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| Status |
Public on Apr 18, 2018 |
| Title |
Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs (SNP60v2 BeadChip data set) |
| Organism |
Sus scrofa |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
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.
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| Overall design |
Genomic DNA was extracted from ham muscle of 48 Danish Landrace pigs with low- medium and high genetic merit of boar taint and genotyped with Illumina Porcine SNP60v2 BeadChip.
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| Contributor(s) |
Drag M, Hansen MB, Skinkyté-Juskiené R, Do DN, Kogelman LJ, Kadarmideen HN |
| Citation(s) |
29438444 |
| Submission date |
Apr 18, 2018 |
| Last update date |
Apr 18, 2018 |
| Contact name |
Haja N Kadarmideen |
| E-mail(s) |
hajak@dtu.dk
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| Organization name |
Technical University of Denmark
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| Department |
Department of Applied Mathematics and Computer Science
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| Lab |
Quantitative Genomics, Bioinformatics & Computational Biology (QBC) Group
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| Street address |
Richard Petersens Plads, Building 324
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| City |
Kongens Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platforms (1) |
| GPL22170 |
Illumina Porcine SNP60v2 BeadChip |
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| Samples (48)
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| This SubSeries is part of SuperSeries: |
| GSE93734 |
Genomics and transcriptomics of boar taint in pigs |
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