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A skewed male-to-female ratio in cattle is believed to be due to the biased embryo losses during pregnancy. The changes in biochemical secretion such as miRNAs by the embryo due to altered maternal environment could cause a sex biased selective implantation resulting in a skewed male to female ratio at birth. Nevertheless, it is still not clear whether the male and female embryos could modify their miRNA expression patterns differently in response to altered physiological developmental conditions. Therefore, this study was focused on identifying sex specific miRNA expression patterns induced in the embryo during the elongation period in response to the maternal environment. For this, in vitro produced day female and male embryos were transferred to Holsteins Frisian cows and heifers. The elongated female and male embryos were then recovered at day 13 of the gestation period. Total RNA including the miRNAs was isolated from each group of elongated embryo samples were subjected to the next generation miRNA sequencing. Sequence alignment, identification and quantification of miRNAs were done using the miRDeep2 software package and differential miRNA expression analyses were performed using the edgeR bioconductor package. The recovery rate of viable elongating embryos at day 13 of the gestation period was 26.6%. In cows, 2.8 more viable elongating male embryos were recovered than female embryos, while in heifers the sex ratio of the recovered elongating embryos was close to one (1.05). The miRNA analysis showed that 254 miRNAs were detected in both male and female elongated embryos developed either in cows or heifers, of which 14 miRNAs including bta-miR-10b, bta-miR-148a, bta-miR-26a, and bta-miR-30d were highly expressed. Moreover, the expression level of 32 miRNAs including bta-let-7c, bta-let-7b, bta-let-7g, bta-let-7d and bta-let-7e was significantly different between the male and female embryos developed in cows, but the expression level of only 4 miRNAs (bta-miR-10, bta-mR-100, bta-miR-155 and bta-miR-6119-5p) was different between the male and female embryos that were developed in heifers. Furthermore, 19 miRNAs including those involved in cellular energy homeostasis pathways were differentially expressed between the male embryos developed in cows and heifers, but no significantly differentially expressed miRNAs were detected between the female embryos of cows and heifers. Thus, this study revealed that the sex ratio skewed towards males in embryos developed in cows was accompanied by increased embryonic sexual dimorphic miRNA expression divergence in embryos developed in cows compared to those developed in heifers. Moreover, male embryos are more sensitive to respond to the maternal reproductive microenvironment by modulating their miRNA expression. [ABSTRACT FROM AUTHOR]

Improving the immunocompetence towards pathogens represents a desirable objective of breeding strategies to increase resilience. However, the immune system is complex and the genetic foundation of the underlying components is not yet clarified. In the present study, we focused on 22 blood parameters of 1,144 Landrace (LR) and Large White (LW) piglets at the age of 6–7 weeks. The immune profiles covered immune cells, red blood cell characteristics and cytokines. Genetic parameters based on pedigree information along with possible environmental effects were estimated. Litter effects play an important role in the expression of immune parameters of their young progenies. Hence, litter impacts on the piglet's immune profile including the immune parameters of the dam itself were investigated by different models. To incorporate the complexity of the immune network, the data were further investigated with a principal component analysis. Immune traits showed low to high breed‐specific heritabilities (h2). Strong positive rg were estimated among red blood cell characteristics (0.77–0.99) and among cytokines (0.48–0.99). Neutrophils and lymphocytes illustrated a high negative rg (−0.96 to −0.98). The litter impact on piglet's immunity was examined and strengthened already observed breed differences. In LR, h2 (0.22–0.15) and litter effect (c2) (0.52–0.44) for IFN‐γ decreased after statistical consideration of maternal impact. In LW, a decrease in h2 (0.32–0.18) for IFN‐γ and an increase in c2 (0.54–0.56) were observed. Here, sufficient correlations were detected within various immune traits and functional biological networks of principal components. Most immune traits are heritable and are promising to cover global breed‐specific immunocompetence in pigs. The analysis of immune traits has to be extended in order to find an optimal range and to characterize relationships between immunity and performance to gain an improved immune system without accidental losses in productivity. [ABSTRACT FROM AUTHOR]

