Deciphering genetic variants from whole genome affecting duodenum, liver and muscle transcriptomes in pigs

With the aim of deciphering genetic variants affecting gene expression levels of duodenum, liver and muscle, the DNA and RNA of 300 pigs from three different breeds (Duroc, Landrace and Large White) was extracted and sequenced. After filtering and normalizing both the genomic and the transcriptomic datasets, expression genome-wide association studies (eGWAS) were conducted between 25,315,878 polymorphisms and the expression of 16,753 genes in duodenum, 15,710 genes in liver, and 13,887 genes in muscle. In total, more than 1.17×1012 combinations were performed, obtaining 19,926,590 significantly associated polymorphisms, which were grouped in 148,639 expression quantitative trait locus (eQTL) regions. Half of the polymorphisms were located in close proximity to their associated gene, but only 7,773 cis-eQTL regions were defined, the remaining being trans-eQTLs regions. Out of the cis-eQTL regions, 18 shared the same top polymorphism among the three tissues; thus, they were considered the strongest candidates for gene expression regulation.

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