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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #369528

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Genome-wide associations for fatty acid composition of pork identifies novel candidate SNP on chromosome 14

item Nonneman, Danny - Dan
item Clancy, Meghan
item Rohrer, Gary
item ARKFELD, EMILY - University Of Illinois
item BOLER, DUSTIN - University Of Illinois
item DILGER, ANNA - University Of Illinois
item King, David - Andy
item Wheeler, Tommy
item Shackelford, Steven

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/24/2019
Publication Date: 1/15/2020
Citation: Nonneman, D.J., Clancy, M.D., Rohrer, G.A., Arkfeld, E., Boler, D.D., Dilger, A.C., King, A., Wheeler, T.L., Shackelford, S.D. 2020. Genome-wide associations for fatty acid composition of pork identifies novel candidate SNP on chromosome 14 [abstract]. In proceedings: Plant and Animal Genome Conference XXVIII, San Diego, CA, January 11-15, 2020. Abstract PE0396. Available:

Interpretive Summary:

Technical Abstract: Fat content and fatty acid composition are attributes that contribute to the nutritional value, sensory properties and quality of pork. Fatty acid composition is dependent upon genetic background, is easily modified through diet and should respond to genetic selection. A genome-wide association study of clear plate (s.c.) fatty acid composition was done in 818 commercial pigs using the GGPHD.v1 beadchip. Thirty-one QTL were identified for fatty acids myristic (14:0), palmitic (16:0), palmitoleic (16:1), stearic (18:0), oleic (18:1(n-9)), arachidic (20:0), SFAs, MUFAs and PUFAs near the genes FADS2 (SSC2), ELOVL5 (SSC7), ELOVL6 (SSC8), SCD and ELOVL3 (SSC14), and ELOVL7 (SSC16) Zero to 3 QTL were identified for individual traits and about 4 to 10 percent of the variance was explained by markers. Thirty-four potentially functional variants in ELOVL6 on SSC8 (12 SNP), and SCD (10 SNP), HIF1AN (5 SNP), PPRC1 (6 SNP) and ELOVL3 (1 SNP) on SSC14 were genotyped in 718 of the same pigs using Agena MassArray. Twenty-one SNP were located in the 5’-UTR or promoter region and 13 SNP were missense substitutions. The most significant associations were found with SNP in the promoter regions of SCD for 18:0, and HIF1AN for 18:1(n-9), the ratio of 18:1 to 18:0, SFAs and MUFAs. Although SCD and HIF1AN are 158kb apart, low LD was observed between SCD and HIF1AN markers. These results indicate that these markers could be used for selection for increased fatty acid saturation to mitigate pork fat quality issues that affect belly slicing yields and bacon quality.