Pig production depends on a health and performance balance. An approach to improve intestinal health is the oregano essential oil (OEO) supplementation within a conventional diet. Intestinal integrity regulating effects, for example gene expression, of some feed ingredients are important key factors for that balance. We hypothesized that OEO affects the expression of genes associated with pigs' intestinal integrity. In four trials, a total of 86 pigs have been used. From weaning, the 'treated' group (n = 42) was additionally fed an oregano flavour additive [1500 mg/kg (7.5% pure OEO)] within the basal diet. The 'control' group (n = 44) was kept under identical environmental conditions, except the OEO. At age of 6 months, pigs were slaughtered with an average weight of 111.1 ± 10.9 kg. In addition to automatically generated 'Fat‐o‐Meter' (AutoFOM) data, carcass quality factors have been measured manually. Valuable cuts of meat, such as ham and belly, were significantly reduced in the OEO group. Effects of OEO on pigs' haematologic parameters were very limited. For transcriptome analysis, the most interesting microarray expression results have been listed in a table (topTable). Selected genes were technically validated by qPCR. As a result, few significant differences in animal development and meat quality have been found between the OEO treated and the control group. Depending on OEO supplementation, we found 93 differently regulated genes in the jejunal tissue (70 up, 23 down) and 60 in the ileal tissue (48 up, 12 down). Just three genes (GRIN3B [glutamate ionotropic receptor NMDA type subunit 3B], TJP1/ZO‐1 [tight junction protein ZO‐1] and one uncharacterized gene) were affected by OEO both in jejunum and ileum. qPCR validation revealed AKT serine/threonine kinase 3 (AKT3), Interferon (IFN) ‐ε, ‐ω, tight junction protein (TJP1)/ZO‐1 (ZO‐1) to be upregulated in the jejunum and C‐C motif chemokine ligand 21 (CCL21) was upregulated in the ileum of pigs that were supplemented with OEO. OEO supplementation had limited effects on pigs' performance traits. However, we were able to demonstrate that OEO alters the expression of genes associated with adaptive immune response in pigs' small intestine. These findings help to explain OEOs' beneficial impact on pigs' intestinal integrity. [ABSTRACT FROM AUTHOR]

Next-generation sequencing is a promising approach for the detection of causal variants within previously identified quantitative trait loci. Because of the costs of re-sequencing experiments, this application is currently mainly restricted to subsets of animals from already genotyped populations. Imputation from a lower to a higher marker density could represent a useful complementary approach. An analysis of the literature shows that several strategies are available to select animals for re-sequencing. This study demonstrates an animal selection workflow under practical conditions. Our approach considers different data sources and limited resources such as budget and availability of sampling material. The workflow combines previously described approaches and makes use of genotype and pedigree information from a Landrace and Large White population. Genotypes were phased and haplotypes were accurately estimated with AlphaPhase. Then, AlphaSeqOpt was used to optimize selection of animals for re-sequencing, reflecting the existing diversity of haplotypes. AlphaSeqOpt and ENDOG were used to select individuals based on pedigree information and by taking into account key animals that represent the genetic diversity of the populations. After the best selection criteria were determined, a subset of 57 animals was selected for subsequent re-sequencing. In order to evaluate and assess the advantage of this procedure, imputation accuracy was assessed by setting a set of single nucleotide polymorphism (SNP) chip genotypes to missing. Accuracy values were compared to those of alternative selection scenarios and the results showed the clear benefits of a targeted selection within this practical-driven approach. Especially imputation of low-frequency markers benefits from the combined approach described here. Accuracy was increased by up to 12% compared to a randomized or exclusively haplotype-based selection of sequencing candidates. [ABSTRACT FROM AUTHOR]

Abstract Background Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs. Methods Three hundred and ten F2 pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software. Results Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level. Conclusions Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs.

Abstract Background Quantitative trait loci (QTL) analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig. Methods Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP) spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. Results A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Conclusions Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.

Porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting the swine industry worldwide. Genetic variation in host immunity has been considered as one of the potential determinants to improve the immunocompetence, thereby resistance to PRRS. Therefore, the present study aimed to investigate the breed difference in innate immune response to PRRSV vaccination between German Landrace (DL) and Pietrain (Pi) pigs. We analyzed microarray-based transcriptome profiles of peripheral blood mononuclear cells (PBMCs) collected before (0 h) and 24 h after PRRSV vaccination from purebred DL and Pi pigs with three biological replicates. In total 4,269 transcripts were identified to be differentially expressed in PBMCs in at least any of four tested contrast pairs (i.e. DL-24h vs. DL-0h, Pi-24h vs. Pi-0h, DL-0h vs. Pi-0h and DL-24h vs. Pi-24h). The number of vaccine-induced differentially expressed genes (DEGs) was much higher (2,459) in DL pigs than that of Pi pigs (291). After 24 h of PRRSV vaccination, 1,046 genes were differentially expressed in PMBCs of DL pigs compared to that of Pi (DL-24h vs. Pi-24h), indicating the breed differences in vaccine responsiveness. The top biological pathways significantly affected by DEGs of both breeds were linked to immune response functions. The network enrichment analysis identified ADAM17, STAT1, MMS19, RPA2, BAD, UCHL5 and APC as potential regulatory genes for the functional network of PRRSV vaccine response specific for DL; while FOXO3, IRF2, ADRBK1, FHL3, PPP2CB and NCOA6 were found to be the most potential hubs of Pi specific transcriptome network. In conclusion, our data provided insights of breed-specific host transcriptome responses to PRRSV vaccination which might contribute in better understanding of PPRS resistance in pigs. [ABSTRACT FROM AUTHOR]

The porcine reproductive and respiratory syndrome (PRRS) is an infectious disease that leads to high financial and production losses in the global swine industry. The pathogenesis of this disease is dependent on a multitude of factors, and its control remains problematic. The immune system generally defends against infectious diseases, especially dendritic cells (DCs), which play a crucial role in the activation of the immune response after viral infections. However, the understanding of the immune response and the genetic impact on the immune response to PRRS virus (PRRSV) remains incomplete. In light of this, we investigated the regulation of the host immune response to PRRSV in porcine lung DCs using RNA-sequencing (RNA-Seq). Lung DCs from two different pig breeds (Pietrain and Duroc) were collected before (0 hours) and during various periods of infection (3, 6, 9, 12, and 24 hours post infection (hpi)). RNA-Seq analysis revealed a total of 20,396 predicted porcine genes, which included breed-specific differentially expressed immune genes. Pietrain and Duroc infected lung DCs showed opposite gene expression courses during the first time points post infection. Duroc lung DCs reacted more strongly and distinctly than Pietrain lung DCs during these periods (3, 6, 9, 12 hpi). Additionally, cluster analysis revealed time-dependent co-expressed groups of genes that were involved in immune-relevant pathways. Key clusters and pathways were identified, which help to explain the biological and functional background of lung DCs post PRRSV infection and suggest IL-1β1 as an important candidate gene. RNA-Seq was also used to characterize the viral replication of PRRSV for each breed. PRRSV was able to infect and to replicate differently in lung DCs between the two mentioned breeds. These results could be useful in investigations on immunity traits in pig breeding and enhancing the health of pigs. [ABSTRACT FROM AUTHOR]

The porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting swine production, health and welfare throughout the world. A synergistic action of the innate and the adaptive immune system of the host is essential for mounting a durable protective immunity through vaccination. Therefore, the current study aimed to investigate the transcriptome profiles of peripheral blood mononuclear cells (PBMCs) to characterize the innate and the adaptive immune response to PRRS Virus (PRRSV) vaccination in Pietrain pigs. The Affymetrix gene chip porcine gene 1.0 ST array was used for the transcriptome profiling of PBMCs collected at immediately before (D0), at one (D1) and 28 days (D28) post PRRSV vaccination with three biological replications. With FDR <0.05 and log2 fold change ±1.5 as cutoff criteria, 295 and 115 transcripts were found to be differentially expressed in PBMCs during the stage of innate and adaptive response, respectively. The microarray expression results were technically validated by qRT-PCR. The gene ontology terms such as viral life cycle, regulation of lymphocyte activation, cytokine activity and inflammatory response were enriched during the innate immunity; cytolysis, T cell mediated cytotoxicity, immunoglobulin production were enriched during adaptive immunity to PRRSV vaccination. Significant enrichment of cytokine-cytokine receptor interaction, signaling by interleukins, signaling by the B cell receptor (BCR), viral mRNA translation, IFN-gamma pathway and AP-1 transcription factor network pathways were indicating the involvement of altered genes in the antiviral defense. Network analysis revealed that four network modules were functionally involved with the transcriptional network of innate immunity, and five modules were linked to adaptive immunity in PBMCs. The innate immune transcriptional network was found to be regulated by LCK, STAT3, ATP5B, UBB and RSP17. While TGFß1, IL7R, RAD21, SP1 and GZMB are likely to be predictive for the adaptive immune transcriptional response to PRRSV vaccine in PBMCs. Results of the current immunogenomics study advances our understanding of PRRS in term of host-vaccine interaction, and thereby contribute to design a rationale for disease control strategy. [ABSTRACT FROM AUTHOR]

