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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]

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]

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]

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]

Studies the marker polymorphisms in the porcine gene for muscle glycogen synthase (GYS1) and muscle glycogen phosphorylase. Analysis of polymerase chain reaction conditions; Examination of Mendelian inheritance of polymorphism; Association of GYS1 with prenatal muscle glycogen reserve.

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]

Ten genes ( ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain × (Landrace × Large White), Duroc × (Landrace × Large White) as well as in an experimental F2 population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human–porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of ≤ 0.05; PDGFRA revealed no association reaching the P ≤ 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical–genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations. [ABSTRACT FROM AUTHOR]

Leptin concentrations in body fluids and tissues undergo dynamic changes during the periparturient period. Polymorphisms in the leptin gene have been shown to be associated with differences in leptin concentration during late pregnancy but not during lactation. As the promoter of leptin regulates the expression of leptin, polymorphisms in this region could play an important role in the differences in leptin expression observed during the periparturient period. We sequenced the leptin promoter and discovered 20 SNP in a 1.6-kbp region of the bovine leptin promoter. Fourteen of these SNP were genotyped for all animals and these were found to be associated with leptin concentrations during late pregnancy but not during lactation. Three of these SNP are located in a 135-bp promoter region and together explained 14.3% of the variance in prepartum leptin concentrations which indicates that this region might be important for pregnancy-induced leptin synthesis. In the association study of the 14 SNP with dairy traits three were separately found to be associated with fertility, energy balance and protein yield. These might serve as markers for future breeding programmes for better fertility and energy balance without significantly influencing milk yield in dairy cattle. [ABSTRACT FROM AUTHOR]

The full-length cDNA of porcine genes (PSME1andPSME2) encoding proteasome activators PA28α- andβ-subunits were obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with their mammalian counterparts. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that porcinePSME1andPSME2genes are expressed in all eight tissues studied (liver, spleen, bladder, small intestine, kidney, heart, skeletal muscle and lung). The full-length genomic DNA of the porcinePSME1andPSME2genes were amplified by PCR. These two genes shared the same structure and were similar in size. A C/T single nucleotide polymorphism inPSME1intron 8 detected as anSphI PCR-restriction fragment length polymorphism (PCR–RFLP) shows allele frequency differences between Meishan, Tibetan, Large White, Qingping, and Duroc pigs. The association analysis using two experimental GY selection lines selected for growth rate or leanness suggested that thePSME1genotype was associated with weaning weight. Analyses of somatic cell hybrid (SCHP) and radiation hybrid (IMpRH) panels revealed that both genes map to SSC7q15.3-q21 and closely linked to the T-cell receptorα (TCRA) gene. [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]

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.

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]

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]