title: Analysis of non-synonymous SNPs of the porcine SERPINA6 gene as potential causal variants for a QTL affecting plasma cortisol levels on SSC7.
abstract: Recently, the SERPINA6 gene encoding corticosteroid-binding globulin (CBG) has been proposed as a candidate gene for a quantitative trait locus (QTL) affecting cortisol level on pig chromosome 7. The QTL was repeatedly detected in different lines, including a Piétrain × (German Landrace × German Large White) cross (PiF1) and purebred German Landrace (LR). In this study, we investigated whether the known non-synonymous polymorphisms c.44G>T, c.622C>T, c.770C>T, c.793G>A, c.832G>A and c.919G>A of SERPINA6 are sufficient to explain the QTL in these two populations. Our investigations revealed that SNPs c.44G>T, c.622C>T, c.793G>A and c.919G>A are associated with cortisol level in PiF1 (P < 0.01). Haplotype analysis showed that these associations are largely attributable to differences between a major haplotype carrying SNPs c.793G>A and c.919G>A and a haplotype carrying SNPs c.44G>T and c.622C>T. Furthermore, some SNPs, particularly c.44G>T and c.622C>T and the carrier haplotype, showed association with meat quality traits including pH and conductivity (P < 0.05). In LR, the non-synonymous SNPs segregate at very low frequency (<5%) and/or show only weak association with cortisol level (SNPs c.832G>A and c.919G>A; P < 0.05). These findings suggest that the non-synonymous SNPs are not sufficient to explain the QTL across different breeds. Therefore, we examined whether the expression of SERPINA6 is affected by cis-regulatory polymorphisms in liver, the major organ for CBG production. We found allelic expression imbalance of SERPINA6, which suggests that its expression is indeed affected by genetic variation in cis-acting elements. This represents candidate causal variation for future studies of the molecular background of the QTL.
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196, Dummerstorf, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Görres
authors.forename: S
authors.initials: S
authors.lastname: Ponsuksili
authors.forename: K
authors.initials: K
authors.lastname: Wimmers
authors.forename: E
authors.initials: E
authors.lastname: Muráni
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D005260:Female; D005838:Genotype; D006239:Haplotypes; D006854:Hydrocortisone / Q000097:blood*; D007030:Hypothalamo-Hypophyseal System / Q000502:physiology; D008297:Male; D008460:Meat; D010913:Pituitary-Adrenal System / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics* / Q000502:physiology; D014156:Transcortin / Q000235:genetics*
chemical_list: D014156:Transcortin; D006854:Hydrocortisone
keywords: allelic expression imbalance; corticosteroid-binding globulin; glucocorticoid; hypothalamus-pituitary-adrenal axis; meat quality; pig