Genome-wide Association Studies For Intramuscular Fat Content In Swine

The intramuscular fat content(IMF)is one of the most important meat quality of pork which is controlled by multiple genes and it has a very strong impact on pig industry.We can improve it through molecular breeding.in the past 20 years,gene mapping about pork meat quality have made significant progress and so many candidate genes correlating with intramuscular fat content have been found out by family-based linkage analysis.But researchers in this area is very few based on Chinese indigenous pig.The rapid development of Next Generation Sequencing(NGS)made it possible to apply Genome-Wide Association Study(GWAS)with single nucleotide polymorphism(SNP).A total of 601 F2 offsprings from a porcine Large White?Minzhu? intercross resource population were used as the experimental animals.High-throughput sequencing technology was used to implement whole genome resequencing.GWAS analysis on the intramuscular fat content was applied by mixed model method.The results are as follows:(1)The result of descriptive statistical analysis of 601 pigs IMF data according with the character of resource family segregating population.We used Sus scrofa build 10.2 as reference to apply pre-analysis.As a result,we got about 26M SNP?(2)Whole-genome single nucleotide polymorphism(SNPs)was used as genetic maker to conducted linkage disequilibrium(LD)analysis.The LD decay rate was measured as the chromosomal distance at which the average pairwise correlation coefficient(r2)dropped to half its maximum value and it is 20Kb.(3)After conducting the GWAS analysis and function annotation according to the database of Ensembl,GeneCards,NCBI,we got 6833 SNPs associated with intramuscular fat content.The range of QTL in the chromesome 3 and 6 is 131Kb and 10M,respectively.The genes MYH1 MYH2,MYH3,MYH4,MYOCD,MED31 are involved in muscle contraction and lipid metabolism.The motifs PU.1,EBF1,USF1 contain significant SNPs associated with IMF and their functions relate to adipocyte differentiation and lipid metabolism(4)The SNPs on the chromesome 12 with peak significant value of p(p<le-32)were used to detect haplotype block.Then haplotype association analysis was apply to the result of haplotype block and IMF phenotype use the haplo.stats package under R statistics environment.The result indicates that two haplotypes in the block 1 and two haplotypes in the block 2 were all significantly associated with IMF.The block2 contains MYH1,MYH2,MYH3,MYH4,which were involved in muscle contraction for 468Kb.In conclusion,the MYH gene family and the MYOCD,MED31,motifs PU.1.EBF1 USF1 were selected as candidate genes for IMF.