New insight into the SSC8 genetic determination of fatty acid composition in pigs

abstract: ...Background Fat content and fatty acid composition in swine are becoming increasingly studied because of their effect on sensory and nutritional quality of meat. A QTL (quantitative trait locus) for fatty acid composition in backfat was previously detected on porcine chromosome 8 (SSC8) in an Iberian x Landrace F 2 intercross. More recently, a genome-wide association study detected the same genomic region for muscle fatty acid composition in an Iberian x Landrace backcross population. ELOVL6 , a strong positional candidate gene for this QTL, contains a polymorphism in its promoter region ( ELOVL6:c.-533CMAML3 and SETD7 are positional candidate genes in the 93Mb region and two novel microsatellites in MAML3 and nine SNPs in SETD7 were identified. No significant association for the MAML3 microsatellite genotypes was detected. The SETD7:c.700G>T SNP, although statistically significant, was not the strongest signal in this region. In addition, the expression of MAML3 and SETD7 in liver and adipose tissue varied among animals, but no association was detected with the polymorphisms in these genes. In the 119Mb region, the ELOVL6:c.-533C>T polymorphism showed a strong association with percentage of palmitic and palmitoleic fatty acids and elongation ratios in backfat. Conclusions Our results suggest that the polymorphisms studied in MAML3 and SETD7 are not the causal mutations for the QTL in the 93Mb region. However, the results for ELOVL6 support the hypothesis that the ELOVL6:c.-533C>T polymorphism has a pleiotropic effect on backfat and intramuscular fatty acid composition and that it has a role in the determination of the QTL in the 119Mb region.

... analyze backfat fatty acid composition in 470 animals of an Iberian x Landrace F 2 intercross genotyped with 144 SNPs (single nucleotide polymorphisms) distributed along SSC8. Results Two trait-associated SNP regions were identified at 93Mb and 119Mb on SSC8. The strongest statistical signals of both regions were observed for palmitoleic acid (C16:1(n-7)) content and C18:0/C16:0 and C18:1(n-7)/C16:1(n-7) elongation ratios. MAML3 and SETD7 are positional candidate genes in the 93Mb region and two novel microsatellites in MAML3 and nine SNPs in SETD7 were identified. No significant association for the MAML3 microsatellite genotypes was detected. The SETD7:c.700G>T SNP, although statistically significant, was not the strongest signal in this region. In addition, the expression of MAML3 and SETD7 in liver and adipose tissue varied among animals, but no association was detected with the polymorphisms in these genes. In the 119Mb region, the ELOVL6:c.-533C>T polymorphism showed a strong association with percentage of palmitic and palmitoleic fatty acids and elongation ratios in backfat. Conclusions Our results suggest that the polymorphisms studied in MAML3 and SETD7 are not the causal mutations for the QTL in the 93Mb region. However, the results for ELOVL6 support the hypothesis that the ELOVL6:c.-533C>T polymorphism has a pleiotropic effect on backfat and intramuscular fatty acid composition and that it has a role in the determination of the QTL in the 119Mb region. Background One of the main sources

... subsequent analysis. Genotypes of all the parents were obtained with the 60K SNP chip (Illumina) [ 17 ] or by pyrosequencing [ 21 , 22 ]. SNPs SETD7:c.-1034T>G , SETD7:c.700G>T and ELOVL6:c.-533C>T were genotyped using the KASP SNP genotyping system platform ( http://www.lgcgenomics.com/genotyping/ ). Besides these, two new microsatellites in the MAML3 gene were genotyped by PCR amplification and capillary electrophoresis and fluorescent detection using an ABI Prism 3730 DNA Analyzer (Applied Biosystems). Fifty-six animals of the BC1_LD were genotyped for SNPs SETD7:c.-1034T>G and SETD7:c.700G>T and the two MAML3 microsatellites for gene-expression studies. In addition, a subset of 168F 2 animals were genotyped for SNPs ELOVL6:c.-533C>T , SETD7:c.700G>T and the two MAML3 microsatellites for association studies. All parents and grandparents of these animals were also genotyped in the same way. Association analysis Association analysis was performed for FA composition and indices of FA metabolism in

... for the most significant traits C16:1(n-7), C18:0/C16:0, C16:1(n-7)/C18:1(n-7), and the FA average chain-length (ACL) by applying the mixed model: y = Xb + Z h h + Z u u + e , in which b is a vector of fixed effects (sex and batch), h is the vector of random QTL effects corresponding to the K cluster defined by the Hidden State, u is the vector of random individual polygenic effects and e is the vector of individual error. Amplification and sequencing of the pig MAML3 and SETD7 genes Genomic DNA samples from 10 individuals of the BC1_LD and two Iberian boars were used to amplify and sequence the proximal promoter and exon 1 of the MAML3 and SETD7 genes. A 931-bp region of the MAML3 gene was amplified and sequenced in two overlapping fragments of 517bp and 663bp. Primers [See Additional file 2 : Table S2] were designed based on a SSC8 sequence of a Sus scrofa mixed breed [ENSSSCG00000009060] available from the Sscrofa10.2 database and conserved with the human MAML3 gene [ENSG00000196782]. For

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Gene: MAML3 - mastermind-like 3 (Drosophila) - (NCBI)

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