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The effect of residual feed intake (a measure of feed efficiency) adjusted for backfat thickness (RFIfat) on pregnancy rate (PR) was examined in Angus heifers over 2 yr. High- or Low-RFI heifers were timed artificially inseminated (TAI) with semen from High- or Low-RFI sires, respectively. There was a negative association (P fat value and PR in Year II for Low-RFI heifers. In Year I, the interaction between RFIfat and AI sires was significant in High-RFI heifers (P

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 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.

Effects of residual feed intake (RFI) and genetic group on growth, carcass, and meat quality characteristics of bovine longissimus lumborum (LL), triceps brachii (TB), semimembranosus (SM), and gluteus medius (GM) muscles were investigated using 72 purebred Angus, purebred Charolais, and Angus crossbred steers (n = 24 per genetic group) classified as either high (inefficient) or low (efficient) RFI (n = 12 high and low RFI steers within genetic group). There was no RFI effect (P > 0.05) on growth, carcass, and meat quality measurements except high RFI steers had the highest dry matter intake (P

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.

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.

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. Electronic supplementary material The online version of this article (10.1186/s40168-019-0699-1) contains supplementary material, which is available to authorized users.

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.

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

Objective The objective was to evaluate the effects of fat supplementation and source on reproductive performance of young lactating Angus beef cows grazing cool-season grass (CSG) pastures. Materials and Methods Over 3 yr, 36 second- and third-calving, lactating (38 ± 1.5 d postpartum) Angus cows (554 ± 15.5 kg of BW) were assigned randomly to 9 paddocks (4 cows per paddock) of CSG pastures. Each paddock was assigned randomly to a nonsupplemented control (CON) or 2 supplemented (SUP) treatments in which cows received 300 g/cow per day of supplemental fat (ether extract) from a canola seed–based (CAN) or flaxseed-based (FLX) pellet for 42 d before start of the breeding period. Data were analyzed as a randomized complete block design contrasting the effects of fat supplementation (CON vs. SUP) and fat source (CAN vs. FLX). Results and Discussion Results indicate that cows in CON had greater (P = 0.01) forage utilization and tended (P = 0.08) to have greater estimated forage DMI compared with cows in SUP, whereas no difference (P ≥ 0.76) was observed between CAN and FLX treatments. By the end of the trial, all treatments resulted in positive ADG, maintained or increased BCS and s.c. fat thickness, and reduced serum nonesterified fatty acid concentrations with no difference (P ≥ 0.20) among treatments. No differences (P ≥ 0.12) were observed for pregnancy rate, calving distribution, and calving-to-calving interval. The failure to find treatment differences in growth and reproductive performance is likely a result of greater-than-expected nutrient content (CP: 12.5 ± 2.5%; TDN: 56.5 ± 2.9%) of CSG pastures and similar nutritional status across treatments. Implications and Applications These results indicate that prebreeding fat supplementation and source had no beneficial effects on reproductive performance of young, lactating Angus beef cows grazing good quality CSG pastures.

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.

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.

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 &gt, 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.

Reduction in greenhouse gas emission from beef production is essential to the survival of the beef industry from environmental and social-economic perspectives. There are different systems available to measure methane from animals, but they are expensive, not easily accessible, and not suitable for large-scale methane measurements on the farm. Therefore exploring indicator traits, which are easy to measure, cost-effective, and suitable for large-scale measurement, are recommended. The objectives of this study were to examine the diversity of fecal methanogen profile among efficient and inefficient beef heifers on pasture and investigate methanogen profile as a possible proxy to predict methane emission in beef cattle consuming a forage diet. Forty pregnant (1st trimester) heifers previously classified for postweaning residual feed intake adjusted for off-test back fat (RFIfat; 20 high and 20 low) were included in this study. To determine individual pasture grazing intake, heifers were dosed with 1 kg of C32 labeled pellets once per day from Day 0 to Day 12, and fecal samples were collected twice daily from Day 8 to Day 15. Fecal samples from Days 8, 10, and 12 were analyzed for their methanogen profile. Animals were monitored individually for methane and carbon dioxide production using a GreenFeed Emissions Monitoring system. Total methanogen population and methanogenic community diversity of fecal samples were not different (P > 0.1) between low and high RFIfat groups, as measured by quantitative PCR and α- and β-diversity indices. However, both groups had a different methanogen profile; the relative abundance of Methanobrevibacter wolinii and relatives were higher (P

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&ndash, tandem mass spectrometry (LC&ndash, MS/MS), and inductively coupled plasma&ndash, mass spectrometry (ICP&ndash, 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.

