Journal article
Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis
Statistics and Data Analysis, Department of Applied Mathematics and Computer Science, Technical University of Denmark1
Department of Applied Mathematics and Computer Science, Technical University of Denmark2
Dynamical systems, Department of Mathematics, Technical University of Denmark3
University of Copenhagen4
SEGES5
Danish Technological Institute6
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.
Language: | English |
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Year: | 2019 |
Pages: | 488-499 |
ISSN: | 15312267 and 10948341 |
Types: | Journal article |
DOI: | 10.1152/physiolgenomics.00125.2018 |
ORCIDs: | Drag, Markus H. and Kadarmideen, Haja N. |
Androsterone Animal Welfare Animals Breeding Cichorium intybus DNA Female Genotype Male Odorants Orchiectomy Osmolar Concentration Plant Extracts Polymorphism, Single Nucleotide Quantitative Trait Loci Reverse Transcriptase Polymerase Chain Reaction Sus scrofa Testis androstenone boar taint chicory expression quantitative trait loci