Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle.

BACKGROUND: This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneous (SC) fat depots in Bos taurus beef cattle. RESULTS: We confirmed many findings previously made at the biochemical level and made new discoveries. The fundamental lipogenic machinery, such as ACACA and FASN encoding the rate limiting Acetyl CoA carboxylase and Fatty Acid synthase were expressed at 1.6-1.8 fold lower levels in IMF, consistent with previous findings. The FA elongation pathway including the rate limiting ELOVL6 was also coordinately downregulated in IMF compared to SC as expected. A 2-fold lower expression in IMF of ACSS2 encoding Acetyl Coenzyme A synthetase is consistent with utilisation of less acetate for lipogenesis in IMF compared to SC as previously determined using radioisotope incorporation. Reduced saturation of fat in the SC depot is reflected by 2.4 fold higher expression of the SCD gene encoding the Δ9 desaturase enzyme. Surprisingly, CH25H encoding the cholesterol 25 hydroxylase enzyme was ~ 36 fold upregulated in IMF compared to SC. Moreover, its expression in whole muscle tissue appears representative of the proportional representation of bovine marbling adipocytes. This suite of observations prompted quantification of a set of oxysterols (oxidised forms of cholesterol) in the plasma of 8 cattle exhibiting varying IMF. Using Liquid Chromatography-Mass Spectrometry (LC-MS) we found the levels of several oxysterols were significantly associated with multiple marbling measurements across the musculature, but (with just one exception) no other carcass phenotypes. CONCLUSIONS: These data build on our molecular understanding of ruminant fat depot biology and suggest oxysterols represent a promising circulating biomarker for cattle marbling.

Current situation and future prospects for global beef production: overview of special issue.

The demand for beef as a protein source is increasing worldwide, although in most countries beef accounts for considerably less than half of total meat consumption. Beef also provides a highly desirable eating experience in developed countries and, increasingly, in developing countries. The sustainability of beef production has different meanings in the various geographical and socio-economic regions of the world. Natural resources including land mass and uses, rainfall and access to livestock feed, and the robustness of the economy are major determinants of the perception of beef sustainability. In this overview of the 2016 International Symposium on "Future Beef in Asia" and this subsequent Special Edition of the Asian-Australasian Journal of Animal Sciences on "Current Situation and Future Prospects for Global Beef Production", the contributions have been grouped into the following categories: Countries in Southeast Asia; Europe; and Countries producing highly marbled beef for export and/or domestic consumption. They also include reference to Special Topics including marbled beef production, and use of "omics" technologies to enhance beef quality assurance. Among these broad categories, notable differences exist across countries in the production and marketing of beef. These reflect differences in factors including natural resource availability and climate, population size, traditional culture and degree of economic development including industrial and technological developments. We trust that the International Symposium and this Special Edition on Current Situation and Future Prospects for Global Beef Production, the contents of which that are briefly summarized in this paper, will serve as a valuable resource for the livestock industries, researchers and students with an interest in enhancing the prospects for sustainable, efficient beef production that satisfies the growing size and complexity of consumer demands and markets for beef.

Current situation and future prospects for the Australian beef industry - A review.

Beef production extends over almost half of Australia, with about 47,000 cattle producers that contribute about 20% ($A12.7 billion gross value of production) of the total value of farm production in Australia. Australia is one of the world's most efficient producers of cattle and was the world's third largest beef exporter in 2016. The Australian beef industry had 25 million head of cattle in 2016-17, with a national beef breeding herd of 11.5 million head. Australian beef production includes pasture-based cow-calf systems, a backgrounding or grow-out period on pasture, and feedlot or pasture finishing. Feedlot finishing has assumed more importance in recent years to assure the eating quality of beef entering the relatively small Australian domestic market, and to enhance the supply of higher value beef for export markets. Maintenance of Australia's preferred status as a quality assured supplier of high value beef produced under environmentally sustainable systems from 'disease-free' cattle is of highest importance. Stringent livestock and meat quality regulations and quality assurance systems, and productivity growth and efficiency across the supply chain to ensure price competiveness, are crucial for continued export market growth in the face of increasing competition. Major industry issues, that also represent research, development and adoption priorities and opportunities for the Australian beef industry have been captured within exhaustive strategic planning processes by the red meat and beef industries. At the broadest level, these issues include consumer and industry support, market growth and diversification, supply chain efficiency, productivity and profitability, environmental sustainability, and animal health and welfare. This review provides an overview of the Australian beef industry including current market trends and future prospects, and major issues and opportunities for the continued growth, development and profitability of the industry.

Transcriptome analysis of cattle muscle identifies potential markers for skeletal muscle growth rate and major cell types.

BACKGROUND: This study aimed to identify markers for muscle growth rate and the different cellular contributors to cattle muscle and to link the muscle growth rate markers to specific cell types. RESULTS: The expression of two groups of genes in the longissimus muscle (LM) of 48 Brahman steers of similar age, significantly enriched for "cell cycle" and "ECM (extracellular matrix) organization" Gene Ontology (GO) terms was correlated with average daily gain/kg liveweight (ADG/kg) of the animals. However, expression of the same genes was only partly related to growth rate across a time course of postnatal LM development in two cattle genotypes, Piedmontese x Hereford (high muscling) and Wagyu x Hereford (high marbling). The deposition of intramuscular fat (IMF) altered the relationship between the expression of these genes and growth rate. K-means clustering across the development time course with a large set of genes (5,596) with similar expression profiles to the ECM genes was undertaken. The locations in the clusters of published markers of different cell types in muscle were identified and used to link clusters of genes to the cell type most likely to be expressing them. Overall correspondence between published cell type expression of markers and predicted major cell types of expression in cattle LM was high. However, some exceptions were identified: expression of SOX8 previously attributed to muscle satellite cells was correlated with angiogenesis. Analysis of the clusters and cell types suggested that the "cell cycle" and "ECM" signals were from the fibro/adipogenic lineage. Significant contributions to these signals from the muscle satellite cells, angiogenic cells and adipocytes themselves were not as strongly supported. Based on the clusters and cell type markers, sets of five genes predicted to be representative of fibro/adipogenic precursors (FAPs) and endothelial cells, and/or ECM remodelling and angiogenesis were identified. CONCLUSIONS: Gene sets and gene markers for the analysis of many of the major processes/cell populations contributing to muscle composition and growth have been proposed, enabling a consistent interpretation of gene expression datasets from cattle LM. The same gene sets are likely to be applicable in other cattle muscles and in other species.

Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle.

Molecular mechanisms in skeletal muscle associated with anabolic steroid treatment of cattle are unclear and we aimed to characterize transcriptional changes. Cattle were chronically exposed (68 ± 20 days) to a steroid hormone implant containing 200 mg trenbolone acetate and 20 mg estradiol (Revalor-H). Biopsy samples from 48 cattle (half treated) from longissimus dorsi (LD) muscle under local anesthesia were collected. Gene expression levels were profiled by microarray, covering 16,944 unique bovine genes: 121 genes were differentially expressed (DE) due to the implant (99.99% posterior probability of not being false positives). Among DE genes, a decrease in expression of a number of fat metabolism-associated genes, likely reflecting the lipid storage activity of intramuscular adipocytes, was observed. The expression of IGF1 and genes related to the extracellular matrix, slow twitch fibers, and cell cycle (including SOX8, a satellite cell marker) was increased in the treated muscle. Unexpectedly, a very large 21- (microarray) to 97 (real time quantitative PCR)-fold higher expression of the mRNA encoding the neuropeptide hormone oxytocin was observed in treated muscle. We also observed an ∼50-fold higher level of circulating oxytocin in the plasma of treated animals at the time of biopsy. Using a coexpression network strategy OXTR was identified as more likely than IGF1R to be a major mediator of the muscle response to Revalor-H. A re-investigation of in vivo cattle LD muscle samples during early to mid-fetal development identified a >128-fold increased expression of OXT, coincident with myofiber differentiation and fusion. We propose that oxytocin may be involved in mediating the anabolic effects of Revalor-H treatment.

Review: An overview of beef production from pasture and feedlot globally, as demand for beef and the need for sustainable practices increase.

Beef is a high-quality source of protein that also can provide highly desirable eating experiences, and demand is increasing globally. Sustainability of beef industries requires high on-farm efficiency and productivity, and efficient value-chains that reward achievement of target-market specifications. These factors also contribute to reduced environmental and animal welfare impacts necessary for provenance and social licence to operate. This review provides an overview of beef industries, beef production, and beef production systems globally, including more productive and efficient industries, systems and practices. Extensive beef production systems typically include pasture-based cow-calf and stocker-backgrounding or grow-out systems, and pasture or feedlot finishing. Cattle in pasture-based systems are subject to high levels of environmental variation to which specific genotypes are better suited. Strategic nutritional supplementation can be provided within these systems to overcome deficiencies in the amount and quality of pasture- or forage-based feed for the breeding herd and for younger offspring prior to a finishing period. More intensive systems can maintain more control over nutrition and the environment and are more typically used for beef and veal from dairy breeds, crosses between beef and dairy breeds, and during finishing of beef cattle to assure product quality and specifications. Cull cows and heifers from beef seedstock and cow-calf operations and dairy enterprises that are mostly sent directly to abattoirs are also important in beef production. Beef production systems that use beef breeds should target appropriate genotypes and high productivity relative to maintenance for the breeding herd and for growing and finishing cattle. This maximizes income and limits input costs particularly feed costs which may be 60% or more of production costs. Digital and other technologies that enable rapid capture and use of environmental and cattle performance data, even within extensive systems, should enhance beef industry productivity, efficiency, animal welfare and sustainability.

Advancements in sensor technology and decision support intelligent tools to assist smart livestock farming.

Remote monitoring, modern data collection through sensors, rapid data transfer, and vast data storage through the Internet of Things (IoT) have advanced precision livestock farming (PLF) in the last 20 yr. PLF is relevant to many fields of livestock production, including aerial- and satellite-based measurement of pasture's forage quantity and quality; body weight and composition and physiological assessments; on-animal devices to monitor location, activity, and behaviors in grazing and foraging environments; early detection of lameness and other diseases; milk yield and composition; reproductive measurements and calving diseases; and feed intake and greenhouse gas emissions, to name just a few. There are many possibilities to improve animal production through PLF, but the combination of PLF and computer modeling is necessary to facilitate on-farm applicability. Concept- or knowledge-driven (mechanistic) models are established on scientific knowledge, and they are based on the conceptualization of hypotheses about variable interrelationships. Artificial intelligence (AI), on the other hand, is a data-driven approach that can manipulate and represent the big data accumulated by sensors and IoT. Still, it cannot explicitly explain the underlying assumptions of the intrinsic relationships in the data core because it lacks the wisdom that confers understanding and principles. The lack of wisdom in AI is because everything revolves around numbers. The associations among the numbers are obtained through the "automatized" learning process of mathematical correlations and covariances, not through "human causation" and abstract conceptualization of physiological or production principles. AI starts with comparative analogies to establish concepts and provides memory for future comparisons. Then, the learning process evolves from seeking wisdom through the systematic use of reasoning. AI is a relatively novel concept in many science fields. It may well be "the missing link" to expedite the transition of the traditional maximizing output mentality to a more mindful purpose of optimizing production efficiency while alleviating resource allocation for production. The integration between concept- and data-driven modeling through parallel hybridization of mechanistic and AI models will yield a hybrid intelligent mechanistic model that, along with data collection through PLF, is paramount to transcend the current status of livestock production in achieving sustainability.

Understanding intake on pastures: how, why, and a way forward.

An assessment of dietary intake is a critical component of animal nutrition. Consumption of feed resources is the basis upon which feeding strategies and grazing management are based. Yet, as far back as 1948, researchers have lauded the trials and tribulations of estimation of the phenomenon, especially when focused on grazing animals and pasture resources. The grazing environment presents a unique situation in which the feed resource is not provided to the animal but, rather, the animal operates as the mechanism of harvest. Therefore, tools for estimation must be developed, validated, and applied to the scenario. There are a plethora of methods currently in use for the estimation of intake, ranging from manual measurement of herbage disappearance to digital technologies and sensors, each of which come with its share of advantages and disadvantages. In order to more firmly grasp these concepts and provide a discussion on the future of this estimation, the Forages and Pastures Symposium at the 2020 ASAS-CSAS-WSASAS Annual Meeting was dedicated to this topic. This review summarizes the presentations in that symposium and offers further insight into where we have come from and where we are going in the estimation of intake for grazing livestock.

Developmental Programming and Growth of Livestock Tissues for Meat Production.

Maternal regulation of fetal development has consequences for growth and development of carcass tissues. Severely restricted fetal growth can reduce postnatal growth capacity, resulting in smaller-for-age animals that take longer to reach market weights but has little effect on feedlot efficiency or carcass and meat quality. Specific nutritional supplementation, particularly during later pregnancy, may limit fetal growth retardation and enhance postnatal growth capacity and carcass characteristics, and may improve development of intramuscular fat. Continued improvements in understanding developmental processes and their regulation will increase future capacity to improve growth, efficiency, carcasses, and meat quality through developmental programming.

Cellular development in muscle differs between Angus steers from low and high muscle score selection lines1.

This study assessed cellular characteristics of longissimus lumborum (LL) and semitendinosus (ST) muscles in steers genetically selected for low (Low) or high (High) muscling using live muscle scoring, and High steers with 1 copy of the loss-of-function 821 del11 MSTN allele (HighHet). We hypothesized High and HighHet have altered muscle cellular characteristics and mechanisms influencing muscling compared with Low steers. Angus steers 25 mo old comprising 14 High, 19 Low, and 11 HighHet were backgrounded to 20 mo of age, grain finished for 150 d, and then slaughtered. Body and carcass weights did not differ due to muscling line (P = 0.46). Weight of LL was 16% greater (P = 0.004) and total protein in LL was 18% greater (P = 0.012) in HighHet than Low steers. ST weight in HighHet was 10% and 13% greater than in High and Low steers (P = 0.007), respectively, and of total ST protein 12% and 17% greater in HighHet than High or Low (P = 0.002). Cross-sectional area (CSA) of LL was greater in HighHet than in High and greater in High than in Low (85.0 vs. 77.0 vs. 70.4 cm2, P < 0.001). Apparent number of myofibers and myofibers per unit CSA did not differ between the muscling lines in LL (P = 0.14) or ST (P = 0.47). Myofiber CSA was greater in the ST of Low than of High and HighHet for type 1 (36% and 31% respectively, P = 0.005) and 2A (22% and 25%, P < 0.001). HighHet steers had greater area of glycolytic (type 2X) relative to more oxidative myofiber types within LL (P = 0.02; 11% and 43% more than High and Low, respectively) and ST (P < 0.001; 27% and 75%). Concentration of RNA in LL was 13% and 10% greater (P = 0.005) in High than in Low and HighHet, respectively, and total amount of RNA in LL was 22% greater in High and 20% greater in HighHet than in Low (P < 0.001). The LL of High steers had less protein to RNA (P = 0.03; 57.4 vs. 65.6) and more RNA to DNA (P = 0.007; 9.03 vs. 7.83) than Low. HighHet steers had 11% more DNA in ST than High (P = 0.04) and 19% more RNA in ST than Low (P = 0.012). The shift towards glycolytic myofibers was consistent with loadings in a principal component that explained 39% of the variation in LL and 38% in ST. Overall, these findings show that selection for increased muscling using live cattle muscle scoring, and 1 copy of the 821 del11 MSTN allele, results in more glycolytic muscle. They also suggest that increased muscling of the High compared with Low steers may be associated with increased translational capacity in the LL.

Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds.

BACKGROUND: The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60), secondary myogenesis (d 135), as well as beginning (d 195) and final stages (birth) of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24) were from Hereford dams and crossed with either Wagyu (high intramuscular fat) or Piedmontese (GDF8 mutant) sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. RESULTS: We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5) RNA at birth. The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth. We also document evidence for timing differences in differentiation events between the two breeds. CONCLUSION: Taken together, these findings provide a detailed description of molecular events accompanying skeletal muscle differentiation in the bovine, as well as gene expression differences that may underpin the phenotype differences between the two breeds. In addition, this study has highlighted a non-coding RNA, which is abundantly expressed and developmentally regulated in bovine fetal muscle.

A gene coexpression network for bovine skeletal muscle inferred from microarray data.

We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and we explore 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism, and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP, and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins or of titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast-twitch muscle structural proteins and enzymes was observed, but slow-twitch-specific proteins were not correlated with the fast-twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.

Proliferation rates of bovine primary muscle cells relate to liveweight and carcase weight in cattle.

Muscling in cattle is largely influenced by genetic background, ultimately affecting beef yield and is of major interest to the beef industry. This investigation aimed to determine whether primary skeletal muscle cells isolated from different breeds of cattle with a varying genetic potential for muscling differ in their myogenic proliferative capacity. Primary skeletal muscle cells were isolated and cultured from the Longissimus muscle (LM) of 6 month old Angus, Hereford and Wagyu X Angus cattle. Cells were assessed for rate of proliferation and gene expression of PAX7, MYOD, MYF5, and MYOG. Proliferation rates were found to differ between breeds of cattle whereby myoblasts from Angus cattle were found to proliferate at a greater rate than those of Hereford and Wagyu X Angus during early stages of growth (5-20 hours in culture) in vitro (P < 0.05). The proliferation rates of myoblasts during early stages of culture in vitro were also found to be positively related to the liveweight and carcase weight of cattle (P < 0.05). Gene expression of MYF5 was also found to be significantly down-regulated in WagyuX compared with Angus cattle (P < 0.05). These findings suggest that early events during myogenesis are important for determining liveweight and caracase weights in cattle.

Prediction of stage of pregnancy in prolific sheep using ultrasound measurement of fetal bones.

The use of ultrasound to estimate stage of pregnancy was assessed in 32 ewes of a prolific genotype carrying 7 singleton fetuses and 9 twin, 10 triplet and 6 quadruplet litters that were scanned on six occasions from 60 to 120 days of gestation. At least one ultrasound measurement per ewe of fetal metacarpal bone length (MCL), biparietal diameter (BPD), or of both bones was made on over 90% of attempts (n = 152). Measurement of MCL was made on 78% of attempts (n = 371), of BPD on 73% of attempts, and of both bones on 62% of attempts. The equation developed from BPD (mean absolute error (MAE) = 3.2 days) was similar to that developed from measurement of MCL (MAE = 3.3 days) in its capacity to predict stage of pregnancy. Accuracy of prediction was improved using equations that included mean values within litters for BPD (MAE = 2.5 days) and MCL (MAE = 2.6 days). Further improvement in predictive capacity was achieved using multiple regression equations developed from measurement of both bones (individual fetuses: MAE = 2.6 days; equations including mean values within litters: MAE = 2.2 days). The results demonstrate that ultrasound can be used to estimate stage of pregnancy in prolific ewes, and that the use of mean values for bone measurements from different fetuses within litters and/or measurement of bones with different growth allometry can increase the reliability of estimates. The utility of the procedure depends on the number of fetuses measured per ewe, the number of bones measured per fetus and, hence, the time required to measure bones and the degree of accuracy required.

A gene expression estimator of intramuscular fat percentage for use in both cattle and sheep.

BACKGROUND: The expression of genes encoding proteins involved in triacyglyceride and fatty acid synthesis and storage in cattle muscle are correlated with intramuscular fat (IMF)%. Are the same genes also correlated with IMF% in sheep muscle, and can the same set of genes be used to estimate IMF% in both species? RESULTS: The correlation between gene expression (microarray) and IMF% in the longissimus muscle (LM) of twenty sheep was calculated. An integrated analysis of this dataset with an equivalent cattle correlation dataset and a cattle differential expression dataset was undertaken. A total of 30 genes were identified to be strongly correlated with IMF% in both cattle and sheep. The overlap of genes was highly significant, 8 of the 13 genes in the TAG gene set and 8 of the 13 genes in the FA gene set were in the top 100 and 500 genes respectively most correlated with IMF% in sheep, P-value = 0. Of the 30 genes, CIDEA, THRSP, ACSM1, DGAT2 and FABP4 had the highest average rank in both species. Using the data from two small groups of Brahman cattle (control and Hormone growth promotant-treated [known to decrease IMF% in muscle]) and 22 animals in total, the utility of a direct measure and different estimators of IMF% (ultrasound and gene expression) to differentiate between the two groups were examined. Directly measured IMF% and IMF% estimated from ultrasound scanning could not discriminate between the two groups. However, using gene expression to estimate IMF% discriminated between the two groups. Increasing the number of genes used to estimate IMF% from one to five significantly increased the discrimination power; but increasing the number of genes to 15 resulted in little further improvement. CONCLUSION: We have demonstrated the utility of a comparative approach to identify robust estimators of IMF% in the LM in cattle and sheep. We have also demonstrated a number of approaches (potentially applicable to much smaller groups of animals than conventional methods) to using gene expression to rank animals for IMF% within a single farm/treatment, or to estimate differences in IMF% between two farms/treatments.

Impacts of the Callipyge mutation on ovine plasma metabolites and muscle fibre type.

The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. Using muscle fibre typing immunohistochemistry, we confirmed muscle specific effects and demonstrated that affected muscles had greater prevalence and hypertrophy of type 2X fast twitch glycolytic fibres and decreased representation of types 1, 2C, 2A and/or 2AX fibres. To investigate potential systemic effects of the mutation, proton NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. Microarray analysis of the perirenal adipose tissue depot did not reveal a transcriptional effect of the mutation in this tissue. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.

Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data.

We outline an in vivo cellular program of bovine longissimus muscle development inferred from expression data from 60 days post conception to 3months postnatal. Analytic challenges included changes in cellular composition, ambiguous 'diagnostic' markers of cell type and contrasts between cattle human and mouse myogenesis. Nevertheless, the expression profiles of the myosin isoforms support slow and fast muscle fibres emanating from primary and secondary myogenesis respectively, while expression of the prenatal myosin subunits is down regulated prior to birth. Of the canonical pro-myogenic transcription factors (TF), MYF6 and MYF5 are negatively co-expressed, with MYF6 displaying higher expression in the post-natal samples and MYF5, MYOG, HES6 and PAX7 displaying higher expression in early development. A set of TFs (SIX1, EYA2 and DACH2) considered important in undifferentiated murine cells were equally abundant in differentiated bovine cells. An examination of mammalian regulators of fibre composition, muscle mass and muscle metabolism, underscored the roles of PPARGC1A, TGFß signalling and the NHR4 Nuclear Hormone Receptors on bovine muscle development. Enriched among the most variably expressed genes from the entire data set were molecules regulating mitochondrial metabolism of carbohydrate (PDK4), fat (UCP3), protein (AGXT2L1) and high energy phosphate (CKMT2). The dramatic increase in the expression of these transcripts, which may enable the peri-natal transition to metabolic independence critical for new-born herbivores, provides surprising evidence for substantial developmental remodelling of muscle mitochondria and reflects changes in nutrient availability. Overall, despite differences in size, metabolism and physiology, the muscle structural subunit expression program appears very similar in ruminants, rodents and humans.

Maternal and paternal genomes differentially affect myofibre characteristics and muscle weights of bovine fetuses at midgestation.

Postnatal myofibre characteristics and muscle mass are largely determined during fetal development and may be significantly affected by epigenetic parent-of-origin effects. However, data on such effects in prenatal muscle development that could help understand unexplained variation in postnatal muscle traits are lacking. In a bovine model we studied effects of distinct maternal and paternal genomes, fetal sex, and non-genetic maternal effects on fetal myofibre characteristics and muscle mass. Data from 73 fetuses (Day153, 54% term) of four genetic groups with purebred and reciprocal cross Angus and Brahman genetics were analyzed using general linear models. Parental genomes explained the greatest proportion of variation in myofibre size of Musculus semitendinosus (80-96%) and in absolute and relative weights of M. supraspinatus, M. longissimus dorsi, M. quadriceps femoris and M. semimembranosus (82-89% and 56-93%, respectively). Paternal genome in interaction with maternal genome (P<0.05) explained most genetic variation in cross sectional area (CSA) of fast myotubes (68%), while maternal genome alone explained most genetic variation in CSA of fast myofibres (93%, P<0.01). Furthermore, maternal genome independently (M. semimembranosus, 88%, P<0.0001) or in combination (M. supraspinatus, 82%; M. longissimus dorsi, 93%; M. quadriceps femoris, 86%) with nested maternal weight effect (5-6%, P<0.05), was the predominant source of variation for absolute muscle weights. Effects of paternal genome on muscle mass decreased from thoracic to pelvic limb and accounted for all (M. supraspinatus, 97%, P<0.0001) or most (M. longissimus dorsi, 69%, P<0.0001; M. quadriceps femoris, 54%, P<0.001) genetic variation in relative weights. An interaction between maternal and paternal genomes (P<0.01) and effects of maternal weight (P<0.05) on expression of H19, a master regulator of an imprinted gene network, and negative correlations between H19 expression and fetal muscle mass (P<0.001), suggested imprinted genes and miRNA interference as mechanisms for differential effects of maternal and paternal genomes on fetal muscle.

Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks.

BACKGROUND: Despite modern technologies and novel computational approaches, decoding causal transcriptional regulation remains challenging. This is particularly true for less well studied organisms and when only gene expression data is available. In muscle a small number of well characterised transcription factors are proposed to regulate development. Therefore, muscle appears to be a tractable system for proposing new computational approaches. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a simple algorithm that asks "which transcriptional regulator has the highest average absolute co-expression correlation to the genes in a co-expression module?" It correctly infers a number of known causal regulators of fundamental biological processes, including cell cycle activity (E2F1), glycolysis (HLF), mitochondrial transcription (TFB2M), adipogenesis (PIAS1), neuronal development (TLX3), immune function (IRF1) and vasculogenesis (SOX17), within a skeletal muscle context. However, none of the canonical pro-myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6 and MEF2C) were linked to muscle structural gene expression modules. Co-expression values were computed using developing bovine muscle from 60 days post conception (early foetal) to 30 months post natal (adulthood) for two breeds of cattle, in addition to a nutritional comparison with a third breed. A number of transcriptional landscapes were constructed and integrated into an always correlated landscape. One notable feature was a 'metabolic axis' formed from glycolysis genes at one end, nuclear-encoded mitochondrial protein genes at the other, and centrally tethered by mitochondrially-encoded mitochondrial protein genes. CONCLUSIONS/SIGNIFICANCE: The new module-to-regulator algorithm complements our recently described Regulatory Impact Factor analysis. Together with a simple examination of a co-expression module's contents, these three gene expression approaches are starting to illuminate the in vivo transcriptional regulation of skeletal muscle development.

Plasma leptin is regulated predominantly by nutrition in preruminant lambs.

In juvenile and mature animals, the plasma concentration of leptin is regulated by adiposity and nutrition. However, the timing of these influences on plasma leptin, and their relative importance in early postnatal life, are unknown. We investigated these plasma leptin influences in sheep, a species characterized during fetal life by leanness and insensitivity of leptin to variation in maternal nutrition. Small and large neonatal lambs were randomly assigned to either a diet sustaining an average daily weight gain (ADG) of 148 g/d (Low plane) or ate ad libitum a diet sustaining an ADG of 337 g/d (High plane). A subset of animals were slaughtered at 7.5, 10, 15 and 20 kg of body weight. Birth size had no effect on plasma leptin concentrations and adiposity at birth or at later times. Plasma leptin concentrations increased within 6 d of birth in the High plane lambs (P < 0.01) and continued to rise over time. In contrast, plasma leptin concentrations never changed in the Low plane lambs despite increasing adiposity. The positive association between plasma leptin concentration and adiposity was greater in the High plane than in the Low plane lambs, suggesting an independent effect of nutrition. Consistent with this finding, lipid accretion rates, a variable that is mostly independent of adiposity, was a strong predictor of plasma leptin concentrations only in the High plane lambs (R(2) = 0.77, P < 0.01). A positive association between plasma insulin and leptin developed over time in the High plane lambs (R(2) = 0.75, P < 0.01 on d 40), but was not seen in the Low plane lambs. These data indicate that both nutrition and adiposity regulate plasma leptin synthesis in early postnatal life, but in contrast to adulthood, the effects of nutrition appear to be predominant.