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.

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.

Carcass attributes of steers were examined for influences of selection for residual feed intake (RFI), and exposure to different levels of prenatal nutrition. Heifers characterized for RFI corrected for backfat were mated to bulls with genetic potential for either High-RFI or Low-RFI, such that the progeny were expected to be H/H or L/L RFI (sire/dam). Pregnant heifers were assigned to a low diet (Ldiet; 0.40 kg/d ADG), or moderate diet (Mdiet; 0.57 kg/d ADG), from 30 to 150 days of gestation, after which all heifers were managed similarly. Steer offspring (n = 23) were also managed similarly until slaughter. Dressing percentage of steers from H-RFI dams/sires exposed to Ldiet during gestation was lower than all other groups (P = 0.02). Marbling was greater for steers from H-RFI parents, as was fat content of longissimus thoracis et lumborum and triceps brachii (P ≤ 0.02). Results suggest that parental selection for RFI and prenatal maternal diet can influence carcass characteristics of progeny.

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.

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 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.

Genomic selection for feed efficiency in beef cattle offers an opportunity to reduce feed costs and greenhouse gas (GHG) emissions while increasing profitability and environmental sustainability in beef production. Data from a selection experiment using three beef cattle populations maintained at the University of Alberta Roy Berg Kinsella Research Ranch namely, the Kinsella beef composite (KC - split into efficient and control lines), purebred Angus (AN), and purebred Charolais (CH) were analyzed following three years of selection (2013–2016) to obtain an evaluation of selection responses. Selection was carried out using multiple trait selection indexes based on molecular breeding values (MBVs). For the KC and AN population, a maternal profitability index (MPI) for improved feed efficiency, i.e. low residual feed intake (RFI), higher direct (DWWT) and maternal weaning weights (MWWT) was applied, while for the CH population a feedlot profitability index (FPI) for low RFI, low dry matter intake (DMI), higher average daily gain (ADG), greater carcass marbling (CMAR), greater hot carcass weight (HCW), increased lean meat yield (LMY), and increased average back fat thickness (AFAT) was applied. Across the three populations, average estimated breeding values (EBVs) obtained from a multivariate animal model showed significant differences at P

A two-year study was conducted to evaluate the effects of level and source of fat in the diet of gestating beef cows on progeny performance. Each year, 75 multiparous pregnant Angus cows (182 ± 4.8 d pre-calving) were randomly assigned to 15 pens, which were randomly assigned to one of three dietary treatments: a low-fat diet (LF; 1.4 ± 0.03% EE) comprised of 72% forage and 28% barley grain, and two high-fat diets (HF; 3.3 ± 0.03% EE) where a canola seed (CAN) or a flaxseed (FLX) based pellet were included to provide 300 g/cow/d of fat as MUFA or PUFA sources, respectively. Diets were formulated to be iso-caloric, iso-nitrogenous, and to meet nutrient requirements for the last two trimesters of gestation. All cows and calves were fed and managed similarly after calving. 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. Calving dates were not different (P=0.80) among treatments. Calves from HF cows were heavier (P≤0.04) at birth (43.0 ± 0.5 vs. 40.0 ± 0.3 kg) and slaughter (627 ± 7.1 vs. 601 ± 11.4 kg) than those from LF cows. When data were analyzed according to sex, bull-calves from HF cows were heavier (P

