Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis (RNASeq Database)
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ABSTRACT:
PROVIDER: PRJNA489302 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7786300_1.fastq.gz | Fastqsanger.gz | |||
| SRR7786300_2.fastq.gz | Fastqsanger.gz | |||
| SRR7786310_1.fastq.gz | Fastqsanger.gz | |||
| SRR7786310_2.fastq.gz | Fastqsanger.gz | |||
| SRR7786320_1.fastq.gz | Fastqsanger.gz |
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Project description:Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis - RNASeq Database
| PRJNA470616 | 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 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:Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis - SNP Genotype Database
| PRJNA471674 | 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: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 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: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 is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
2018-04-18 | GSE113318 | GEO