Identification of lipid deposition related genes in Tibetan pigs based on whole genome re-sequencing

【Objective】Exploring the genetic differences between Tibetan pigs（TIB）and Large white pigs（LW）at the whole-genome level，and identifying genes related to lipid deposition in TIB，to provide informative insights into the genetic utilization of its high meat quality traits.【Method】Whole genome re-sequencing data of 5 Yunnan Diqing TIB and whole-genome re-sequencing data of 34 TIB from Tibet，Sichuan and Gansu，and 14 LW with low fat characteristics in NCBI database were selected，which were totally 53 whole genome re-sequencing data for followed analysis.Whole genome SNPs were obtained and selection sweep analysis was performed using VCFtools. Allele frequencies for candidate SNPs in TIB and LW populations were calculated using VCFtools，and candidate SNPs were annotated using in house Pythonscript and all annotation files. Then，DAVID was used for GO functional annotation and KEGG pathway enrichment analysis to further identify genes related to lipid deposition.【Result】 By mapping whole genome sequence to reference genome，19374832 high quality SNPs were obtained. The selection region contained 370778 candidate SNPs，among which 152877 SNPs met the condition of allele frequency>0.5 in TIB and <0.5 in LW and were annotated into 1486 genes. The GO analysis showed that 1486 candidate genes were enriched into 17 GO functional clusters（Cluster 1-Cluster 17）， among which Cluster 11 and Cluster 12 were related to lipid synthesis. The two clusters included genes involved in lipid droplet transport，binding processes（NME4，C4BPA，AP2M1，CD36，FABP5，PMP2，PDZD8，OSBPL6， APOD and OSBPL1A），fatty acid synthesis，elongation，and metabolism（TECR，ELOVL7，and HACD2），as well as extracellular matrix genes （CCN3，EGFL6，KAZALD1，ASPN，ADAMTS18，ECM2，COL18A1，COL3A1 and COL4A5）. In addition， by surveying literature，eight genes（APOOL，PLAG1，PLAUR，SUCLG2，CPE，AKR1B1， SLC4A4 and CHPT1）were found to have differential expression in subcutaneous adipose tissue or muscle tissue between TIB and LW，and related to lipid formation.【Conclusion】This study reveals that the difference in lipid deposition between TIB and LW involves multiple processes and genes related to lipid formation，extracellular matrix genes might also involved in fat depostition of TIB， and these genes have a relatively high allele frequencies in TIB.