In beef cattle, skeletal muscle tissue represents a large energy sink within the animal, accounting for over 60% of the animal’s systemic metabolism. Therefore, identifying the differentially expressed (DE) genes between the muscle tissues of beef cattle with divergent feed intake and growth rate would enhance our understanding of the molecular mechanisms that regulate feed efficiency in beef cattle. Using RNAseq analyses we investigated transcriptome expression differences of Gluteus medias muscle tissues between crossbred steers with divergent residual feed intake (RFI), daily dry matter intake (DMI), or average daily gain (ADG). For each of these traits, RNAseq data of six (n=6) Kinsella Composite (KC) steers with extreme high and six (n=6) with extreme low phenotypes were analyzed to identify DE genes. On average, we obtained 26.4 million reads per sample with an average quality score of 36, and 97.5% were of the desired length (90-101bp) with 92% of the reads uniquely mapped to the bovine reference genome (UMD3.1). At a false discovery rate < 0.05 and fold change > 2, we identified 271, 383, and 22 DE genes between RFI, ADG, and DMI divergent steers, respectively. Of the identified DE genes, 17 (TFRC, AFF4, NBEAL1, PHIP, NFAT5, HSPA6, FRAS1, HSPA1A, UHMK1, KMT2A, HOOK3, KLHL24, SMG1, ZBED6, RPL12, ROCK2 and ENSBTAG00000017233) were common among the three traits, of which 16 DE genes except for RPL12 were downregulated in steers of low phenotypic values for all the traits. The DE genes between the steers divergent in RFI were primarily involved in gene expression regulation, cellular development, cellular growth and proliferation, cellular function and maintenance and carbohydrate metabolism. Results from this study provide insight into the molecular control of skeletal muscle tissue contributing to divergence in feed efficiency potential in beef cattle.

Approximately 70% of the cost of beef production is impacted by feed utilization. Maximizing production efficiency of beef cattle requires not only genetic selection to maximize feeding efficiency (i.e. residual feed intake - RFI), but also adequate nutrition throughout all stages of growth and development to maximize productivity of growth and reproductive capacity, even during gestation. Nutrient restriction during gestation has been shown to negatively affect post-natal growth and development. This, when combined with efforts to minimize RFI, may significantly affect energy partitioning in the offspring and subsequently important performance traits. Therefore, we decided to investigate the impacts of prenatal under-nutrition during the first half of gestation, as well as selection for divergent RFI, upon gene expression in select tissues, including Longissimus thoracis (LT) and semimembranosus (SM) muscles, liver, and testis, in Angus bull progeny. The genes monitored in this study included metabolic drivers of animal growth, especially muscle growth and development, and those that were aspects of detoxification/immune function. The results showed that the mRNA abundance of protocadherin 19 [PCDH19] in liver, and myocyte enhancer factor 2A [MEF2A] in LT muscle, was significantly higher in Low-diet (Ldiet), and Normal-diet (Ndiet) prenatal maternal diet groups, respectively. The results also showed that in all four tissues, expression of MEF2A was significantly higher in the Low-RFI (LRFI) group as compared to its High-RFI (HRFI) counterpart. We also reported correlations between gene expression in these four tissues with phenotypic measures of feed efficiency and body weight.

Context Selection for residual feed intake (RFI) and its impact on male reproductive development has had mixed reviews in the past. Our previous studies demonstrated earlier puberty, larger testes and greater percentage of progressively motile sperm in high-RFI bulls. However, the molecular mechanisms within testes of bulls with varying RFI remain unclear. Aims To determine the effect of RFI and pre-natal diet on the expression patterns of testicular genes and use this information to explain differences observed across RFI. Methods The study included 25 purebred-Angus bulls with a genetic background of either high or low RFI and fed either normal or low pre-natal nutrition from 30 to 150 days post conception. After slaughter (17 months), testicular tissue was recovered, and RNA was extracted and sequenced. Key results Of 19218 expressed genes, 17 were differentially expressed for RFI (including PLCD1, INPP4B), with no differences being observed for pre-natal diet or diet × RFI interaction (false discovery rate) < 0.1%). KEGG pathway analysis indicated that differentially expressed genes were associated with inositol phosphate metabolism, and phosphatidylinositol signalling. On the basis of a candidate gene-expression study, IGF1R was upregulated in high-RFI bulls (P < 0.1). Conclusions Increased expression of IGF1R and lowered PLCD1 and INPP4B expression could activate PI3K–Akt signalling responsible for cell growth, proliferation and steroid metabolism in high-RFI bulls. Implications Selecting bulls for feed efficiency might affect molecular networks associated with reproduction and fertility.

