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http://dx.doi.org/10.5713/ajas.17.0779

Genome wide association study of fatty acid composition in Duroc swine  

Viterbo, Vanessa S. (Department of Animal Science and Technology, Sunchon National University)
Lopez, Bryan Irvine M. (Department of Animal Science and Technology, Sunchon National University)
Kang, Hyunsung (Department of Animal Science and Technology, Sunchon National University)
Kim, Hoonseop (Department of Animal Science and Technology, Sunchon National University)
Song, Choul-won (Department of Animal Science and Technology, Sunchon National University)
Seo, Kang Seok (Department of Animal Science and Technology, Sunchon National University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.31, no.8, 2018 , pp. 1127-1133 More about this Journal
Abstract
Objective: Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods: A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following genome-wide rapid association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results: A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively. Genome wide significant variants were located on the same region of swine chromosome 14 (SSC14) that spanned from 120 to 124 Mb. Top SNP ALGA008191 was located at 5 kb near the stearoyl-CoA desaturase (SCD) gene. This gene is directly involved in desaturation of stearic acid into oleic acid. General relationship of significant SNPs showed high linkage disequilibrium thus genome-wide signals was attributed to SCD gene. However, understanding the role of other genes like elongation of very long chain fatty acids-3 (ELOVL3) located on this chromosomal segment might help in further understanding of metabolism and biosynthesis of fatty acids. Conclusion: Overall, this study provides evidence that validates SCD gene as strong candidate gene associated with fatty acid composition in Duroc pigs. Moreover, this study confirms significant SNPs near ELOVL3 gene.
Keywords
Duroc; Fatty Acid; Genome Wide Association Study (GWAS); Stearoyl-CoA Desaturase (SCD) Gene;
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1 Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA 2008;299:1335-44.   DOI
2 Folch J, Lees M, Sloane-Stanley G. A simple method for the isolation and purification of total lipids from animal tissues. J Biol Chem 1957;226:497-509.
3 Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75.   DOI
4 Aulchenko YS, De Koning D-J, Haley C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 2007;177:577-85.   DOI
5 Amin N, Van Duijn CM, Aulchenko YS. A genomic background based method for association analysis in related individuals. PloS One 2007;2:e1274.   DOI
6 Aguilar I, Misztal I, Tsuruta S, Legarra A, Wang H. PREGSF90-POSTGSF90: computational tools for the implementation of single-step genomic selection and genome-wide association with ungenotyped individuals in BLUPF90 programs. Proceedings 10th World Congress Genetics Applied Livestock Production; 2014.
7 Barrett J, Fry B, Maller J, Daly M. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005;21:263-5.   DOI
8 National Center for Biotechnology Information (NCBI) [Internet]. Bethesda, MD, USA: National Library of Medicine (US), National Center for Biotechnology Information; 1988 [cited 2017 Oct 20]. Available from: http://www.ncbi.nlm.nih.gov
9 Klensporf-Pawlik D, Szydlowski M, Kaczmarek A, et al. The fatty acid composition of the Longissimus dorsi muscle, subcutaneous and visceral fats differ in four commercial pig breeds. J Anim Feed Sci 2012;21:661-76.   DOI
10 Jiao X, Sherman BT, Huang DW, et al. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics 2012;28:1805-6.   DOI
11 Uemoto Y, Nakano H, Kikuchi T, et al. Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population. Anim Genet 2012;43:225-8.   DOI
12 Yang B, Zhang W, Zhang Z, et al. Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues. PloS One 2013;8:e65554.   DOI
13 Munoz M, Rodriguez MC, Alves E, et al. Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics 2013;14:845.   DOI
14 Guillou H, Zadravec D, Martin PG, Jacobsson A. The key roles of elongases and desaturases in mammalian fatty acid metabolism: Insights from transgenic mice. Prog Lipid Res 2010;49:186-99.   DOI
15 Miyazaki M, Ntambi JM. Role of stearoyl-coenzyme A desaturase in lipid metabolism. Prostaglandins Leukot Essent Fatty Acids 2003;68:113-21.   DOI
16 Jakobsson A, Westerberg R, Jacobsson A. Fatty acid elongases in mammals: their regulation and roles in metabolism. Prog Lipid Res 2006;45:237-49.   DOI
17 Zhao S, Ren L, Chen L, et al. Differential expression of lipid metabolism related genes in porcine muscle tissue leading to different intramuscular fat deposition. Lipids 2009;44:1029-37.   DOI
18 Zhang W, Zhang J, Cui L, et al. Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genet Sel Evol 2016;48:5.   DOI
19 Henriquez-Rodriguez E, Tor M, Pena R, Estany J. A polymorphism in the stearoyl-CoA desaturase gene promoter increases monounsaturated fatty acid content in dry-cured ham. Meat Sci 2015;106:38-43.   DOI
20 Wilkinson S, Lu ZH, Megens H-J, et al. Signatures of diversifying selection in European pig breeds. PLoS Genet 2013;9:e1003453.   DOI
21 Gjerlaug-Enger E, Aass L, Odegard J, Kongsro J, Vangen O. Genetic parameter of fat quality in pigs measured by near-infrared spectroscopy. Animal 2011;5:1495-505.   DOI
22 Kobayashi T, Fujimori K. Very long-chain-fatty acids enhance adipogenesis through coregulation of Elovl3 and $PPAR{\gamma}$ in 3T3-L1 cells. Am J Physiol Endocrinol Metab 2012;302:E1461-E71.   DOI
23 Ros-Freixedes R, Gol S, Pena RN, et al. Genome-wide association study singles out SCD and LEPR as the two main loci influencing intramuscular fat content and fatty acid composition in Duroc pigs. PloS One 2016;11:e0152496.   DOI
24 Wood J, Enser M, Fisher A, et al. Fat deposition, fatty acid composition and meat quality: a review. Meat Sci 2008;78:343-58.   DOI