Pulmonary alveolar macrophages (AMs) are important in defense against bacterial lung inflammation. Cluster of differentiation 14 (CD14) is involved in recognizing bacterial lipopolysaccharide (LPS) through MyD88-dependent and TRIF pathways of innate immunity. Sulforaphane (SFN) shows anti-inflammatory activity and suppresses DNA methylation. To identify CD14 epigenetic changes by SFN in the LPS-induced TRIF pathway, an AMs model was investigated in vitro. CD14 gene expression was induced by 5 µg/ml LPS at the time point of 12 h and suppressed by 5 µM SFN. After 12 h of LPS stimulation, gene expression was significantly up-regulated, including TRIF, TRAF6, NF-κB, TRAF3, IRF7, TNF-α, IL-1β, IL-6, and IFN-β. LPS-induced TRAM, TRIF, RIPK1, TRAF3, TNF-α, IL-1β and IFN-β were suppressed by 5 µM SFN. Similarly, DNMT3a expression was increased by LPS but significantly down-regulated by 5 µM SFN. It showed positive correlation of CD14 gene body methylation with in LPS-stimulated AMs, and this methylation status was inhibited by SFN. This study suggests that SFN suppresses CD14 activation in bacterial inflammation through epigenetic regulation of CD14 gene body methylation associated with DNMT3a. The results provide insights into SFN-mediated epigenetic down-regulation of CD14 in LPS-induced TRIF pathway inflammation and may lead to new methods for controlling LPS-induced inflammation in pigs. [ABSTRACT FROM AUTHOR]

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes. [ABSTRACT FROM AUTHOR]

Background: Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important viral diseases affecting swine industry worldwide. Despite routine farm vaccination, effective control strategies for PRRS remained elusive which underscores the need for in-depth studies to gain insight into the host immune response to vaccines. The current study aimed to investigate transcriptional responses to PRRS Virus (PRRSV) vaccine in the peripheral blood mononuclear cells (PBMCs) within 3 days following vaccination in German Landrace pigs. Results: Transcriptome profiling of PBMCs from PRRSV vaccinated and age-matched unvaccinated pigs at right before (0 h), and at 6, 24 and 72 h after PRRSV vaccination was performed using the Affymetrix gene chip porcine gene 1.0 st array. Comparison of PBMCs transcriptome profiles between vaccinated and unvaccinated pigs revealed a distinct host innate immune transcriptional response to PRRSV vaccine. There was a significant temporal variation in transcriptional responses of PRRSV vaccine in PBMCs accounting 542, 2,263 and 357 differentially expressed genes (DEGs) at 6, 24 and 72 h post vaccination, respectively compared to the time point before vaccination (controls). Gene ontology analysis revealed the involvement of these DEGs in various biological process including innate immune response, signal transduction, positive regulation of MAP kinase activity, TRIF-dependent toll-like receptor signaling pathway, T cell differentiation and apoptosis. Immune response specific pathways such as cytokine-cytokine receptor interaction, chemokine signaling pathway, signal transduction, JAK-STAT pathway and regulation, TRAF6 mediated induction of NF-kB and MAPK, the NLRP3 inflammasome, endocytosis and interferon signaling were under regulation during the early stage of PRRSV vaccination. Network enrichment analysis revealed APP, TRAF6, PIN1, FOS, CTNNB1, TNFAIP3, TIP1, CDKN1, SIRT1, ESR1 and HDAC5 as the highly interconnected hubs of the functional network of PRRSV vaccine induced transcriptome changes in PBMCs. Conclusions: This study showed that a massive gene expression change occurred in PBMCs following PRRSV vaccination in German Landrace pigs. Within first 3 days of vaccine exposure, the highest transcript abundance was observed at 24 h after vaccination compared to that of control. Results of this study suggest that APP, TRAF6, PIN1, FOS, CDKN1A and TNFAIP3 could be considered as potential candidate genes for PRRSV vaccine responsiveness. [ABSTRACT FROM AUTHOR]

