Identification Of Gene Expression Patterns Affecting Porcine Fat Depositionusing GEO Public Database

Intramuscular fat(IMF)and subcutaneous fat are two important pork traits.IMF content affects p H,meat color,tenderness,odor and other related pork quality traits,while subcutaneous fat is also associated with pork quality traits and economic value.As we all know,the indigenous pig breeds in China have stronger fat deposition ability than thatin foreign pig breeds,and the meat quality ofindigenous pig breeds is also good and favored by consumers.In addition,fat deposition is regulated by multiple genes,signaling pathways,and Lnc RNAs.Therefore,we could provide a theoretical basis for pig breeding by studying the molecular mechanism of fat deposition in different pig breeds.The GEO database is the world's largest public database and freely accessible to researchers worldwide.Data mining the microarray and RNA-seq data related to pigs in the GEO database will facilitate the elucidation of the molecular mechanisms for fat deposition in different pig breeds.In this study,by analyzing the longissimus dorsi muscle(LD)GEO data of Large White and indigenous pig breeds in China,we screened three signaling pathways related to porcine IMF deposition,including AMPK,PPAR and fatty acid metabolism signaling pathways.q RT-PCR microarray results revealed that in the LD of Large White,the expression levels of fatty acid oxidation-related genes were up-regulated in the AMPK signaling pathway.The expression levels of genes related to fatty acid oxidation and transport in the PPAR signaling pathway were up-regulated.The expression levels of fatty acid metabolism and oxidation-related genes were up-regulated in fatty acid metabolic pathway.Moreover,the genes involved in fatty acid synthesis were down-regulated.These results indicate that the AMPK,PPAR and fatty acid metabolic pathways play important roles in reducing INF content in the LD of Large White pigs.At the same time,we also detected the expression of AMPK,LKB1,Ca MKK2,CPT1 A and ACC1 by western blot.The results showed that the expression trends of these proteins were consistent with the corresponding gene expression patterns in LD muscle of Large White pigs.In our study,by analyzing the GEO data of subcutaneous adipose tissue of Large White and local pig breeds in China,we found that the ribosomes,metabolic pathways,and oxidative phosphorylation pathways were related to the depositon of subcutaneous adipose tissue.The expression levels of three pathway-related genes were quantified by q RT-PCR array.We found that 11 genes of the ribosomal pathway in subcutaneous adipose tissueof Large White were up-regulated.The expression levels of five genes in the metabolic pathway were up-regulated,and four genes in the oxidative phosphorylation pathway were up-regulated.These results suggested that these three signaling pathways were involved in the regulation of subcutaneous fat deposition in Large White pigs.In the present study,Lnc RNAs associated with fat deposition were identified by data minging the RNA-seq data in GEO database.One Lnc RNA(NONSUST005598.1)associated with IMF deposition was identified in the LD muscle.Three Lnc RNAs(NONSUST011681.1,NONSUST018163.1 and NONSUST011273.1)associated with subcutaneous fat deposition were identified in the subcutaneous adipose tissue.In summary,the object of this study was to investigate the genes,signaling pathways and Lnc RNAs that affect pig fat deposition in different pig breeds.It will provide more theoretical basis for pig breeding in the future.