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) 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.

Exploring pre-natal nutrition to modulate and improve post-natal growth and development in cattle continues to reveal new opportunities for researchers, and ultimately cattle producers. Effects of pre-natal dietary interventions have been shown to be markedly time- and treatment-specific, although a few particular patterns of changes in post-natal growth present themselves recurrently. Male calves, both bulls and steers, appear to be more susceptible to alterations in pre-natal maternal nutrition and, when the opportunity presents, turn it into increased growth performance at a later stage of life (Fitzsimmons unpublished, Añez-Osuna et al. 2018). Male calves may also develop differences in growth patterns in association with pre-natal nutrition even if no differences in weight are detected at birth. Elucidating the how and why behind these changes is more challenging, as well as any long-term effects upon animal health and longevity. Examination of gene expression patterns within tissues that are highly connected with growth and metabolism in cattle, for example skeletal muscles and liver, shows that expression of genes connected to overall growth such as the IGF family, myogenesis (MYOD1, MYOG, etc.), adipogenesis (PPARG), as well as microRNAs that modulate proliferation and differentiation in skeletal muscle, can be associated with pre-natal maternal diet (Paradis et al. 2017). Furthermore, DNA methylation patterns of differentially-methylated regions (DMRs) near the genes for IGF2 and IGF2R in the bovine have been found to be significantly associated with pre-natal maternal diet, and the degree of methylation of IGF2 DMR2 to be negatively correlated with IGF2 expression (Paradis et al. 2017, Fitzsimmons et al. 2017). Dissecting the causes and effects of these associations still presents a great challenge, but the possibility of explaining more of the ‘E’ in the classic equation of Phenotype = Genotype (G) + Environment (E) + G X E is a fascinating and exciting opportunity.

In beef cattle, production feedstuffs are the largest variable input cost. Beef cattle also have a large carbon footprint, raising concern about their environmental impact. Unfortunately, only a small proportion of dietary energy is directed toward protein deposition and muscle growth whereas the majority supports body maintenance. Improving feed efficiency would, therefore, have important consequences on productivity, profitability, and sustainability of the beef industry. Various measures of feed efficiency have been proposed to improve feed utilization, and currently, residual feed intake (RFI) is gaining popularity. However, the cost associated with measuring RFI and the limited knowledge of the biology underlying improved feed efficiency make its adoption prohibitive. Identifying molecular mechanisms explaining divergence in RFI in beef cattle would lead to the development of early detection methods for the selection of more efficient breeding stock. The objective of this study was to identify hepatic markers of metabolic feed efficiency in replacement beef heifers. A group of 87 heifers were tested for RFI adjusted for off-test backfat thickness (RFIfat). Preprandial liver biopsies were collected from 10 high- and 10 low-RFIfat heifers (7 Hereford–Aberdeen Angus and 3 Charolais–Red Angus–Main Anjou per group) and gene expression analysis was performed using RNA sequencing and quantitative real-time PCR. The heifers used in this study differed in RFIfat averaging 0.438 vs. –0.584 kg DM/d in high- and low-RFIfat groups, respectively. As expected, DMI was correlated with RFIfat and ADG did not differ between high- and low-RFIfat heifers. Through a combination of whole transcriptome and candidate gene analyses, we identified differentially expressed genes involved in inflammatory processes including hemoglobin β (HBB), myxovirus resistance 1 interferon-inducible protein p78 (MX1), ISG15 ubiquitin-like modifier (ISG15), hect domain and RLD 6 (HERC6), and interferon-induced protein 44 (IFI44) whose mRNA abundance was lower (HBB) or higher (MX1, ISG15, HERC6, and IFI44) in low-RFIfat heifers. These genes have been shown to be directly or indirectly modulated by interferon signaling and involved with innate immunity. Our results suggest that more efficient heifers respond differently to hepatic proinflammatory stimulus, potentially expending less energy toward combating systemic inflammation and redirecting nutrients toward growth and protein accretion.