The aim of this study was to elucidate the underlying biochemical processes to identify potential key molecules of meat quality traits drip loss, pH of meat 1 h post-mortem (pH1), pH in meat 24 h post-mortem (pH24) and meat color. An untargeted metabolomics approach detected the profiles of 393 annotated and 1,600 unknown metabolites in 97 Duroc × Pietrain pigs. Despite obvious differences regarding the statistical approaches, the four applied methods, namely correlation analysis, principal component analysis, weighted network analysis (WNA) and random forest regression (RFR), revealed mainly concordant results. Our findings lead to the conclusion that meat quality traits pH1, pH24 and color are strongly influenced by processes of post-mortem energy metabolism like glycolysis and pentose phosphate pathway, whereas drip loss is significantly associated with metabolites of lipid metabolism. In case of drip loss, RFR was the most suitable method to identify reliable biomarkers and to predict the phenotype based on metabolites. On the other hand, WNA provides the best parameters to investigate the metabolite interactions and to clarify the complex molecular background of meat quality traits. In summary, it was possible to attain findings on the interaction of meat quality traits and their underlying biochemical processes. The detected key metabolites might be better indicators of meat quality especially of drip loss than the measured phenotype itself and potentially might be used as bio indicators. [ABSTRACT FROM AUTHOR]

The aim of the study was to investigate single nucleotide polymorphisms (SNPs) and expression of SOX-6 to support its candidacy for growth, carcass, and meat quality traits in pigs. The first SNP, rs81358375, was associated with pH 45 min post mortem in loin (pH1 L ), the thickness of backfat and side fat, and carcass length in Pietrain (Pi) population, and related with backfat thickness and daily gain in Duroc × Pietrain F 2 (DuPi) population. The other SNP, rs321666676, was associated with meat colour in Pi population. In DuPi population, the protein, not mRNA, level of SOX-6 in high pH1 L pigs was significantly less abundant compared with low pH1 L pigs, where microRNAs targeting SOX-6 were also differently regulated. This paper shows that SOX-6 could be a potential candidate gene for porcine growth, carcass, and meat quality traits based on genetic association and gene expression. [ABSTRACT FROM AUTHOR]

Background: The aim of this study was to perform a genome-wide association analyses (GWAS) for androstenone, skatole and indole in different Pietrain sire lines and compare the results with previous findings in purebred populations. Furthermore, the genetic relationship of androstenone and skatole were investigated with respect to pleiotropy. In order to characterize the performance of intact boars, crossbred progenies of 136 Pietrain boars mated to crossbred sows from three different breeding companies were tested on four test stations. A total of 598 boars were performance tested according to the rules of stationary performance testing in Germany. Beside common fattening and carcass composition traits, the concentrations of the boar taint components and testicular size parameters were recorded. All boars were genotyped with the PorcineSNP60 Illumina BeadChip. The GWAS were performed using the whole data set as well as in sub groups according to the line of origin. Besides an univariate GWAS approach, principal component (PC) techniques were applied to identify common expression pattern affecting the biosynthesis and the metabolism of androstenone. Results: In total, 33 SNPs were significantly associated with at least one of the boar taint components. Only one SNP was identified being significant in both subgroups. The analyses of the testes size parameters revealed 31 significant associations. The numbers of significant SNPs within the genetic groups evidenced the strong population specific effects. A multivariate approach using PC revealed 33 significant associations for five different PC. Conclusions: Based on Pietrain sired cross bred boars, the mayor objective of our study was to identify QTL for boar taint components and to detect pleiotropy among boar taint and testes traits. The high number of identified QTL revealed that boar taint traits are influenced by a large number of loci. Analyzing pleiotropy allowed identifying a QTL affecting androstenone and the gonasomatic index. In this region, QTL for ovulation rate and age at puberty of sows have been described in literature. This supports the physiological findings that the androstenone level of boars and reproduction performance of sows might be linked by an antagonistic relationship. [ABSTRACT FROM AUTHOR]

The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected. [ABSTRACT FROM AUTHOR]

