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.

中文翻译：

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通过猪睾丸 RNA 测序表征与雄烯酮相关的 eQTL。


影响猪睾丸全基因组基因表达水平（表达数量性状位点或 eQTL）的遗传变异的表征可以提高我们对公猪异味（动物福利性状）遗传结构的理解，并有助于基因组辅助或基因组选择计划。本研究的目的是鉴定与雄烯酮相关的 eQTL，寻找低雄烯酮的候选 eQTL，并通过逆转录酶定量 PCR (RT-qPCR) 验证顶级 eQTL。通过丹麦杂交猪睾丸中的 RNA 测序获得基因表达谱，并通过 80K 单核苷酸多态性面板获得基因型数据。使用两个软件包：Matrix eQTL 和 Krux eQTL，总共鉴定了 262 个 eQTL [错误发现率 (FDR) < 0.05]。其中，149 个顺式作用 eQTL 与雄烯酮浓度和基因表达显着相关 (FDR < 0.05)。 eQTL 与公猪异味相关的多个基因相关，包括 CYP1A2、CYB5D1 和 SPHK2。一种 eQTL 基因 AMPH 存在差异表达（FDR < 0.05）并受到菊苣的影响。发现了五个与低雄烯酮浓度相关的候选 eQTL，包括与 CYP1A2 相关的顶级 eQTL。 RT-qPCR 证实，根据 eQTL 基因型，目标基因表达存在显着差异 (P < 0.05)。此外，eQTL 被丰富为 PigQTLdb 中 15 个公猪异味相关性状的 QTL。这是第一项报告用于猪肉生产的商业杂交猪睾丸中的 eQTL 并揭示公猪异味的遗传结构的研究。潜在的应用包括开发 DNA 测试和先进的公猪异味基因组选择模型。