Integrating Transcriptome And Whole Genome Resequencing To Target Key Genes And Variations Affecting Swine Fat Deposition

Fat deposition in pigs impact on production efficiency and meat quality. In this study, differential expression genes were detected between Songliao black pigs and Landrace with extreme backfat thickness in adipose tissue(three pairs) and liver (two pairs) using high-throughput sequencing technology. At the same time, genome of each group with extreme phenotypes in each species was pool ed for resequencing, to find genetic variations between the2groups. By integrating transcriptome sequencing and re-sequencing technology and using functional genomics, bioinformatics methods, we analysised differentially expressed genes, gene mutation and their relationship, to screen and identify fat deposition candidate genes and their variations in pigs.The study found that the meat quality were different between Songliao black pigs and Landrace. Fleshcolor has significant differences between Songliao black pigs and Landrace, while the higher intramuscular fat content and lower water loss rate in Songliao black pigs. And between different groups of the same species with extreme backfat thickness, only intramuscular fat content there was a significant difference. Others showed no difference.By transcriptome sequencing, in adipose tissue and liver in Songliao black pigs with extreme backfat thickness,188and91differentially expressed genes were found respectively. In Landrace, adipose tissue and liverwere also found552and72differentially expressed genes. Through biological function analyse, differentially expressed genes were found to involve in fatty acid synthesis, activating lipid metabolism, insulin signaling pathway, PPAR signaling pathway, MAPK signaling pathways and so on. These genes related to fat synthesis, metabolism can be considered a candidate gene affecting fat deposition. Meanwhile, we found large number of differentially expressed genes related to immunity in adipose tissue. The results indicate that adipose tissue is an immune organ, and fat deposition directly affects the role of adipose tissue in immunity.A large number of genetic variations were found in genome re-sequencing, including deletion and insertion SNP. Most of these genetic variants located in intergenic or introns. Missense and frameshift mutations may affect gene expression and function. Genes containing missense and frameshift mutations were functional enrichment analysis. We found that fat synthesis, transport, storage, metabolism pathway contains a lot of genetic variation. A large number of sites were found for the study of fat deposition providing a foundation.Finally, the integration of the results of transcriptome sequencing and re-sequencing of genomes, find the key differentially expressed gene and gene variants. We find a lot of genetic variation in fatty acid synthesis key genes such as FASN, ACACA,ME1and PCK1. Especially missense mutations and UYR mutations in these genes, may affect fat deposition are key mutation. This study found two SNP in ME1and one SNP in PCK1are effect on the fat deposition of pigs significant.In summary, the strong fatty acid synthesis capability in adipose tissue are the key factor of backfat thickness,while the liver and adipose tissue metabolism also plays important roles. A comprehensive understanding of Songliao and Landrace pig adipose tissue and liver in Songliao black pigs and landrace gene expression profiling and genome variation for further studying molecular mechanisms.