Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues

• Published in: BMC genomics 2024-07, Vol.25 (1), p.684-13, Article 684
• Main Authors: Farhangi, Samin, Gòdia, Marta, Derks, Martijn F L, Harlizius, Barbara, Dibbits, Bert, González-Prendes, Rayner, Crooijmans, Richard P M A, Madsen, Ole, Groenen, Martien A M
• Format: Article
• Language: English
• Subjects: Analysis; Animals; Bioinformatics; Biological activity; Diseases; DNA binding proteins; DNA sequencing; eGWAS; Female; Gene expression; Gene Expression Regulation; Gene mapping; Gene regulation; Gene sequencing; Genes; Genetic aspects; Genetic diversity; Genetic polymorphisms; Genetic transcription; Genetic variance; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomic analysis; Genomics; Genotype; Genotype & phenotype; Genotypes; Genotyping; Liver; Liver - metabolism; Lung - immunology; Lung - metabolism; Lungs; Meat; Muscles; Organ Specificity - genetics; Pig; Polymorphism, Single Nucleotide; Quality control; Quantitative genetics; Quantitative Trait Loci; Regulatory sequences; Regulatory variants; RNA; RNA-seq; Scientific equipment and supplies industry; Single nucleotide polymorphisms; Spleen; Spleen - metabolism; Swine; Swine - genetics; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptome; Transcriptomes
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10583-w

Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status. Here, the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred female finishers were studied, with the aim of identifying novel eQTL regulatory regions and transcription factors (TFs) associated with regulation of porcine metabolism and health-related traits. An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression. This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.