Genome-wide association study of intramuscular fat content in a Duroc-Landrace-Yorkshire pig population

【Objective】Genome-wide association analysis was performed to locate SNP loci and their important candidate genes affecting intramuscular fat content in a Duroc-Landrace-Yorkshire pig population,thus providing a scientific basis for the improvement of intramuscular fat content in pigs by molecular biology.【Method】981 Duroc-Landrace-Yorkshire pigs were selected for the experiment,including 447 castrated boars and 534 sows. All pigs were reared under uniform conditions until 150 days of age and then slaughtered for determination of intramuscular fat content after slaughter using the Soxhlet leaching method. GeneSeek GGP 50 K was used for genotyping and the FarmCPU model of the rMVP software package was used to analyze the whole genome association of intramuscular fat content traits.【Result】The average intramuscular fat content of Duroc-Landrace-Yorkshire pig was 2.27%,with a coefficient of variation of 34.24%. Its genomic heritability(h²)was 0.39,which belonged to medium heritability trait,indicating that this trait has more room for genetic improvement. After quality control,the remaining 30600 SNPs were used for genome-wide association analysis and 8 potential SNP loci were found to be associated with intramuscular fat content and distributed on chromosomes 2,3,5,11,12,13 and 14. The GO function annotation analysis on candidate genes that may affect intramuscular fat content was conducted using the Gene Ontology database. It was found that these candidate genes were involved in the metabolic pathways of muscle development,organ growth and metabolism,gene expression regulation and RNA transcription,but mainly in muscle growth and development,indicating that there was a close relationship between intramuscular fat content and muscle growth and development.【Conclusion】Based on genome-wide association analysis that is conducted with high density chips,8 SNPs loci are found related to intramuscular fat content. According to the gene biological function and related research literature,it is further speculated that C2orf74,HS6ST3 and ROBO2 genes,mainly participating in cell proliferation and differentiation,fat metabolism and biological processes,can be used as important candidate genes affecting intramuscular fat content,which provides a reference basis for the breeding and improvement of pork quality traits.