Sus scrofa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA188941 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR689211.fastq.gz | Fastqsanger.gz | |||
| SRR689212.fastq.gz | Fastqsanger.gz | |||
| SRR689213.fastq.gz | Fastqsanger.gz | |||
| SRR689214.fastq.gz | Fastqsanger.gz | |||
| SRR689215.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Boar taint described as an offensive odor that is released while cooking pork. Androstenone, a steroid mainly synthesized in testis and metabolized in liver is one of the major causes of 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). For this purpose, mRNA expression from testis and liver tissue samples from 10 boars, 5 samples each for high and low androstenone levels were quantified and analyzed. The results shows that in testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver. Digital gene expression analysis identified genes in keratin family, desmoplakin and Interferon-induced protein family for as candidate genes for low androstenone testis sample and genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family as candidate genes for low androstenone liver sample. Additionally, the results revealed that mutations in genes IRG6, DSP, IFIT2 were specific for low androstenone testis tissues and mutations in genes FMO5, HIST1H4K and TSKU were specific for low androstenone liver samples. Testis and liver mRNA profile of high and low androstenone level were generated by RNA deep sequencing, in five animal for each group, Ilumina HiSeq 2000
2013-02-09 | E-GEOD-44171 | biostudies-arrayexpress
Project description:Boar taint described as an offensive odor that is released while cooking pork. Androstenone, a steroid mainly synthesized in testis and metabolized in liver is one of the major causes of 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). For this purpose, mRNA expression from testis and liver tissue samples from 10 boars, 5 samples each for high and low androstenone levels were quantified and analyzed. The results shows that in testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver. Digital gene expression analysis identified genes in keratin family, desmoplakin and Interferon-induced protein family for as candidate genes for low androstenone testis sample and genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family as candidate genes for low androstenone liver sample. Additionally, the results revealed that mutations in genes IRG6, DSP, IFIT2 were specific for low androstenone testis tissues and mutations in genes FMO5, HIST1H4K and TSKU were specific for low androstenone liver samples.
2013-02-09 | GSE44171 | GEO
Project description:Gene expression profiles in testis of pigs with extreme high and low levels of androstenone.
| PRJNA100377 | ENA
Project description:Characterization of genetic variants affecting genome-wide gene expression levels (expression quantitative trait loci or eQTLs) in pig testes may improve our understanding of genetic architecture of boar taint (an animal welfare trait) and helps in genome-assisted or genomic selection programs. The aims of this study were to identify eQTLs associated with androstenone, to find candidate eQTLs for low androstenone, and to validate the top eQTL by reverse transcriptase quantitative PCR (RT-qPCR). Gene expression profiles were obtained by RNA sequencing in testis from Danish cross-bred pigs and genotype data by 80K single nucleotide polymorphism panel. A total of 262 eQTLs [false discovery rate (FDR) < 0.05] were identified by using two software packages: Matrix eQTL and Krux eQTL. Of these, 149 cis-acting eQTLs were significantly associated with androstenone concentrations and gene expression (FDR < 0.05). The eQTLs were associated with several genes of boar taint relevance including CYP1A2, CYB5D1, and SPHK2. One eQTL gene, AMPH, was differentially expressed (FDR < 0.05) and affected by chicory. Five candidate eQTLs associated with low androstenone concentrations were discovered, including the top eQTL associated with CYP1A2. RT-qPCR confirmed target gene expression to be significantly (P < 0.05) different based on eQTL genotypes. Furthermore, eQTLs were enriched as QTLs for 15 boar taint related traits from the PigQTLdb. This is the first study to report eQTLs in testes of commercial crossbred pigs used in pork production and to reveal genetic architecture of boar taint. Potential applications include development of a DNA test and in advanced genomic selection models for boar taint.
2019-08-22 | GSE114225 | GEO
Project description:Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26.877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten of the most significant genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint. Keywords: high vs low Testicle samples from animals with extreme androstenone values, 30 high and 30 low from each of the two breeds Norwegian Landrace and Duroc, were used for the experiment. Each microarray was hybridised with one high and one low androstenone sample from the same breed, giving a total of 30 arrays for each breed.