Background: Boar taint is principally caused by accumulation of androstenone and skatole in adipose tissues. Studies have shown high heritability estimates for androstenone whereas skatole production is mainly dependent on nutritional factors. Androstenone is a lipophilic steroid mainly metabolized in liver. Majority of the studies on hepatic androstenone metabolism focus only on a single breed and very few studies account for population similarities/differences in gene expression patterns. In this work, we concentrated on population similarities in gene expression to identify the common genes involved in hepatic androstenone metabolism of multiple pig populations. Based on androstenone measurements, publicly available gene expression datasets from three porcine populations were compiled into either low or high androstenone dataset. Gene expression correlation coefficients from these datasets were converted to rank ratios and joint probabilities of these rank ratios were used to generate dataset specific co-expression clusters. Finally, these networks were clustered using a graph clustering technique. Results: Cluster analysis identified a number of statistically significant co-expression clusters in the dataset. Further enrichment analysis of these clusters showed that one of the clusters from low androstenone dataset was highly enriched for xenobiotic, drug, cholesterol and lipid metabolism and cytochrome P450 associated metabolism of drugs and xenobiotics. Literature references revealed that a number of genes in this cluster were involved in phase I and phase II metabolism. Physical and functional similarity assessment showed that the members of this cluster were dispersed across multiple clusters in high androstenone dataset, possibly indicating a weak co-expression of these genes in high androstenone dataset. Conclusions: Based on these results we hypothesize that majority of the genes in this cluster forms a signature co-expression cluster in low androstenone dataset in our experiment and that majority of the members of this cluster might be responsible for hepatic androstenone metabolism across all the three populations used in our study. We propose these results as a background work towards understanding breed similarities in hepatic androstenone metabolism. Additional large scale experiments using data from multiple porcine breeds are necessary to validate these findings. [ABSTRACT FROM AUTHOR]

Histone acetylation, regulated by histone deacetylases (HDACs) is a key epigenetic mechanism controlling gene expressions. Although dendritic cells (DCs) are playing pivotal roles in host immune responses, the effect of epigenetic modulation of DCs immune responses remains unknown. Sulforaphane (SFN) as a HDAC inhibitor has anti-inflammatory properties, which is used to investigate the epigenetic regulation of LPS-induced immune gene and HDAC family gene expressions in porcine monocyte-derived dendritic cells (moDCs). SFN was found to inhibit the lipopolysaccharide LPS induced HDAC6, HDAC10 and DNA methyltransferase (DNMT3a) gene expression, whereas up-regulated the expression of DNMT1 gene. Additionally, SFN was observed to inhibit the global HDAC activity, and suppressed moDCs differentiation from immature to mature DCs through down-regulating the CD40, CD80 and CD86 expression and led further to enhanced phagocytosis of moDCs. The SFN pre-treated of moDCs directly altered the LPS-induced TLR4 and MD2 gene expression and dynamically regulated the TLR4-induced activity of transcription factor NF-κB and TBP. SFN showed a protective role in LPS induced cell apoptosis through suppressing the IRF6 and TGF-ß1 production. SFN impaired the pro-inflammatory cytokine TNF-α and IL-1ß secretion into the cell culture supernatants that were induced in moDCs by LPS stimulation, whereas SFN increased the cellular-resident TNF-α accumulation. This study demonstrates that through the epigenetic mechanism the HDAC inhibitor SFN could modulate the LPS induced innate immune responses of porcine moDCs. [ABSTRACT FROM AUTHOR]

Background: Different genome wide association methods (GWAS) including multivariate analysis techniques were applied to identify quantitative trait loci (QTL) and pleiotropy in the simulated data set provided by the QTL-MAS workshop 2012 held in Alghero (Italy). Methods: Genetic correlations and heritabilities for all three quantitative traits were obtained by a multivariate animal model. In a second step the data were corrected for a polygenic component containing the genomicbased kinship matrix. Residuals from this model were later used for QTL detection in a regression analysis, to achieve genome-wide rapid association (GRAMMAR). In order to take pleiotropic effects into account, all three traits were condensed via principle component techniques to two principal components (PC) which reflect the phenotypic variance covariance structure of all traits. The PCs were analyzed by single trait analysis by GRAMMAR. As an alternative to GRAMMAR, the data set was analyzed by Bayesian methods implemented in the package snptest. The program allows the analysis of the data in a univariate and a multivariate way, where all three traits are investigated simultaneously. Results: According to the polygenic model, analyses the three traits revealed high heritability (0.56, 0.55, and 0.66). Traits 1 and 2 were highly correlated (rg = 0.84). All applied GWAS revealed 10 QTL on four different chromosomes. No QTL was detected on chromosome 5. The Bayesian multivariate analysis revealed significant pleiotropic SNPs. Conclusions: Principal component and multivariate analyses seem to be promising in order to characterize the genetic basis of trait relationships. [ABSTRACT FROM AUTHOR]

