Genome wide association study of fatty acid composition in Duroc swine

Abstract

ObjectiveGenome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork.MethodsA 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.ResultsA 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.ConclusionOverall, 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.

Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig

“…A similar QTL signal was detected on SSC12, where the FASN gene was located, on GWAS performed for the abundance of C14:0 in adipose tissue and muscle in Erhualian and Duroc pigs 21,23 . The signal found on SSC14 for the percentages of C16:0, C16:1(n-7), C18:0, C18:1(n-9), SFAs, and MUFAs was also found on GWAS performed in different pig populations for FA composition in adipose tissue and IMF, which reported SCD and ELOVL3 as candidate genes [19][20][21][22][23][24][25][26] . On a previous study in the BC1_LD animals, the FADS genes were proposed as potential candidate genes for the SSC2 QTL associated with the percentages of C16:1(n-9), C18:2(n-6), C18:3(n-3), and PUFAS in backfat 109 .…”

“…As some of the QTL signals found in our study were previously reported in other GWAS for FA composition in adipose tissue and muscle in several swine populations 16 – 26 , we decided to genotype polymorphisms in the most recurrent candidate genes reported in these studies: FADS2 , FASN , ELOVL6 , ELOVL7 and SCD . A total of 21 SNPs were genotyped among these positional candidate genes.…”

“…These chips allow the genotyping of markers distributed along the pig genome to perform Genome-Wide Association Studies (GWAS) for production traits. Through the use of GWAS, significant Quantitative Trait Loci (QTLs) in the pig genome have been identified for the FA composition in adipose tissue and muscle in several populations of crossed and purebred pigs such as Duroc, Landrace, Large White, and Erhualian [16][17][18][19][20][21][22][23][24][25][26] . In these studies, strong candidate genes related with lipid metabolism have been found for the FA composition in adipose tissue and muscle: ELOVL fatty acid elongases 6 and 7 (ELOVL6 17,18,21,22,24,25 and ELOVL7 16,19,21,22 ), fatty acid synthase (FASN) [21][22][23] , and stearoyl-CoA desaturase (SCD) [19][20][21][22][23][24][25][26] .…”

Enhancing the Nutritional Value of Red Meat through Genetic and Feeding Strategies

“…Inter- and intra-breed differences are well known in terms of total IMF variability, with very obvious cases of genetic groups with higher marbling [ 127 , 128 ], while populations selected for other traits correlated to total fat, such as lean meat yield, have seen a decrease in IMF as a negative side effect [ 129 , 130 , 131 ] Studies show a medium to high heritability not only for total IMF, but also for the majority of fatty acid groups which can be endogenously synthesized in both ruminants and monogastrics [ 132 , 133 ]. According to GWAS studies in different species, both total IMF and fatty acid composition in meat are influenced by key regulatory genes with major effects and multiple genes with smaller effects, and have shown moderate to high heritability estimates for IMF and low to medium heritability for specific fatty acids [ 134 , 135 , 136 , 137 , 138 , 139 ]. However, despite the potential to include IMF fatty acids in breeding programs, antagonistic genetic relationships with performance have usually minimized the emphasis on selection for these traits.…”

Literature review of genes responsible for intramusculat fat content and its methodology in swine

“…The genome-wide association studies (GWAS) make it possible to study over one-hundred thousand individual nucleotides (SNP) (Pearson et al, 2008). As a result of GWAS, several illnesses associated genes, genes associated with economically important properties and genes associated with various metabolic and biological functions have been identified (Viterbo et al, 2018). The fatty acid composition of Duroc swine showed that saturated fatty acids (SFA) and mono-unsaturated fatty acids (MUFA) are highly heritable, according to genetic estimations they are at 0.50-0.57, while polyunsaturated fatty acids (PUFA) are moderately at between 0.25 and 0.46.…”