Genome-wide Association Study For Fat Deposition Traits And Assessment Of The Positional Candidate Gene IRS4in Pig

Fat deposition is one of the most important trait in pig production and breedingprograms. Subcutaneous fat content, such as backfat depth, mainly infulences carcassquality, Intramuscular fat (IMF) contributes to the tenderness, juiciness and flavour aftercooked. This study aims to localize QTLs for fat deposition traits, and assess the positionalcandidate gene IRS4on SSCX, furter investigate the molecular mechanisms of fatdeposition in pigs.First part of this study, we performed a genome-wide association (GWA) study forabdominal fat weight and chest backfat thickness using the Illumina PorcineSNP60KBeadchip in five swine populations:926F2pigs from a White Duroc×Erhualian intercross,408purebred Sutai pigs(a newly developed line which contains50%Duroc and50%Chinese Taihu breed),317purebred Erhualian pigs,316purebred Laiwu pigs and610commercial DLY trispecific hybrid pigs. And also, we performed a GWAS meta analysisby combining the F2and Sutai pigs both were both slaughered at240days after birth. Themain results are as follows.1、2SNPs on SSC7were identified only in F2pigs, and there were no SNP identifiedassociated with abdominal fat weight trait in other populations.2、Totally identified246SNPs on SSC4, SSC7, SSC13significantly associated withchest backfat thickness in F2pigs. There was only1SNP locate on SSC4and SSC13,respectively.And all of the other SNPs were mapped to34.8Mb region on SSC7.3、3SNPs on SSC8were identified significantly associated with chest backfatthickness in laiwu pigs.4、43SNPs on the chromosomes1,5,6,12,14, X and Y were detected significantlyassociated with chest backfat thickness in commercial pigs. All the SNPs detected onSSCX were mapped around to11.3Mb,40.2Mb and105.3Mb region.5、There was no SNP detected significantly associated with chest backfat thickness inSutai and Erhualian pigs.6、Totally245SNPs on SSC4, SSC7and SSCX were identified significantlyassociated with chest backfat thickness through the GWAS meta analyses. And the resultson SSC4and SSC13showed no different with the F2pigs. Except the SNPs detected onSSC7were mapped around to34.8Mb region, there were58SNPs on SSCX identifiedsignificantly associated with fat deposition traits.Next, the correlations of gene expression profiles with fat deposition were evaluatedusing loin musle samples of586F2intercross pigs, total22,92transcripts were correlatedwith abdominal weight fat and chest backfat thicnkess phenotypes (P <5×10-4),respectively. And7transcripts were correlated with this two phenotypes. Except for1 transcript which is poorly annotated, other transcripts represent the candidate gene MTMR7,AHSP, ALAS2, GSPT2, CPXM2, TM4SF4.Second part of this study, we studied on the candidate gene IRS4on the SSCX. IRS4gene encodes the insulin receptor substrate4, and it is abundantly expressed inhypothalamus. participates in the control of food intake The functions of the IRS4geneindicate that polymorphisms in the gene could explain associated effects, and it may be astrong candidate gene for fat deposition traits in the QTL region. Comparative sequencingrevealed a substitution g.96C<G in the promoter region, a missense variant substitutionc.1294T<C(Phe432Leu) and a synonymous substitution c.1329T<C in the coding sequence.PCR-RFLP genotyping assays for3SNPs were performed in the resource populations,sutai pigs and erhualian pigs. Then, we choose c.1294T>C and c.1329T>C and performedthe association analysis between these genotypes and phenotypes, including BFT at4sites,abdominal fat weight, IMF and loin area. The result showed that missense variantsubstitution c.1294T<C was very significantly associated with all these fat deposition traitsin F2pigs(P <0.01), and only significantly associated with IMF in sutai pigs.Non-significant association showed in erhualian pigs. c.1329T<C was also verysignificantly associated with all these fat deposition traits in F2pigs(P <0.01), and it wasboth very significantly associated with backfat and loin area in sutai pigs, but there was nopolymorphisms in erhualian pigs. After that we performed association analyses of the threehaplotypes T-T, C-C and T-T with the phenotypes. As a result, the haplotypes, T-T and T-C,derived from Erhualian pigs showed a similar effection on phenotypes(P>0.05), but asignificant differences with the T-T derived from Duroc. That indicated the secondSNP(c.1329T>C) share a similar QTL allele associated with the phenotypes. Mean while,we predicted the effect of the Missense variant c.1294T>C on IRS4protein function usingthe online bioimformatic softwares, and the results shown the change of amino acid fromPhe to Leu in IRS4protein was tolerated. A conclusion of this study showed that themissense variant substitution c.1294T<C may not be the causative gene causes fatdeposition on porcine, while the synonymous substitution c.1329T<C was significantlyassociated with fat deposition traits that need to be further studied.