Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs

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 x 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 x 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 x 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 x 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.