Dissection Of Genetic Architecture Of Fatty Acid Composition In Pork

Fatty acid composition is an important phenptypic trait in pigs as it affects meat nutrition,quality and tasting flavor.In this study,a series of genetic analyses were conducted to investigate the genetic architecture of porcine fatty acid composition.First,we reported a genome-wide association study?GWAS?for fatty acid composition in the longissimus dorsi muscle and abodominal fat tissues of 598 White Duroc×Erhualian F₂animals?F₂?and in muscle samples of 282 Chinese Sutai pigs.A total of 46 loci surpassing the suggestive significance level were identitied on 15 pig chromosomes?SSC?for 12major fatty acids.Of the 46 loci,15 on SSC5,7,14,and 16 reached the genome-wide significane level.The longissimus dorsi muscle and abdominal fat showed consistent association profiles at most of the identified loci and distinct association signals at several loci.All loci have specific effects on fatty acid composition,except for two loci on SSC4and SSC7 affecting multiple fatness traits.Several promising candidate genes were found in the neighboring regions of the lead SNPs at the genome-wide significant loci,such as SCD for C18:0 and C16:1 on SSC14 and ELOVL7 for C20:0 on SSC16.The findings provide insights into the molecular basis of fatty acid composition in pigs,and would benefit the final identification of the underlying mutations.To investigate the genetic mechanism of fatty acid metabolic traits in pork,we then conducted GWAS for 33 fatty acid metabolic traits in F₂,Sutai,Duroc×?Landrace×Yorkshire??DLY?,Erhualian and Laiwu populations.We identified a total of 865 single nucleotide polymorphisms?SNPs?,corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes.Our findings not only confirmed seven previously reported QTL with stronger association strength,but also revealed four novel population-specific loci,showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes.We proposed a list of candidate genes at the identified loci,including three novel genes?FADS2,SREBF1 and PLA2G7?.Further,we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway.These findings advance our understanding of the genetic basis of fatty acid composition in pigs.The results from European hybrid commercial pigs can be transited into breeding practice to benefit the fatty acid composition in the related pig populations.To further characterize the non-addition effects on porcine fatty acid composition,we performed a two-dimensional genome scan for the epistatic loci for fatty acid composition in the longissimus dorsi muscle in the F₂ and DLY populations.A total of 66 and 583significant(P value<1×10^-10)interactive SNP pairs were detected in the F₂ and DLY populations,respectively.Both top epistatic loci in the two populations have not been detected in our previously GWAS under an additive model.We highlighted three candidate genes including FABP5,ACADL,and DGAT2 for the most significant epistatic loci.Our results illustrate that epistasis is an important non-additive genetic factor underlying phenotypic variation in fatty acid composition in pork.To identify the responsible gene and causative mutation?s??QTNs?underlying the major QTL for C18:0,C18:1,C16:0 and C16:1 contents in longissimus dorsi samples on SSC14,we explored a series of genetic assays and defined this major QTL into a region of430 kb.By resequencing the positional candidate gene SCD,we found that two variants in the promoter region and one variant in the 3'UTR were significantly associated with the contents of these four fatty acids.Further analysis in Sutai and DLY pigs indicated that the two variants in the promoter region were in high linkage disequilibrium with the QTN.We identified 105 candidate QTNs by conducting a concordance analysis of genotypes of all variants in the 430 kb region with QTL genotypes.These variants warrants further investigations in a large sample of DLY or Duroc-derived pigs to characterize the QTNs together with functional validation assays.The phylogenetic tree analysis of the haplotypes in the 430 kb region supports that the QTN underlying the major QTL on SSC14 exists exclusively in Duroc and Duroc-derived pigs.The results provide critical steps towards the identification of the QTN at the SSC14 locus,and the candidate QTNs in the SCD gene provide important molecular markers to optimize fatty acid composition in pork.