0.59 indicating that up to 35% of the observed carcass trait variability can be predicted, which suggests utility of MBV as a marker-assisted management tool to sort feeder cattle into uniform carcass endpoint groups under similar environmental and management conditions. Further investigation is warranted to evaluate the performance of feeder cattle sorted based on MBV and managed for different carcass endpoints as well as the cost-benefit implications for feedlot operations.

Effects of maternal feed intake restriction during pregnancy on the expression of growth regulation, imprinting and epigenetic transcription-related genes in foetal goats.

Maternal nutrition during gestation is a leading factor of modifying the foetal epigenome and phenotype for mammals. Imprinting genes have important roles in regulating foetal growth, programming and development. There, however, are limited data available on the effects of feed intake restriction on the expression of imprinting genes in pregnant goats. The present study, therefore, was conducted to assess the effects of maternal feed intake restriction on the relative abundance of mRNA for growth imprinting, DNA methyltransferase (DNMT) and epigenetic transcription-related genes in the liver and heart of foetal goats during gestation. A total of 24 Liuyang black goats (2.0±0.3 yr) with similar body weight (BW, 31.22±8.09 kg) and parity (2) were allocated equally to either a control group (CG) or a restriction group (RG) during both early (from 26 to 65 days) and late (from 96 to 135 days) gestation. All goats were fed a mixed diet and had free access to fresh water. The feed of the RG was 40% less than that of the CG. The early and late gestation goats were weighed, bled and slaughtered on days 65 and 135 of gestation, respectively. In early gestation, the foetal weight, body length, the weight of foetal heart and liver were greater (P < 0.05) in the RG. The CpG methylation of genomic DNA in the foetal heart was less (P = 0.0001) in the RG. The relative abundance of mRNA of methyl-CpG-binding domain protein 2 (MBD2) and methyl-CpG-binding domain protein 3 (MBD3) genes in the foetal liver were greater (P < 0.05) in the RG. During the late gestation, the foetal weight, heart weight and liver weight were less (P < 0.05) in the RG. The relative abundance of mRNA for the MBD2 gene (P = 0.043) in the foetal heart, and the ten-eleven translocation protein 1 (TET1) gene (P < 0.05) in both the foetal heart and liver were greater in the RG. These results indicate feed intake restriction during gestation influenced foetal development and regulated the relative abundance of mRNA for epigenetic transcription-related genes.

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle.

The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds.