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A recently developed mechanistic mathematical model of the bovine estrous cycle was parameterized to fit empirical data sets collected during one estrous cycle of 31 individual cows, with the main objective to further validate the model. The a priori criteria for validation were (1) the resulting model can simulate the measured data correctly (i.e. goodness of fit), and (2) this is achieved without needing extreme, probably non-physiological parameter values. We used a least squares optimization procedure to identify parameter configurations for the mathematical model to fit the empirical in vivo measurements of follicle and corpus luteum sizes, and the plasma concentrations of progesterone, estradiol, FSH and LH for each cow. The model was capable of accommodating normal variation in estrous cycle characteristics of individual cows. With the parameter sets estimated for the individual cows, the model behavior changed for 21 cows, with improved fit of the simulated output curves for 18 of these 21 cows. Moreover, the number of follicular waves was predicted correctly for 18 of the 25 two-wave and three-wave cows, without extreme parameter value changes. Estimation of specific parameters confirmed results of previous model simulations indicating that parameters involved in luteolytic signaling are very important for regulation of general estrous cycle characteristics, and are likely responsible for differences in estrous cycle characteristics between cows. [ABSTRACT FROM PUBLISHER]

The expression of oestrous behaviour in Holstein Friesian dairy cows has progressively decreased over the past 50 years. Reduced oestrus expression is one of the factors contributing to the current suboptimal reproductive efficiency in dairy farming. Variation between and within cows in the expression of oestrous behaviour is associated with variation in peripheral blood oestradiol concentrations during oestrus. In addition, there is evidence for a priming role of progesterone for the full display of oestrous behaviour. A higher rate of metabolic clearance of ovarian steroids could be one of the factors leading to lower peripheral blood concentrations of oestradiol and progesterone in high-producing dairy cows. Oestradiol acts on the brain by genomic, non-genomic and growth factor-dependent mechanisms. A firm base of understanding of the ovarian steroid-driven central genomic regulation of female sexual behaviour has been obtained from studies on rodents. These studies have resulted in the definition of five modules of oestradiol-activated genes in the brain, referred to as the GAPPS modules. In a recent series of studies, gene expression in the anterior pituitary and four brain areas (amygdala, hippocampus, dorsal hypothalamus and ventral hypothalamus) in oestrous and luteal phase cows, respectively, has been measured, and the relation with oestrous behaviour of these cows was analysed. These studies identified a number of genes of which the expression was associated with the intensity of oestrous behaviour. These genes could be grouped according to the GAPPS modules, suggesting close similarity of the regulation of oestrous behaviour in cows and female sexual behaviour in rodents. A better understanding of the central genomic regulation of the expression of oestrous behaviour in dairy cows may in due time contribute to improved (genomic) selection strategies for appropriate oestrus expression in high-producing dairy cows. [ABSTRACT FROM PUBLISHER]

The expression of estrous (sexually receptive) behavior (EB), a key fertility trait in dairy cows, has been declining over the past few decades both in intensity and duration. Improved knowledge of the genomic factors underlying EB, which is currently lacking, may lead to novel applications to enhance fertility. Our objective was to identify genes and biological processes shared among the bovine anterior pituitary (AP) and four brain areas that act together to regulate EB by investigating networks of coexpressed genes between these tissues. We used a systems biology approach called weighted gene coexpression network analysis for defining gene coexpression networks using gene expression data from the following tissues collected from 14 cows at estrus: AP, dorsal hypothalamus (DH), ventral hypothalamus (VH), amygdala (AM), and hippocampus (HC). Consensus modules of coexpressed genes were identified between the networks for the AM-DH, HC-DH, VH-DH, AP-DH, and AM-HC tissue pairs. The correlation between the module's eigengene (weighted average gene expression profile) and levels of EB exhibited by the experimental cows were tested. Estrous behavior-correlated modules were found enriched for gene ontology terms like glial cell development and regulation of neural projection development as well as for Kyoto Encyclopedia of Genes and Genomes pathway terms related to brain degenerative diseases. General cellular processes like oxidative phosphorylation and ribosome and biosynthetic processes were found enriched in several correlated modules, indicating increased transcription and protein synthesis. Stimulation of ribosomal RNA synthesis is known from rodent studies to be a primary event in the activation of neuronal cells and pathways involved in female reproductive behavior and this precedes the estrogen-driven expansion of dendrites and synapses. Similar processes also operate in cows to affect EB. Hub genes within EB-correlated modules (e.g. NEFL, NDRG2, GAP43, THY1, and TCF7L2, among others) are strong candidates among genes regulating EB expression. The study improved our understanding of the genomic regulation of EB in dairy cows by providing new insights into genes and biological processes shared among the bovine AP and brain areas acting together to regulate EB. The new knowledge could lead to the development of novel management strategies to monitor and improve reproductive performance in dairy cows (for example, biomarkers for estrus detection). [ABSTRACT FROM AUTHOR]

Improved understanding of the biology of traits of livestock species necessitates the use and combination of information that is stored in a variety of different sources such as databases and literature. The ability to effectively combine information from different sources, however, depends on a high level of standardization within and between various resources, at least with respect to the used terminology. Ontologies represent a set of concepts that facilitate standardization of terminology within specific domains of interest. The biological mechanisms underlying quantitative traits of farm animal species related to reproduction and host pathogen interactions are complex and not well understood. This knowledge could be improved through the availability of domain-specific ontologies that provide enhanced possibilities for data annotation, data retrieval, data integration, data exchange, data analysis, and ontology-based searches. Here we describe a framework for domain-specific ontologies and the development of 2 first-generation ontologies: Reproductive Trait and Phenotype Ontology (REPO) and Host Pathogen Interactions Ontology. In these first-generation ontologies, we focused on "female fertility in cattle" and "interactions between pigs and Salmonella". Through this, we contribute to the global initiative toward the development of an Animal Trait Ontology for livestock species. To demonstrate its usefulness, we show how REPO can be used to select candidate genes for fertility. [ABSTRACT FROM AUTHOR]

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed ‘omics’ technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A ‘system’ approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with ‘system approaches’ in animal sciences, providing exciting opportunities to predict and modulate animal traits. [ABSTRACT FROM AUTHOR]

Reduced oestrus behaviour expression or its absence (silent oestrus) results in subfertility in high-producing dairy cows. Insight into the genomic regulation of oestrus behaviour is likely to help alleviate reproduction problems. Here, gene expression was recorded in the ventral tegmental area (VTA) of high milk production dairy cows differing in the degree of showing oestrus behaviour (H - highly expressing versus L - lowly expressing), which was then analysed. Genes regulating cell morphology and adhesion or coding for immunoglobulin G (IgG) chains were differentially expressed in VTA between cows around day 0 and 12 of the oestrus cycle, but only in cows that earlier in life tended to show high levels of oestrus behaviour (H0 versus H12). The comparisons between H and L groups of cows also revealed differential expression of several genes (e.g. those of the IgG family or encoding for pro-melanin-concentrating hormone). However, any significant changes in VTA genes expression were detected in the comparison of L0 versus L12 cows. Altogether, the genes expression profile in VTA of cows highly expressing oestrus behaviour changes together with phases of the oestrus cycle, while in case of cows expressing oestrus behaviour lowly it remains stable. This supports the existence of genomic regulation by centrally expressed genes on the expression of oestrus behaviour in dairy cows. [ABSTRACT FROM AUTHOR]

In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21-35 and 63-91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos' development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63-77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs. [ABSTRACT FROM AUTHOR]

High quality pork is consumed as fresh meat, whereas other carcasses are used in the processing industry. Meat quality is determined measuring technical muscle variables. The objective of this research was to investigate the molecular regulatory mechanisms underlying meat quality differences of pork originating from genetically different Piétrain boars. Piétrain boars were approved for high meat quality using a DNA marker panel. Other Piétrain boars were indicated as average. Both groups produced litters in similar Piétrain sows. The LM were sampled from 9 carcasses produced by approved boars and 8 carcasses of average boars. Total RNA was isolated, and an equal portion of each sample was pooled to make a reference sample representing the mean of all samples. Each sample was hybridized on microarrays against the reference in duplicate using a dye swaps design. After normalization and subtraction of 2 times the background, only genes expressed in at least 5 carcasses were analyzed. For all analyses the mean of the M-values relative to the reference (i.e., fold change), were used. Sixteen genes showed significant linear or quadratic associations between gene expression and meat color (Minolta a* value, Minolta L* value, reflection, pH 24 h) after Bonferroni correction. All these genes had expression levels similar to the reference in all carcasses. Studying association between gene expression levels and meat quality using only genes with expression statistically differing from the reference in at least 5 carcasses revealed 29 more genes associating with the technological meat quality variables, again with meat color as a main trait. These associations were not significant after Bonferroni correction and explained less of the phenotypic variation in the traits. Bioinformatics analyses with The Database for Annotation, Visualization and Integrated Discovery (DAVID) using the list of genes with more than 2-fold changed expression level revealed that these genes were mainly found in muscle-specific processes, protein complexes, and oxygen transport, and located to muscle-specific cellular localizations. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed pathways related to protein metabolism, cellular proliferation, signaling, and adipose development differing between the 2 groups of carcasses. Approved meat carcasses showed less variation in gene expression. The results highlight biological molecular mechanisms underlying the differences between the high meat quality approved and average boars. [ABSTRACT FROM AUTHOR]

Intensive selection for high milk yield in dairy cows has raised production levels substantially but at the cost of reduced fertility, which manifests in different ways including reduced expression of oestrous behaviour. The genomic regulation of oestrous behaviour in bovines remains largely unknown. Here, we aimed to identify and study those genes that were associated with oestrous behaviour among genes expressed in the bovine anterior pituitary either at the start of oestrous cycle or at the mid-cycle (around day 12 of cycle), or regardless of the phase of cycle. Oestrous behaviour was recorded in each of 28 primiparous cows from 30 days in milk onwards till the day of their sacrifice (between 77 and 139 days in milk) and quantified as heat scores. An average heat score value was calculated for each cow from heat scores observed during consecutive oestrous cycles excluding the cycle on the day of sacrifice. A microarray experiment was designed to measure gene expression in the anterior pituitary of these cows, 14 of which were sacrificed at the start of oestrous cycle (day 0) and 14 around day 12 of cycle (day 12). Gene expression was modelled as a function of the orthogonally transformed average heat score values using a Bayesian hierarchical mixed model on data from day 0 cows alone (analysis 1), day 12 cows alone (analysis 2) and the combined data from day 0 and day 12 cows (analysis 3). Genes whose expression patterns showed significant linear or non-linear relationships with average heat scores were identified in all three analyses (177, 142 and 118 genes, respectively). Gene ontology terms enriched among genes identified in analysis 1 revealed processes associated with expression of oestrous behaviour whereas the terms enriched among genes identified in analysis 2 and 3 were general processes which may facilitate proper expression of oestrous behaviour at the subsequent oestrus. Studying these genes will help to improve our understanding of the genomic regulation of oestrous behaviour, ultimately leading to better management strategies and tools to improve or monitor reproductive performance in bovines. [ABSTRACT FROM AUTHOR]

The objectives of this study were to evaluate the influence of different pure pig breeds and muscle types on the expression of muscle proteins, as well as their interactions, and second, to find biomarkers for breed and muscle types. A total of 126 male pigs, including 43 Landrace, 21 Duroc, 43 Large White, 13 Pietrain, and 6 Belgian Landrace, were slaughtered at the age of 174 ± 6 d. Samples from the semimembranosus muscle (SM) and LM were collected 24 h postmortem. Proteomic spectra were generated on an anion exchanger (Q10), a cation exchanger (CM10), and on immobilized metal affinity capture (IJVIAC3O) ProteinChip arrays and analyzed using surface-enhanced laser desorption/ionization time-of-flight inass spectrometry ProteinChip techniques. Breed and muscle type did not affect the number of peaks per spectrum but, interestingly, affected the average intensity of the peaks. Of these peaks, a total of 4 proved to be potential protein biomarkers to differentiate LM or SM muscles, and 2 to classify specific breed types. Additionally, several peaks influenced by the interaction between muscle and breed types could correctly classify pig muscles according to their breed. Further studies need to be carried out to validate and identify these potential protein biomarkers for breed and muscle types in finishing pigs. [ABSTRACT FROM AUTHOR]

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarray data and visualize the results using color codes indicating regulation. To demonstrate the power of the method, we used a previously reported chicken microarray experiment investigating line-specific reactions to Salmonella infection as an example. [ABSTRACT FROM AUTHOR]

The objective of this study was to compare purebred Duroc and Pietrain prenatal muscle tissue transcriptome expression levels at different stages of prenatal development to gain insight into the differences in muscle tissue development in these pig breeds. Commercial western pig breeds have been selected for muscle growth for the past 2 decades. Pig breeds differ for their muscle phenotypes (i.e., myofiber numbers and myofiber types). Duroc and Pietrain pig breeds are extremes; Duroc pigs have redder muscle fiber types with more intramuscular fat, and Pietrain pigs have faster-growing and whiter muscle fiber types. Pietrain pigs are more muscular than Duroc pigs, whereas Duroc pigs are fatter than Pietrain pigs. The genomic background underlying these breed-specific differences is poorly known. Myogenesis is a complex exclusive prenatal process involving proliferation and differentiation (i.e., fusion) of precursor cells called myoblasts. We investigated the difference in the prenatal muscle-specific transcriptome profiles of Duroc and Pietrain pigs using microarray technology. The microarray contained more than 500 genes affecting myogenesis, energy metabolism, muscle structural genes, and other genes from a porcine muscle cDNA library. The results indicated that the expression of the myogenesis-related genes was greater in early Duroc embryos than in early Pietrain embryos (14 to 49 d of gestation), whereas the opposite was found in late embryos (63 to 91 d of gestation). These findings suggest that the myogenesis process is more intense in early Duroc embryos than in Pietrain embryos but that myogenesis is more intense in late Pietrain fetuses than in Duroc fetuses. Transcriptomes of muscle structural genes followed that pattern. The energy metabolism genes were expressed at a higher level in prenatal Pietrain pigs than in prenatal Duroc pigs, except for d 35, when the opposite situation was found. Fatty acid metabolism genes were expressed at a higher level in early (14 to 49 d of gestation) Duroc embryos than in Pietrain embryos. Better understanding of the genomic regulation of tissue formation leads to improved knowledge of the genome under selection and may lead to directed breed-specific changes in the future. [ABSTRACT FROM AUTHOR]

The leptin receptor ( LEPR) gene consists of 20 exons divided over 1.75 Mb. Parts of bovine LEPR exon 4 (79 bp), exon 11 (95 bp) and exon 20 (513 bp) of 20 cows (Holstein-Friesian) were sequenced ( ; ; ) in an attempt to find polymorphisms. In exons 4 and 11 no SNPs were found. In exon 20, a T to C missense mutation was found at nucleotide 115, which causes an amino acid substitution at residue 945 (T945M). Frequencies for alleles C and T were 0.93 and 0.07 respectively, in a population of 323 Holstein-Friesian cows and TT animals were not detected. Using genotypes of these cows an association study was performed for leptin concentrations during late pregnancy and lactation. Leptin concentrations were determined by radioimmunoassay (RIA). The T945M mutation showed an association with circulating leptin concentrations only during late pregnancy ( P < 0.05) but not during lactation ( P > 0.05). The CC genotype had higher concentrations than the CT genotype during this period. A combined effect with previously described leptin polymorphisms on prepartum leptin concentrations was observed, with one genotype combination having significantly lower levels of leptin up to 50 days, but interaction effects were not significant. The T945M polymorphism may have induced a structural change in the intracellular domain of the LEPR, which may have influenced the signal transduction pathway. However, the effect was found only for the heterozygous genotype because the TT genotype was not detected in this population of 323 Holstein-Friesian cows. [ABSTRACT FROM AUTHOR]

Summary Selection for growth rate or backfat thickness (BFT) in pigs is related with changes in the blood plasma concentrations of growth hormone (GH) and insulin-like growth factor-I (IGF-I). Two experimental pig selection lines based upon a common commercial Large White (LW) selection line were selected for increased growth rate (F-line), or decreased BFT (L-line), respectively. We report here on the statistical evaluation of the phenotypic relationships between growth rate and BFT on the one hand, and (1) mRNA expression levels of GH and its transcription factor pituitary-specific transcription factor-1 (Pit-1), (2) GH protein plasma pulse pattern components and (3) IGF-I and insulin plasma concentrations on the other hand. Residual regression coefficients (RRC) and residual correlation coefficients (RCC) were used to evaluate the phenotypic residual relations between the traits and the hormone levels. Growth hormone mRNA levels, and to a lesser extent Pit-1 mRNA levels, were inversely related with BFT and growth rate when these traits were fitted separately in the model suggesting that GH is more closely related to the traits than Pit-1. Within line evaluation showed that GH mRNA levels had significant RRC with the performance traits in both lines, while Pit-1 mRNA levels were only significantly related to BFT in the L-line in both analyses. When growth rate and BFT were fitted together in the model GH mRNA levels had also significantly RRC with growth rate and BFT. Growth hormone mRNA levels seem to be more closely related with BFT than with growth rate. Growth rate was inversely related with the GH plasma baseline value in both lines. Growth hormone baseline concentration, and to a lesser extent GH area under the curve, were inversely related to BFT. However, GH level-line-specific effects were only found for the baseline concentration in the F-line. A positive relationship between growth rate and plasma IGF-I concentrations was found in the L-line. These results suggest a relationship between GH mRNA expression and performance traits in pig lines selected for growth rate or against BFT. No such relationship could be found for its pituitary-specific transcription factor. Furthermore, specific components of the GH blood plasma pulse pattern were related to specific performance traits in these selection lines. The IGF-I blood plasma concentrations were related to growth rate in these selection lines. [ABSTRACT FROM AUTHOR]

An abstract of the article "Leptin Gene Polymorphisms and Their Phenotypic Associations," by T. van der Lende and colleagues is presented.

Describes fluctuations in leptin concentrations during late pregnancy and lactation in dairy cows. Leptin concentrations and reproductive measures; Influence of feed intake on the production of leptin during the lactation period; Recovery of leptin concentrations after the nadir at parturition.

Ethiopia is an ecologically diverse country; the low altitude regions are hot and humid whereas the high altitude regions are cooler. In this study we analyzed the transcriptome response of high altitude (Addis Ababa) and low altitude (Awash) chickens to heat stress conditions that are prevalent in the low altitude regions. The chickens were free ranged for 20 h in an enclosure in Awash, and then the heart, breast muscle and spleen tissues were collected at 6:00 am, 12:00 noon and 6:00 pm to follow a daily circadian cycle. Through RNA-sequencing analysis, we identified differentially expressed genes (DEGs) that were significant (q < 0.05). These DEGs were subjected to protein-protein interaction (PPI) network and gene co-expression network (GCN) analyses to understand their role. KEGG pathway analysis and Gene Ontology analysis of all the identified DEGs and the genes identified from the PPI network and GCN analyses revealed that several immune-related pathways, such as proteasome, focal adhesion, influenza A, the ErbB signaling pathway and glycerophospholipid metabolism, were enriched in response to heat stress. These results suggest that the high altitude chickens were under heat stress and might be immunologically susceptible. Our findings will help in developing a genetic approach to mitigate production loss due to heat stress., (© 2018 Stichting International Foundation for Animal Genetics.)

Chicken skeletal muscle satellite cells are located between the basement membrane and the sarcolemma of mature muscle fibers. Avian broilers have been genetically selected based on their high growth velocity and large muscle mass. The Wuding chicken is a famous local chicken in Yunnan Province that undergoes non-selection breeding and is slow growing. In this study, we aimed to explore differences in the proliferation and differentiation properties of satellite cells isolated from the two chicken breeds. Using immunofluorescence, hematoxylin-eosin staining and real-time polymerase chain reaction analysis, we analyzed the in vitro characteristics of proliferating and differentiating satellite cells isolated from the two chicken breeds. The growth curve of satellite cells was S-shaped, and cells from Wuding chickens entered the logarithmic phase and plateau phase 1 day later than those from Avian chicken. The results also showed that the two skeletal muscle satellite cell lines were positive for Pax7, MyoD and IGF-1. The expression of Pax7 followed a downward trend, whereas that of MyoD and IGF-1 first increased and subsequently decreased in cells isolated from the two chickens. These data indicated that the skeletal muscle satellite cells of Avian chicken grow and differentiate faster than did those of Wuding chickens. We suggest that the methods of breeding selection applied to these breeds regulate the characteristics of skeletal muscle satellite cells to influence muscle growth.

The aim of this study was to validate previously reported associations between microarray gene expression levels and pork quality traits using real-time PCR. Meat samples and meat quality data from 100 pigs were collected from a different pig breed to the one tested by microarray (Large White versus Pietrain) and a different country of origin (Denmark versus Germany). Ten genes (CARP, MB, CSRP3, TNNC1, VAPB, TNNI1, HSPB1, TNNT1, TIMP-1, RAD-like) were chosen from the original microarray study on the basis of the association between gene expression levels and the meat quality traits meat %, back fat, pH24, drip loss %, colour a*, colour b*, colour L*, WB-SF, SFA, MUFA, PUFA. Real-time PCR detection methods were developed for validation of all ten genes, confirming association with drip loss (two of two genes), ultimate pH (three of four genes), a* (redness) (two of six genes) and L*(lightness) (two of four genes). Furthermore, several new correlations for MUFA and PUFA were established due to additional meat quality trait information on fatty acid composition not available for the microarray study. Regression studies showed that the maximum explanation of the phenotypic variance of the meat quality traits was 50% for the ultimate pH trait using these ten genes only. Additional studies showed that the gene expression of several of the genes was correlated with each other. We conclude that the genes initially selected from the microarray study were robust, explaining variances of the genes for the meat quality traits., (© 2014 Blackwell Verlag GmbH.)