Placental function impacts growth and development with lifelong consequences for performance and health. We provide novel insights into placental development in bovine, an important agricultural species and biomedical model.Concepti with defined genetics and sex were recovered from nulliparous dams managed under standardized conditions to study placental gross morphological and histomorphological parameters at the late embryo (Day48) and early accelerated fetal growth (Day153) stages.Placentome number increased 3-fold between Day48 and Day153. Placental barrier thickness was thinner, and volume of placental components, and surface areas and densities were higher at Day153 than Day48. We confirmed two placentome types, flat and convex. At Day48, there were more convex than flat placentomes, and convex placentomes had a lower proportion of maternal connective tissue (P 0.01). However, this was reversed at Day153, where convex placentomes were lower in number and had greater volume of placental components (P 0.01- P 0.001) and greater surface area (P 0.001) than flat placentomes. Importantly, embryo (r = 0.50) and fetal (r = 0.30) weight correlated with total number of convex but not flat placentomes.Extensive remodelling of the placenta increases capacity for nutrient exchange to support rapidly increasing embryo-fetal weight from Day48 to Day153. The cellular composition of convex placentomes, and exclusive relationships between convex placentome number and embryo-fetal weight, provide strong evidence for these placentomes as drivers of prenatal growth. The difference in proportion of maternal connective tissue between placentome types at Day48 suggests that this tissue plays a role in determining placentome shape, further highlighting the importance of early placental development.

Wood, K. M., Montanholi, Y. R., Fitzsimmons, C. F., Miller, S. P., McBride, B. W. and Swanson, K. C. 2014. Characterization and evaluation of residual feed intake measured in mid- to late-gestation mature beef cows and relationships with circulating serum metabolites and linear body measurements. Can. J. Anim. Sci. 94: 499–508. To evaluate the use of residual feed intake (RFI) models measured in mid-to-late gestating beef cows, a dataset was used combining data from five experiments containing nine treatment and/or replicate groups for a total of 321 animal records. Investigations of RFI models included the effects of age, ultrasound measures of body composition, pregnancy corrected gain, and dietary treatment group. A subset of animals had serum analyzed for circulating metabolites (glucose, non-esterified fatty acids, urea, beta-hydroxybutyrate; n=227) and/or linear body measures (hip height and width, body length, body circumference at the heart, mid-body and at flank; n=114) for correlation analysis w...

Our objective was to determine effects of genetic potential for residual feed intake (RFI) and pre-natal diet on post-natal growth and reproductive development of bulls. Twenty-five bull calves with a divergent potential for RFI were produced by mating purebred Angus heifers (60) categorised as high or low RFI and inseminated with semen from high or low RFI bulls. From 30 to 150 days of gestation, half the heifers (balanced for RFI across treatments) in each RFI category were fed to gain 0.7 or 0.5 kg/day (~100% and 75% of recommended feed intake; designated normal- and low-diet, respectively). Birthweights of bull calves (n = 25) did not differ significantly among treatment groups (P ≥ 0.1). However, there was a tendency (P < 0.1) for a maternal diet*time interaction for bull weights, with bulls from low pre-natal diet fed heifers growing faster between 10 and 16 months of age than bulls from normal pre-natal diet fed heifers. Furthermore, high-RFI bulls had a larger scrotal circumference (P < 0.01) and attained puberty (P < 0.05) earlier than low-RFI bulls. Other testes measures, including paired testes volume, epididymal sperm reserves, daily sperm production and total sperm production, were not significantly different among treatment groups (P ≥ 0.1). High RFI bulls tended (P < 0.1) to have better average sperm motility than low RFI bulls. However, sperm morphology, viability and chromatin damage were not different (P ≥ 0.1). In summary, young beef bulls with low RFI had smaller testis, delayed onset of puberty (~1.7 months) and tended to exhibit lower progressive motility compared with high RFI bulls. Pre-natal diet had no direct influence on male reproductive development, nor did it interact with RFI of bulls.