One of the primary factors contributing to boar taint is the level of androstenone in porcine adipose tissues. A majority of the studies performed to identify candidate biomarkers for the synthesis of androstenone in testis tissues follow a reductionist approach, identifying and studying the effect of biomarkers individually. Although these studies provide detailed information on individual biomarkers, a global picture of changes in metabolic pathways that lead to the difference in androstenone synthesis is still missing. The aim of this work was to identify major pathways and interactions influencing steroid hormone synthesis and androstenone biosynthesis using an integrative approach to provide a bird’s eye view of the factors causing difference in steroidogenesis and androstenone biosynthesis. For this purpose, we followed an analysis procedure merging together gene expression data from boars with divergent levels of androstenone and pathway mapping and interaction network retrieved from KEGG database. The interaction networks were weighted with Pearson correlation coefficients calculated from gene expression data and significant interactions and enriched pathways were identified based on these networks. The results show that 1,023 interactions were significant for high and low androstenone animals and that a total of 92 pathways were enriched for significant interactions. Although published articles show that a number of these enriched pathways were activated as a result of downstream signaling of steroid hormones, we speculate that the significant interactions in pathways such as glutathione metabolism, sphingolipid metabolism, fatty acid metabolism and significant interactions in cAMP-PKA/PKC signaling might be the key factors determining the difference in steroidogenesis and androstenone biosynthesis between boars with divergent androstenone levels in our study. The results and assumptions presented in this study are from an in-silico analysis done at the gene expression level and further laboratory experiments at genomic, proteomic or metabolomic level are necessary to validate these findings. [ABSTRACT FROM AUTHOR]

Boar taint is the unpleasant odour of meat derived from non-castrated male pigs, caused by the accumulation of androstenone and skatole in fat. Skatole is a tryptophan metabolite produced by intestinal bacteria in gut and catabolised in liver. Since boar taint affects consumer’s preference, the aim of this study was to perform transcriptome profiling in liver of boars with divergent skatole levels in backfat by using RNA-Seq. The total number of reads produced for each liver sample ranged from 11.8 to 39.0 million. Approximately 448 genes were differentially regulated (p-adjusted <0.05). Among them, 383 genes were up-regulated in higher skatole group and 65 were down-regulated (p<0.01, FC>1.5). Differentially regulated genes in the high skatole liver samples were enriched in metabolic processes such as small molecule biochemistry, protein synthesis, lipid and amino acid metabolism. Pathway analysis identified the remodeling of epithelial adherens junction and TCA cycle as the most dominant pathways which may play important roles in skatole metabolism. Differential gene expression analysis identified candidate genes in ATP synthesis, cytochrome P450, keratin, phosphoglucomutase, isocitrate dehydrogenase and solute carrier family. Additionally, polymorphism and association analysis revealed that mutations in ATP5B, KRT8, PGM1, SLC22A7 and IDH1 genes could be potential markers for skatole levels in boars. Furthermore, expression analysis of exon usage of three genes (ATP5B, KRT8 and PGM1) revealed significant differential expression of exons of these genes in different skatole levels. These polymorphisms and exon expression differences may have impacts on the gene activity ultimately leading to skatole variation and could be used as genetic marker for boar taint related traits. However, further validation is required to confirm the effect of these genetic markers in other pig populations in order to be used in genomic selection against boar taint in pig breeding programs. [ABSTRACT FROM AUTHOR]

Boar taint is an unpleasant smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone (5α-androst-16-en-3-one) and skatole (3-methylindole). It is crucial to understand the genetic mechanism of boar taint to select pigs for lower androstenone levels and thus reduce boar taint. The aim of the present study was to investigate transcriptome differences in boar testis and liver tissues with divergent androstenone levels using RNA deep sequencing (RNA-Seq). The total number of reads produced for each testis and liver sample ranged from 13,221,550 to 33,206,723 and 12,755,487 to 46,050,468, respectively. In testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver. The fold change values ranged from −4.68 to 2.90 in testis samples and −2.86 to 3.89 in liver samples. Differentially regulated genes in high androstenone testis and liver samples were enriched in metabolic processes such as lipid metabolism, small molecule biochemistry and molecular transport. This study provides evidence for transcriptome profile and gene polymorphisms of boars with divergent androstenone level using RNA-Seq technology. Digital gene expression analysis identified candidate genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family. Moreover, polymorphism and association analysis revealed mutation in IRG6, MX1, IFIT2, CYP7A1, FMO5 and KRT18 genes could be potential candidate markers for androstenone levels in boars. Further studies are required for proving the role of candidate genes to be used in genomic selection against boar taint in pig breeding programs. [ABSTRACT FROM AUTHOR]