Expression of water soluble proteins of fresh pork Longissimus thoracis from 4 pure breed pigs (Duroc, Large White, Landrace, and Piétrain) was studied to identify candidate protein markers for meat quality. Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) was used to obtain the soluble protein profiles of Longissimus thoracis muscles. The pure breeds showed differences among the studied meat quality traits (pHu, drip loss, androstenone, marbling, intramuscular fat, texture, and moisture), but no significant differences were detected in sensory analysis. Associations between protein peaks obtained with SELDI-TOF-MS and meat quality traits, mainly water holding capacity, texture and skatole were observed. Of these peaks, a total of 10 peaks from CM10 array and 6 peaks from Q10 array were candidate soluble protein markers for pork loin quality. The developed models explained a limited proportion of the variability, however they point out interesting relationships between protein expression and meat quality., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The relationship between protein profiles of Gluteus medius (GM) muscles of raw hams obtained from 4 pure breed pigs (Duroc, Large White, Landrace, and Piétrain) with the final quality of the Semimembranosus and Biceps femoris muscles of dry-cured hams was investigated. As expected, Duroc hams showed higher levels of marbling and intramuscular fat content than the other breeds. Piétrain hams were the leanest and most conformed, and presented the lowest salt content in dry-cured hams. Even if differences in the quality traits (colour, water activity, texture, composition, intramuscular fat, and marbling) of dry-cured hams were observed among the studied breeds, only small differences in the sensory attributes were detected. Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) was used to obtain the soluble protein profiles of GM muscles. Some associations between protein peaks obtained with SELDI-TOF-MS and quality traits, mainly colour (b*) and texture (F(0), Y(2), Y(90)) were observed. Candidate protein markers for the quality of processed dry-cured hams were identified., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Selection of pigs for increased meat production or improved meat quality changes muscle mass and muscle composition. This will be related to transcriptome expression profile changes in muscle tissue, generating inter-individual differences. This study investigated the differentially expressed genes in the transcriptome profiles of the longissimus muscle of 75 Large White-Duroc cross sows and castrates. The use of a common reference design enabled to investigate the inter-individual transcriptome expression profile differences between the animals as compared with the means of all animals. The aim of the study was to identify the biological processes related to these inter-individual differences. It was expected that these processes underlie the selection effects. In total, 908 transcripts were differentially expressed. Among them, 762 were mainly downregulated and 146 were mainly upregulated. Gene Ontology and Pathways analyses indicated that the differentially expressed genes belong to three groups of processes involved in protein synthesis and amino acid-protein metabolism, energy metabolism and muscle-specific structure and activity processes. Comparing the functional biological analysis results with previously reported data suggested that the protein synthesis, energy metabolism and muscle-specific structure would contribute to meat production and the meat quality., (© 2012 Wageningen University.)

Skeletal muscle development in vertebrates - also termed myogenesis - is a highly integrated process. Evidence to date indicates that the processes are very similar across mammals, poultry and fish, although the timings of the various steps differ considerably. Myogenesis is regulated by the myogenic regulatory factors and consists of two to three distinct phases when different fibre populations appear. The critical times when myogenesis is prone to hormonal or environmental influences depend largely on the developmental stage. One of the main mechanisms for both genetic and environmental effects on muscle fibre development is via the direct action of the growth hormone-insulin-like growth factor (GH-IGF) axis. In mammals and poultry, postnatal growth and function of muscles relate mainly to the hypertrophy of the fibres formed during myogenesis and to their fibre-type composition in terms of metabolic and contractile properties, whereas in fish hyperplasia still plays a major role. Candidate genes that are important in skeletal muscle development, for instance, encode for IGFs and IGF-binding proteins, myosin heavy chain isoforms, troponin T, myosin light chain and others have been identified. In mammals, nutritional supply in utero affects myogenesis and the GH-IGF axis may have an indirect action through the partitioning of nutrients towards the gravid uterus. Impaired myogenesis resulting in low skeletal myofibre numbers is considered one of the main reasons for negative long-term consequences of intrauterine growth retardation. Severe undernutrition in utero due to natural variation in litter or twin-bearing species or insufficient maternal nutrient supply may impair myogenesis and adversely affect carcass quality later in terms of reduced lean and increased fat deposition in the progeny. On the other hand, increases in maternal feed intake above standard requirement seem to have no beneficial effects on the growth of the progeny with myogenesis not or only slightly affected. Initial studies on low and high maternal protein feeding are published. Although there are only a few studies, first results also reveal an influence of nutrition on skeletal muscle development in fish and poultry. Finally, environmental temperature has been identified as a critical factor for growth and development of skeletal muscle in both fish and poultry.

