Evaluation of <i>FABP2</i> as candidate gene for a fatty acid composition QTL in porcine chromosome 8

Estellé, Jordi; Mercadé, A.; Pérez‐Enciso, Miguel; Pena, Ramona N.; Silió, L.; Sánchez, Armand; Folch, Josep María

doi:10.1111/j.1439-0388.2008.00754.x

Cited by 10 publications

(12 citation statements)

References 20 publications

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“…Two other studies of our group analyzed positional candidate genes for this QTL, i.e. FABP2 [21] and MTTP [22], but the localization of the QTL was not refined. In addition, QTL for IMF palmitic (C16:0) FA composition have been reported in a Duroc x Large White F 2 cross [13] and for stearic (C18:0) FA in a White Duroc x Erhualian F 2 cross [14].…”

Section: Resultsmentioning

confidence: 99%

“…A total of 470 animals were genotyped for 144 SNPs located on SSC8; these include a selection of 142 informative SNPs derived from the Porcine SNP60K BeadChip [20] and two SNPs that corresponded to the previously detected polymorphisms in the FABP2 [21] and MTTP [22] genes. These SNPs [See Additional file 1: Table S1] were included in a custom-generated panel, genotyped using a Veracode Golden Gate Genotyping Kit (Illumina Inc.) and analyzed with a Bead Xpress Reader (Illumina Inc.).…”

Section: Methodsmentioning

confidence: 99%

“…In total, 133 SNPs (92%) passed this quality-threshold filter and were used in the subsequent analysis. Genotypes of all the parents were obtained with the 60 K SNP chip (Illumina) [17] or by pyrosequencing [21,22]. …”

Section: Methodsmentioning

confidence: 99%

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

et al. 2014

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BackgroundFat 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 F2 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.-533C < T), which is associated with percentage of palmitic and palmitoleic acids in muscle and adipose tissues. Here, a combination of single-marker association and the haplotype-based approach was used to analyze backfat fatty acid composition in 470 animals of an Iberian x Landrace F2 intercross genotyped with 144 SNPs (single nucleotide polymorphisms) distributed along SSC8.ResultsTwo trait-associated SNP regions were identified at 93 Mb and 119 Mb 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 93 Mb 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 119 Mb region, the ELOVL6:c.-533C > T polymorphism showed a strong association with percentage of palmitic and palmitoleic fatty acids and elongation ratios in backfat.ConclusionsOur results suggest that the polymorphisms studied in MAML3 and SETD7 are not the causal mutations for the QTL in the 93 Mb 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 119 Mb region.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

et al. 2014

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“…CRI-MAP version 2.503, developed by Evans and Maddox [http://www.animalgenome.org/bioinfo/tools/share/crimap], was used to build the linkage map using the genotype information of SSC8. In addition, previously detected polymorphisms in the MTTP and FABP2 genes were also included in the analysis [8], [17]. Raw data had a high genotyping quality (call rate >0.99) and, after selecting SNPs with MAF >5%, markers with genotyping and mapping errors were excluded by using the “Chrompic” option of CRI-MAP and R scripts developed by our group.…”

Section: Methodsmentioning

confidence: 99%

Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs

et al. 2013

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BackgroundThe ELOVL fatty acid elongase 6 (ELOVL6), the only elongase related to de novo lipogenesis, catalyzes the rate-limiting step in the elongation cycle by controlling the fatty acid balance in mammals. It is located on pig chromosome 8 (SSC8) in a region where a QTL affecting palmitic, and palmitoleic acid composition was previously detected, using an Iberian x Landrace intercross. The main goal of this work was to fine-map the QTL and to evaluate the ELOVL6 gene as a positional candidate gene affecting the percentages of palmitic and palmitoleic fatty acids in pigs.Methodology and Principal FindingsThe combination of a haplotype-based approach and single-marker analysis allowed us to identify the main, associated interval for the QTL, in which the ELOVL6 gene was identified and selected as a positional candidate gene. A polymorphism in the promoter region of ELOVL6, ELOVL6:c.-533C>T, was highly associated with the percentage of palmitic and palmitoleic acids in muscle and backfat. Significant differences in ELOVL6 gene expression were observed in backfat when animals were classified by the ELOVL6:c.-533C>T genotype. Accordingly, animals carrying the allele associated with a decrease in ELOVL6 gene expression presented an increase in C16:0 and C16:1(n-7) fatty acid content and a decrease of elongation activity ratios in muscle and backfat. Furthermore, a SNP genome-wide association study with ELOVL6 relative expression levels in backfat showed the strongest effect on the SSC8 region in which the ELOVL6 gene is located. Finally, different potential genomic regions associated with ELOVL6 gene expression were also identified by GWAS in liver and muscle, suggesting a differential tissue regulation of the ELOVL6 gene.Conclusions and SignificanceOur results suggest ELOVL6 as a potential causal gene for the QTL analyzed and, subsequently, for controlling the overall balance of fatty acid composition in pigs.

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“…Two of them are FAPB3 and FABP4 which also well known as H-FABP and A-FABP, respectively. FABPs act mainly as FA transporters in the metabolic pathway (Estelle et al, 2009), where the peroxisome proliferators-activated receptor (PPAR) family members cooperatively participate as transcription factors. The knock-out mouse study indicated that FAPB3 gene is important for FA transportation and metabolism (Binas et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

Investigation of SNPs in FABP3 and FABP4 Genes and Their Possible Relationships with Fatty Acid Composition in Broiler

Maharani¹,

Park²,

Jung³

et al. 2011

Korean Journal of Poultry Science

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There is limited information of the genetic effect for fatty acid composition in chicken meat. This study assessed the association of FABP3 and FABP4 genes affecting fatty acid composition in broilers. Two single nucleotide polymorphisms (SNPs) were detected in FABP3 gene and five SNPs were identified in FABP4 gene. The SNPs located in intron 1 and exon 1 of FABP3 and FABP4, respectively, were used for genotyping using PCR-RFLP method. The SNPg.285C >T in FABP4 showed suggestive association with high arachidonic acid (C20 : 4) in CT genotypes (P = 0.068). However, the SNP g.508C > T in FABP3 showed no significant associations with fatty acid composition. These results are the first report to investigate the SNPs in FABP3 and FABP4 genes and their associations with fatty acid composition, although we only found the possible association of FABP4 SNP with fatty acid composition. These results should provide valuable information for further investigation of the genes affecting fatty acid composition in chicken.

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Evaluation of FABP2 as candidate gene for a fatty acid composition QTL in porcine chromosome 8

Cited by 10 publications

References 20 publications

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

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

Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs

Investigation of SNPs in FABP3 and FABP4 Genes and Their Possible Relationships with Fatty Acid Composition in Broiler

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