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Analysis of non‐synonymous SNP s of the porcine SERPINA 6 gene as potential causal variants for a QTL affecting plasma cortisol levels on SSC 7
Author(s) -
Görres A.,
Ponsuksili S.,
Wimmers K.,
Muráni E.
Publication year - 2015
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12276
Subject(s) - biology , single nucleotide polymorphism , haplotype , quantitative trait locus , genetics , candidate gene , snp , locus (genetics) , gene , linkage disequilibrium , genetic association , allele , genotype
Summary Recently, the SERPINA 6 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 SERPINA 6 are sufficient to explain the QTL in these two populations. Our investigations revealed that SNP s 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 SNP s c.793G>A and c.919G>A and a haplotype carrying SNP s c.44G>T and c.622C>T. Furthermore, some SNP s, 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 SNP s segregate at very low frequency (<5%) and/or show only weak association with cortisol level ( SNP s c.832G>A and c.919G>A; P < 0.05). These findings suggest that the non‐synonymous SNP s are not sufficient to explain the QTL across different breeds. Therefore, we examined whether the expression of SERPINA 6 is affected by cis‐regulatory polymorphisms in liver, the major organ for CBG production. We found allelic expression imbalance of SERPINA 6, 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 .