Selective breeding is an effective tool to improve livestock. Several selection experiments have been conducted to study direct selection responses as well as correlated responses in traits of skeletal muscle growth and function. Moreover, comparisons of domestic with wild-type species and of extreme breeds provide information on the genetic background of the skeletal muscle phenotype. Structural muscular components that differed with increasing distance in lean growth or meat quality in mammals were found to be myofibre number, myofibre size, proportions of fibre types as well as the numbers and proportions of secondary and primary fibres. Furthermore, markers of satellite cell proliferation, metabolic enzyme activities, glycogen and fat contents, the expression of myosin heavy chain isoforms, of activated AMPKα and other proteins in skeletal muscle tissue and circulating IGF1 and IGF-binding proteins have been identified to be involved in selection responses observed in pigs, cattle and/or chicken. The use of molecular methods for selective breeding of fish has only recently been adopted in aquaculture and studies of the genetic basis of growth and flesh quality traits are scarce. Some of the molecular markers of muscle structure/metabolism in livestock have also been identified in fish, but so far no studies have linked them with selection response. Genome scans have been applied to identify genomic regions exhibiting quantitative trait loci that control traits of interest, for example, muscle structure and meat quality in pigs and growth rate in chicken. As another approach, polymorphisms in candidate genes reveal the relationship between genetic variation and target traits. Thus, in large-scale studies with pigs' associations of polymorphisms in the HMGA2, CA3, EPOR, NME1 and TTN genes with traits of carcass and meat quality were detected. Other studies revealed the significance of mutations in the IGF2 and RYR1 genes for carcass lean and muscle fibre traits in pigs. Mutations in the myostatin (MSTN) gene in fish were also examined. Advances in research of the genetic and environmental control of traits related to meat quality and growth have been made by the application of holistic 'omics' techniques that studied the whole muscle-specific genome, transcriptome and proteome in relation to muscle and meat traits, the development of new methods for muscle fibre typing and the adaptation of biophysical measures to develop parameters of muscle fibre traits as well as the application of in vitro studies. Finally, future research priorities in the field are defined.

Subfertility has negative effects for dairy farm profitability, animal welfare and sustainability of animal production. Increasing herd sizes and economic pressures restrict the amount of time that farmers can spend on counteractive management. Genetic improvement will become increasingly important to restore reproductive performance. Complementary to traditional breeding value estimation procedures, genomic selection based on genome-wide information will become more widely applied. Functional genomics, including transcriptomics (gene expression profiling), produces the information to understand the consequences of selection as it helps to unravel physiological mechanisms underlying female fertility traits. Insight into the latter is needed to develop new effective management strategies to combat subfertility. Here, the importance of functional genomics for dairy cow reproduction so far and in the near future is evaluated. Recent gene profiling studies in the field of dairy cow fertility are reviewed and new data are presented on genes that are expressed in the brains of dairy cows and that are involved in dairy cow oestrus (behaviour). Fast-developing new research areas in the field of functional genomics, such as epigenetics, RNA interference, variable copy numbers and nutrigenomics, are discussed including their promising future value for dairy cow fertility.

The research area of animal genomics is moving now from its sequencing era into an integrativefunctional genomics era. Thefast growing sequence information of animal genomes provides exiting opportunities for improving animal health traits by genomics-assisted breeding approaches. In addition, data from functional genomics studies offers deeper insight into the biological mechanisms that underlie animal health phenotypes. Understanding host-pathogen relationships, for example, promises to forward the integration of health genetics into breeding programmes and the development of new tools and strategies for the diagnosis, prognosis, treatment and prevention of infectious diseases. Similarly, increased knowledge on nutrient-gene interactions provides information on the effects of nutrients on biological processes. This knowledge may be used to redefine and optimize the nutritional needs of healthy animals. In this paper, prospects, challenges, and requirements of animal genomics research for improving animal health will be presented.