In mid-to-late gestation, nutrient demand increases to meet the growth requirements of the conceptus and cows may alter metabolism in response to energy demands of pregnancy. By better understanding the metabolic role of pregnancy, there may be opportunities to better understand maintenance energy costs and improve overall feed efficiency. Eighteen mature Simmental/Angus crossbred cows, pregnant (PREG; n = 9) and nonpregnant (OPEN; n = 9), were used to investigate the effect of pregnancy on BW change, carcass traits, visceral organ mass, and circulating serum metabolites. Cows were blocked by day of expected parturition such that each block was slaughtered 4 to 5 wk before parturition. Cows were individually fed for ad libitum intake using Calan gates for 89 to 105 d. Cows were weighed, ultrasounded for rib (over the 12th and 13th rib) and rump fat, and a serum sample obtained at d 1, 56, and 3 to 5 d before slaughter. At slaughter, organs were removed, trimmed of fat, and weighed. Serum was analyzed for β-hydroxybutyrate (BHBA), NEFA, glucose, urea, total cholesterol, and triiodothyronine (T3). Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papillae, pancreas, and small intestinal mucosa were collected at slaughter and snap frozen in liquid N. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na(+)/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1α (PGC1-α), 5'-adenosine monophosphate-activated protein kinase (AMPK) and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Data were analyzed using PROC MIXED in SAS as a replicated randomized complete block. Liver weights (actual, relative to BW, relative to HCW) were heavier (P ≤ 0.02) in OPEN. Rumen mass and kidney fat weight, both relative to BW, were also greater (P ≤ 0.04) in OPEN. On d 56 and at preslaughter, PREG cows had greater (P ≤ 0.04) BHBA, NEFA and urea concentrations and lower (P = 0.04) cholesterol concentration. Hepatic Na(+)/K+ ATPase abundance was greater (P = 0.04) in PREG cows. In rumen papillae, abundance of pAMPKα was increased (P = 0.006) in PREG cows. These data indicate that PREG cows may metabolize energy reserves and alter their metabolism to meet the energetic demands of the growing fetus.

This study evaluated the use of molecular breeding values (MBVs) for carcass traits to sort steers into quality grid and lean meat yield groups. A training set of 2300 animals with genotypes and phenotypes was used to predict MBVs for lean meat yield (LMY) and marbling score (MBS) for 299 Angus, 181 Charolais and 638 Kinsella composite steers using the genomic best linear unbiased prediction method. Steers were placed into MBV-Quality, MBV-Lean, MBV-Marbling and MBV-Other groups on the basis of predicted MBV for LMY and MBS being jointly greater or less than the mean MBV values for both traits. Carcass phenotypes of the steers were then collected and evaluated for consistency with the assigned group using descriptive statistics. Also, the accuracy of genomic predictions was assessed as the additive genetic correlation from a bivariate animal model that fits the observed carcass phenotype and the predicted MBV. 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, MBV-Quality and MBV-Marbling groups had heavier carcasses, greater backfat and more marbling across the three populations while MBV-Lean had leaner carcasses. For most traits, the coefficient of variation suggested less variability and uniform carcass in the MBV-Marbling followed by MBV-Lean and MBV-Quality groups. Greater than 70% of the steers in the MBV-Quality, MBV-Lean and MBV-Marbling groups reached the desired carcass outcome of 70:70 Quality Grid and Y1-lean meat yield in Angus and Charolais but not for Kinsella composite. The accuracy of genomic prediction showed that the MBVs could predict from 60 to 80% of the observed carcass trait values. Thus, genomic profiles can potentially help to streamline the feedlot-finishing process and improve the quality and consistency of beef carcasses.

