Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs Dyah Maharani • Hee-Bok Park • Jae-Bong Lee • Chae-Kyoung Yoo • Hyun-Tae Lim • Sang-Hyun Han • Sung-Soo Lee • Moon-Suck Ko • In-Cheol Cho • Jun-Heon Lee Received: 25 January 2012 / Accepted: 1 October 2012 / Published online: 3 November 2012 Ó Springer Science+Business Media Dordrecht 2012 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 com- position in a Korean native pig 9 Landrace F 2 intercross population, we genotyped six single nucleotide polymor- phisms (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 0 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 9 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 9 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 9 10 -10 ). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population. Keywords Landrace and Korean native pigs  Fatty acid composition  Single nucleotide polymorphism  Association  Stearoyl-CoA desaturase Introduction Dietary fatty acid (FA) in meat is a concern in human health. The ratio of saturated FA (SFA) and unsaturated FA (UFA) levels in membrane fluidity and cell–cell interaction has been implicated in a variety of human diseases such as cancer [1], diabetes [2], obesity [3], hypertension [4], and neurological diseases [5, 6]. High intake of saturated FA Dyah Maharani and Hee-Bok Park contributed equally to this study. Electronic supplementary material The online version of this article (doi:10.1007/s11033-012-2014-0) contains supplementary material, which is available to authorized users. D. Maharani  J.-H. Lee (&) Department of Animal Science and Biotechnology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea e-mail: junheon@cnu.ac.kr D. Maharani Faculty of Animal Science, Gadjah Mada University, Yogyakarta 55281, Indonesia H.-B. Park  J.-B. Lee  C.-K. Yoo  H.-T. Lim Division of Applied Life Science, Graduate School of Gyeongsang National University, Jinju 660-701, Korea H.-B. Park  H.-T. Lim Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Korea S.-H. Han  S.-S. Lee  M.-S. Ko  I.-C. Cho (&) Subtropical Animal Experiment Station, National Institute of Animal Science, RDA, 175-6, O-deung dong, Cheju 690-150, Korea e-mail: choic4753@korea.kr 123 Mol Biol Rep (2013) 40:73–80 DOI 10.1007/s11033-012-2014-0