2007-11-26 | E-GEOD-7409 | biostudies-arrayexpress
Project description:Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26.877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten of the most significant genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint. Keywords: high vs low
2007-11-26 | GSE7409 | GEO
Project description:Boar taint is an offensive odour and flavour from developed in a proportion of non-castrated male pigs (boars). Surgical castration is an effective solution but is under debate due to animal welfare concerns. Gene-based selection for low boar taint has been proposed as concentrations of the main compounds responsible for boar taint (androstenone, skatole and indole [ASI]) exhibit heritability but candidate biomarkers are lacking. The aims of this study were to identify expression quantitative trait loci (eQTLs) associated with ASI in order to aid development of candidate biomarkers and to generate insights into biological pathways. Gene expression profiles were obtained by RNA-Seq from testis of Danish Duroc × Landrace/Yorkshire boars fed either a control or chicory-added diet and genotyping was conducted with a high density SNP panel. A tendency (P = 0.052) of lowered ASI concentrations was found in the chicory group. Furthermore, a high correlation was found between estimated breeding values (EBVs) of androstenone and androstenone concentrations (r2 = 0.48). A total of 213 eQTLs, representing 125 unique genes including MVP, COX1, MAP2K4 and RDH16, contained genotypes associated with summed ASI concentrations and of these, six genes were also differentially expressed across ASI/diet groups. The genes were functionally associated with membrane localised proteins, extracellular exosomes, ATP binding, MAPK cascade and oxidative stress. The highest densities of the eQTLs were on pig chromosomes (SSC) SSC18, SSC12, SSC2, SSC7 and SSC14, in that order. A total of 42 known porcine traits were enriched by the genomic coordinates, including health, meat quality and one reproduction trait. A total of 33 candidate eQTLs enriched known genomic coordinates for androstenone and odour intensity in fat. Our findings suggests that careful monitoring of important productions parameters is necessary, if gene-based selection is performed with markers located within the genomic coordinates of the candidate eQTLs or the eQTLs themselves.
2019-08-22 | GSE114518 | GEO
Project description:Gene expression profiles in liver of pigs with extreme high and low levels of androstenone.
| PRJNA107061 | ENA
Project description:Boar taint is an offensive odour and flavour from developed in a proportion of non-castrated male pigs (boars). Surgical castration is an effective solution but is under debate due to animal welfare concerns. Gene-based selection for low boar taint has been proposed as concentrations of the main compounds responsible for boar taint (androstenone and skatole [AS]) exhibit heritability but candidate biomarkers are lacking. The aims of this study were to identify expression quantitative trait loci (eQTLs) associated with AS in order to aid development of candidate biomarkers and to generate insights into biological pathways.
2019-10-22 | GSE119474 | GEO
Project description:ABSTRACT: BACKGROUND: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs that is primarily caused by high levels of androstenone and skatole in adipose tissue. Androstenone is a steroid and its levels are mainly genetically determined. Studies on androstenone metabolism have, however, focused on a limited number of genes. Identification of additional genes influencing levels of androstenone may facilitate implementation of marker assisted breeding practices. In this study, microarrays were used to identify differentially expressed genes and pathways related to androstenone metabolism in the liver from boars with extreme levels of androstenone in adipose tissue. RESULTS: Liver tissue samples from 58 boars of the two breeds Duroc and Norwegian Landrace, 29 with extreme high and 29 with extreme low levels of androstenone, were selected from more than 2500 individuals. The samples were hybridised to porcine cDNA microarrays and the 1 % most significant differentially expressed genes were considered significant. Among the differentially expressed genes were metabolic phase I related genes belonging to the cytochrome P450 family and the flavin-containing monooxygenase FMO1. Additionally, phase II conjugation genes including UDP-glucuronosyltransferases UGT1A5, UGT2A1 and UGT2B15, sulfotransferase STE, N-acetyltransferase NAT12 and glutathione S-transferase were identified. Phase I and phase II metabolic reactions increase the water solubility of steroids and play a key role in their elimination. Differential expression was also found for genes encoding 17beta-hydroxysteroid dehydrogenases (HSD17B2, HSD17B4, HSD17B11 and HSD17B13) and plasma proteins alpha-1-acid glycoprotein (AGP) and orosomucoid (ORM1). 17beta-hydroxysteroid dehydrogenases and plasma proteins regulate the availability of steroids by controlling the amount of active steroids accessible to receptors and available for metabolism. Differences in the expression of FMO1, NAT12, HSD17B2 and HSD17B13 were verified by quantitative real competitive PCR. CONCLUSIONS: A number of genes and pathways related to metabolism of androstenone in liver were identified, including new candidate genes involved in phase I oxidation metabolism, phase II conjugation metabolism, and regulation of steroid availability. The study is a first step towards a deeper understanding of enzymes and regulators involved in pathways of androstenone metabolism and may ultimately lead to the discovery of markers to reduce boar taint. Liver samples from 116 animals with extreme androstenone values, 29 high and 29 low from each of the two breeds Norwegian Landrace and Duroc, were used for this experiment. Each sample was hybridised together with a common refrence resulting in a total of 116 microarrays.
2008-08-17 | E-GEOD-11073 | biostudies-arrayexpress