Background: Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs. Methods: Three hundred and ten F2 pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software. Results: Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level. Conclusions: Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: Breeding against boar taint compounds androstenone and skatole can be an efficient alternative for surgical castration of young piglets during their first week of life to avoid boar taint. Physiological links of androstenone to steroid hormones in the synthesis pathway are documented and they have to be analyzed for their genetic effects on reproduction and fertility. While using boar taint and hormone data from Landrace and Large White pigs (commercial nucleus populations and herd book populations), the effects of breeding against androstenone on fertility were evaluated. Moreover, the genetic foundation of the chosen hormones' testosterone, 17β-estradiol, luteinizing hormone, follicle-stimulating hormone, and progesterone was analyzed and then checked for possible pleiotropic effects with boar taint compounds. The results showed consistent unfavorable side effects of breeding against androstenone on testosterone and 17β-estradiol in both breeds. The other hormones showed contrary results regarding unfavorable relationships between boar taint and endocrine fertility parameters. The genetic foundation showed a high potential of breeding against boar taint but the impact on fertility potential should be supervised. The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28–0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on Sus Scrofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes. [ABSTRACT FROM AUTHOR]

An association study between polymorphisms of six genes and boar taint related compounds androstenone, skatole and indole was performed in a boar population (n = 370). Significant association ( P < 0.05) was detected for SNP of FMO5 (g.494A>G) with all boar taint compounds, SNP of CYP21 (g.3911T>C) with skatole and indole, and SNP of ESR1 (g.672C>T) with androstenone and indole. mRNA expression of CYP21 and ESR1 was higher in CAB (castrated boar) compared to non-castrated boars; whereas, the expression of FMO5 and ESR1 was higher in LBT (low boar taint) compared to HBT (high boar taint) in liver tissue. FMO5, CYP21 and ESR1 proteins were less detectable in HBT compared with LBT and CAB in liver tissues. These findings suggest that FMO5, CYP21 and ESR1 gene variants might have effects on the boar taint compounds. [ABSTRACT FROM AUTHOR]

Abstract: Cluster-of-differentiation antigen 9 (CD9) gene expressed in the male germ line stem cells is crucial for sperm–egg fusion, and was therefore selected as candidate gene for boar semen quality. The association of CD9 with boar sperm quality and fertility trait was analyzed using a total of 340 boars both from purebred Pietrain and Pietrain×Hampshire crosses. A single nucleotide polymorphism (g.358A>T) in intron 6 was significantly associated with sperm motility (MOT) (P <0.001), plasma droplet rate (PDR) (P <0.001) and abnormal spermatozoa rate (ASR) (P <0.01). Boars were divided into two groups with group 1 (G-I) boars having a higher SCON and SMOT, lower SVOL (sperm volume) and group 2 (G-II) having a lower SCON and SMOT, higher SVOL. The mRNA and protein expression levels were evaluated in reproductive, non-reproductive tissues and spermatozoa from G-I and G-II animals by using quantitative real-time PCR and western blotting. When both reproductive and non-reproductive tissues were examined, highest mRNA was expressed in prostate gland, then in the body of the epididymis, vas deferens and tail of the epididymis. In case of reproductive tissues, CD9 expression was higher in tissues and spermatozoa collected from G-I boars than those collected from G-II boars. The mRNA expression was significantly different (P <0.05) in body of epididymis from G-I and G-II boars. The CD9 protein expression results from western blot were coincided with the results of qRT-PCR. Moreover, CD9 protein localization in Leydig cells, Sertoli cells, epithelial cells and spermatozoa was remarkable which indicated the important role of CD9 in spermatogenesis process. By using mRNA and protein expression profiles, it could be shown that CD9 plays a crucial role during sperm development, especially within the epididymis where the maturation of the sperm, a key process for the sperm quality and motility takes place. These results will improve the understanding of the functions of the CD9 in spermatogenesis within the reproductive tracts and will shed light on CD9 as a candidate gene in the selection of good sperm quality boars. [Copyright &y& Elsevier]