Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population.
ABSTRACT The stearoyl-CoA desaturase (delta-9-desaturase; SCD) gene is a candidate gene for fatty acid composition. It is located on pig SSC14 in a region where quantitative trait loci (QTL) for fatty acid composition were previously detected in a Duroc purebred population. The objective of the present study was to fine map the QTL, to identify polymorphisms of the pig SCD gene and to examine the effects of SCD polymorphisms on fatty acid composition and melting point of fat in the population. The pigs were examined for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat; the number of pigs examined was 479-521. Two SNPs (g.-353C>T and g.-233T>C) were identified in the promoter region of the SCD gene and were completely linked in the pigs from the base generation. In all pigs, 19 microsatellite markers and SCD haplotypes were then genotyped. Different statistical models were applied to evaluate the effects of QTL and the possible causality of the SCD gene variants with respect to the QTL. The results show that all significant QTL for C14:0, C18:0, C18:1 and melting point of fat were detected in the same region, located near the SCD gene. The results also show a significant association between SCD haplotypes and fatty acid composition and fat melting point in this population. These results indicate that the haplotype of the SCD gene has a strong effect on fatty acid composition and melting point of fat.
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ABSTRACT: Fatty acid composition is an important phenotypic trait in pigs as it affects nutritional, technical and sensory quality of pork. Here, we reported a genome-wide association study (GWAS) for fatty acid composition in the longissimus muscle and abdominal fat tissues of 591 White Duroc×Erhualian F2 animals and in muscle samples of 282 Chinese Sutai pigs. A total of 46 loci surpassing the suggestive significance level were identified on 15 pig chromosomes (SSC) for 12 fatty acids, revealing the complex genetic architecture of fatty acid composition in pigs. Of the 46 loci, 15 on SSC5, 7, 14 and 16 reached the genome-wide significance level. The two most significant SNPs were ss131535508 (P = 2.48×10(-25)) at 41.39 Mb on SSC16 for C20∶0 in abdominal fat and ss478935891 (P = 3.29×10(-13)) at 121.31 Mb on SSC14 for muscle C18∶0. A meta-analysis of GWAS identified 4 novel loci and enhanced the association strength at 6 loci compared to those evidenced in a single population, suggesting the presence of common underlying variants. The longissimus muscle and abdominal fat showed consistent association profiles at most of the identified loci and distinct association signals at several loci. All loci have specific effects on fatty acid composition, except for two loci on SSC4 and SSC7 affecting multiple fatness traits. Several promising candidate genes were found in the neighboring regions of the lead SNPs at the genome-wide significant loci, such as SCD for C18∶0 and C16∶1 on SSC14 and ELOVL7 for C20∶0 on SSC16. The findings provide insights into the molecular basis of fatty acid composition in pigs, and would benefit the final identification of the underlying mutations.PLoS ONE 06/2013; 8(6):e65554. DOI:10.1371/journal.pone.0065554 · 3.53 Impact Factor
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ABSTRACT: Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD c.*2041T>C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.Asian Australasian Journal of Animal Sciences 02/2015; 28(2):151-7. DOI:10.5713/ajas.14.0529 · 0.56 Impact Factor
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ABSTRACT: Fatty acid composition in porcine intramuscular fat affects the dietetic value and technological properties of meat. The stearoyl-CoA desaturase (SCD) gene is a strong positional and functional candidate for fatty acid composition. Our sequence analysis in 4 breeds (Duroc, Pietrain, Polish Landrace, and Polish Large White) revealed a novel single-nucleotide polymorphism (SNP) in the 5'-flanking sequence, and 9 novel SNPs and 2 novel InDels in the 3'UTR. Transcript level of the SCD in subcutaneous fat was significantly higher than in muscle tissue (n = 83, P < 0.001) and the interbreed comparison revealed a higher transcript level in the fat tissue of Polish Landrace (P < 0.01). We found no association between the level of the SCD transcript and fatty acid composition in any of the tissues. We performed an association analysis between 4 SNPs (c.-353C>T, c.-233T>C, c.*164A>G, c.*928G>C), 1 InDel (c.*2574_2576delGTC), and production traits in Polish Large White (n = 185) and synthetic line 990 (n = 243). The most pronounced associations were observed for the c.*928G>C polymorphism, which occurs within a predicted target site for 2 microRNAs (ssc-miR-185 and ssc-miR-491). In line 990, this polymorphism was significantly associated with daily gain (P < 0.04 under the general model) and feed conversion ratio (P < 0.0004), but not with fatness traits. The same tendency, but not significant, was observed in the Polish Large White breed. When both breeds were analyzed together, these associations were again highly significant (daily gain P < 0.003; feed conversion ratio P < 0.0001). We conclude that c.*928G>C is a promising marker for both porcine traits.Journal of Animal Science 10/2012; 91(1). DOI:10.2527/jas.2012-5380 · 1.92 Impact Factor