Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population

National Livestock Breeding Center, Nishigo, Fukushima, Japan.
Animal Genetics (Impact Factor: 2.21). 04/2012; 43(2):225-8. DOI: 10.1111/j.1365-2052.2011.02236.x
Source: PubMed


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 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.
    No preview · Article · Oct 2012 · Journal of Animal Science
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    ABSTRACT: Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.
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