In dairy cattle, the increase in milk yield has been accompanied by a more negative energy balance (EB) during early lactation and a decrease in fertility. As the hormone leptin is involved in regulation of nutritional status and reproductive function this hormone is an interesting protein to investigate during the periparturient period in dairy cattle. This study was performed to get insight into the function of leptin during the periparturient period and to perform an association study between polymorphisms in the bovine leptin gene and leptin receptor gene and fertility as well as production traits. Leptin concentrations in the periparturient cow undergo remarkable changes; leptin concentrations were high during late pregnancy and declined to a nadir at parturition. Genetic analysis of the leptin gene indicated that a combination of three polymorphisms located at a 135 bp region of the leptin promoter explained most of the variance in prepartum leptin concentrations. The two extreme genotype combinations could be used to investigate the function of leptin concentrations in pregnant cows. A polymorphism located on intron 2 of the leptin gene explained a significant part of the variation in milk yield. On the promoter region of the leptin gene an SNP was detected that was associated with first postpartum luteal activity (FPLA). This SNP could be a candidate marker for fertility in dairy cows. Another SNP on the leptin promoter was associated with energy balance and dry matter intake (DMI) where a higher dry matter intake occurred together with a higher energy balance. Two genotype combinations of the aforementioned three associated SNPs were defined which had a good milk yield together with a good energy balance and fertility. Calculations of an economical value per trait have to validate if one of these genotype combinations would be a possible candidate to be used in selection.

Leptin is a 16-kDa protein synthesized by adipose tissue and is involved in regulation of feed intake, energy balance, fertility, and immune functions. Since evidence of a genetic correlation between start of luteal activity and energy balance, milk yield, and live weights is present, we investigated the association of genetic differences in the bovine leptin gene with these traits. Between 1990 and 1997, a total of 613 Holstein-Friesian heifers of two genetic groups with known pedigree were followed from parturition until d 105 of lactation. During the first 15 wk of lactation live weight, feed intake, and milk yield were measured for 565 cows. The start of luteal activity was set at the first day with a progesterone concentration higher than 3 ng/ml. In addition to the interval between calving and start of luteal activity, analyses were performed for average milk yield, percentage fat, protein, and lactose in milk, dry matter intake, feed intake, energy balance, and live weight over the first 15 wk of lactation. All 613 cows were genotyped for two restricted fragment length polymorphisms and for the BM1500 microsatellite, all located at the leptin gene locus. Significances of the genotype effects were estimated using the approximated F-statistic provided by ASREML. Fixed effects were year-season, genetic group, and a quadratic polynomial for age at calving. Animal was fitted as a random effect including the additive relationship between animals to account for background genes. Firstly, each genotype effect was fitted in turn, and secondly the other restriction fragment length polymorphisms were fitted as a cofactor to take into account effects of linkage disequilibrium. Thirdly, sire x genotype interaction was investigated. Heifers with the RFLP1-AB genotype produce 1.32 kg/d more milk and consume 0.73 kg/d more food compared with the RFLP1-AA genotype. No effects were found for start of luteal activity. When linkage disequilibrium with the other markers was taken into account and DMI was included as fixed effect in the model a 0.96 kg/d higher milk yield was still found. Assuming that no pleiotropic effects on traits such as immunity and milk production in later lactations exist, future breeding programs favoring the RFLP1 B-allele can yield a higher milk production without negatively affecting energy balance and fertility. The prospects are good because in this study the frequency of the RFLP1 AB- and BB-genotypes were only 18.5 and 0.2%, respectively.

Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple independent sites within the genome and would allow a better definition of the relatedness of different Trypanosome (sub)species. Nine isolates (3 from each T. brucei subspecies) were tested with 40 AFLP primer combinations to identify the most appropriate pairs of restriction endonucleases and selective primers. Primers based on the recognition sequences of EcoRI and BglII were chosen and used to analyse 31 T. brucei isolates. Similarity levels calculated with the Pearson correlation coefficient ranged from 15 to 98%, and clusters were determined using the unweighted pair-group method using arithmetic averages (UPGMA). At the intraspecific level, AFLP fingerprints were grouped by numerical analysis in 2 main clusters, allowing a clear separation of T. b. gambiense (cluster I) from T. b. brucei and T. b. rhodesiense isolates (cluster II). Interspecies evaluation of this customized approach produced heterogeneous AFLP patterns, with unique genetic markers, except for T. evansi and T. equiperdum, which showed identical patterns and clustered together.