Twenty-two nonlactating multiparous pregnant beef cows (639 ± 68 kg) were used to investigate the effect of dietary restriction on the abundance of selected proteins regulating cellular energy metabolism. Cows were fed at either 85% (n = 11; LOW) or 140% (n = 11; HIGH) of total NE requirements. The diet consisted of a haylage-based total mixed ration containing 20% wheat straw. Cows were slaughtered by block (predicted date of parturition), beginning 83 d after the initiation of dietary treatments and every week thereafter for 6 wk, such that each block was slaughtered at approximately 250 d of gestation. Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papilli (ventral sac), pancreas, and small intestinal muscosa were collected at slaughter and snap frozen in liquid N2. Western blots were conducted to quantify abundance of proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1 α (PGC-1α), and 5´-adenosine monophosphate-activated protein kinase (AMPK) and the activated form phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Statistical analysis was conducted using Proc Mixed in SAS and included the fixed effects of dietary treatment, cow age, block, and the random effect of pen. Dietary treatments resulted in cows fed HIGH having greater (P ≤ 0.04) ADG and final BW than cows fed LOW. Abundance of ubiquitin in muscle was greater (P = 0.009) in cows fed LOW, and PCG-1 α in liver was greater (P = 0.03) in cows fed HIGH. Hepatic O2 consumption was greater in HIGH (P ≤ 0.04). Feed intake can influence the abundance of important metabolic proteins and suggest that protein degradation may increase in muscle from moderately nutrient restricted cows and that energy metabolism in liver increases in cows fed above NE requirements.

To determine effects of pregnancy (experiment 1) and plane of nutrition during pregnancy (experiment 2) on pancreatic digestive enzymes and morphology of insulin-containing cell clusters, beef cows...

Long-term selection (> 45 generations) for low or high body weight from the same founder population has generated two extremely divergent lines of chickens, the low (LWS) and high weight (HWS) lines, which at the age of selection (56 days) differs by more than nine-fold in body weight. The HWS line chickens are compulsive feeders, whereas, in the LWS line, some individuals are anorexic and others have very low appetites. The involvement of the central nervous system in these behavioural differences has been experimentally supported. We compared a brain region at 0 and 56 days of age containing the major metabolic regulatory regions, including the hypothalamus and brainstem, using a global cDNA array expression analysis. The results obtained show that the long-term selection has produced minor but multiple expression differences. Genes that regulate neuronal plasticity, such as actin filament polymerisation and brain-derived neurotrophic factor, were identified as being differentially expressed. Genes involved in lipid metabolism were over-represented among differentially expressed genes. The expression data confirm that neural systems regulating feeding behaviours in these lines are different. The results suggest that the lines are set in separate developmental trajectories equipped with slightly different nervous systems. We suggest that the lines adapt behaviourally different to changing situations post hatch, such as the transition from dependence on yolk to feeding, in order to obtain energy. The present study has identified and exemplifies the kind of changes that may underlie the extreme differences in such behaviours.

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.

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 ( = 0.50) 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. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0290-0) contains supplementary material, which is available to authorized users.

We report the generation, assembly and annotation of expressed sequence tags (ESTs) from four chicken cDNA libraries, constructed from brain and testis tissue dissected from red junglefowl and White Leghorn. 21,285 5′-end ESTs were generated and assembled into 2,813 contigs and 9,737 singletons, giving 12,549 tentative unique transcripts. The transcripts were annotated using BLAST by matching to known chicken genes or to putative homologues in other species using the major gene/protein databases. The results for these similarity searches are available on www.sbc.su.se/∼arve/chicken. 4,129 (32.9%) of the transcripts remained without a significant match to gene/protein databases, a proportion of unmatched transcripts similar to earlier non-mammalian EST studies. To estimate how many of these transcripts may represent novel genes, they were studied for the presence of coding sequence. It was shown that most of the unique chicken transcripts do not contain coding parts of genes, but it was estimated that at least 400 of the transcripts contain coding sequence, indicating that 3.2% of avian genes belong to previously unknown gene families. Further BLAST search against dbEST left 1,649 (13.1%) of the transcripts unmatched to any library. The number of completely unmatched transcripts containing coding sequence was estimated at 180, giving a measure of the number of putative novel chicken genes identified in this study. 84.3% of the identified transcripts were found only in testis tissue, which has been poorly studied in earlier chicken EST studies. Large differences in expression levels were found between the brain and testis libraries for a large number of transcripts, and among the 525 most frequently represented transcripts, there were at least 20 transcripts with significant difference in expression levels between red junglefowl and White Leghorn.