Mapping And Fine-mapping QTL Affecting Longissimus Muscle Fatty Acid Composition In Large Scale Multiple Pig Populations

Fatty acid composition in muscle has profound influences on nutrition,taste and process of pork.In our previous study,we performed genome-wide association study（GWAS）between 60K SNP genotypes and fatty acid composition in longissimus dorsi muscle samples from a White Duroc×Erhualian F₂ intercross（hereafter referred to as F₂,n=591）and Sutai pigs（n=282）.Two quantitative trait loci（QLT）with major effect on C18:0 and C20:0 were mapped on pig chromosome（SSC）14 and 16,and the most likely candidate genes of these two loci were SCD and ELOVL7,respectively.We also conducted GWAS for 33 fatty acid metabolic traits in F₂,Sutai,Duroc×（Landrace×Yorkshire）（DLY）,Erhualian and Laiwu populations,and proposed a list of candidate genes at the identified loci,including three novel genes（FADS2,SREBF1 and PLA2G7）which have important role in fatty acid metabolism.To identify new loci and refine known loci influencing fatty acid composition traits,we herein carried out the following studies:1)We performed GWAS for fatty acid contents in longissimus dorsi muscle of 1244 pigs from DLY,Erhualian and Laiwu populations by using Illunima porcine 60K Beadchips.2)To refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs,we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian（n=331）and Bamaxiang（n=315）pigs based on a customized 1.4 million SNP array.3)To further fine-mapping the fatty acid composition traits-related loci,we performed GWAS using imputed whole-genome sequence data followed by meta-analysis,haplotype-sharing and Bayesian fine-mapping analysis in 2248 pigs from F₂,Sutai,DLY,Laiwu,Erhualian and Bamaxiang populations.4)Lead SNPs for fatty acid traits were annotated using VEP and publicly available ChIP-Seq data downloaded from Villar et al.5)To confirm expression of the prime candidate genes,RNA-Seq data from nine tissues of three pigs were analyzed.6)To investigate the genes and gene networks associated with fatty acid composition traits in pigs,we evaluated correlations between liver and muscle transcriptomes and fatty acid composition traits in muscle and abdominal fat tissues in 335 F₂ pigs.Based on the above analysis,we obtained the following novel results:1)We detected genome-wide significant novel loci proximal to FASN for C14:0 and C16:0 on SSC12 in Laiwu and Erhualian for the first time.We further refined the locus to credible intervals of330 Kb with 1.4M SNP arrays and imputed whole-genome sequence data.The lead SNP for C14:0 was only approximately 140 Kb to FASN,and further analysis found that selection against C14:0 and C16:0 using this lead SNP will not adversely affect carcass or fat deposition traits in Erhualian pigs.2)Applying haplotype-sharing and Bayesian fine-mapping approach,we fine mapped the locus for C18:1n-9/C16:1n7 on SSC8 and the locus for C18:0 on SSC14 to credible intervals of 210 and 130 Kb,respectively.3)We proposed a list of candidate genes at the novel loci,including ABCD2,ACSBG1,ELOVL5,HPGDS,DAGT2,ACAD10,ACSL1,PLIN5,APOM,SNCA,ACAA1 genes with function relevant to metabolism of fatty acids.4)The majority of the identified loci located in non-coding region,suggesting most of the QTL were regulatory.5)RNA-Seq data showed that candidate genes associated with saturated and monounsaturated fatty acids,such as ELOVL6,FASN and SCD were specifically expressed in fat tissues,while candidate genes affecting polyunsaturated fatty acids like FADS2 and FADS1 were highly expressed in hypothalamus and also showed moderate expression in other tissues.6)Quantitative trait transcripts and gene co-expression network analysis identified gene and gene network to fatty acid unsaturation index that were enriched in platelet activation and the type I interferon signaling pathway and highlighted the connections between variations in fatty acid composition and genes involved in hematological and immune system.In this study,we integrated phenotype,genotype and gene expression data from multiple populations,and used a series of genetic analyses like QTL mapping,fine-mapping and gene network analysis,we largely narrowed down the QTL intervals near FASN,ELOVL6 and SCD and enriched our understanding of the candidate genes expression pattern in multiple tissues.These results provide an important reference for the design of breeding tool to improve the fatty acid profile of pork.