Identification of key genes affecting porcine fat deposition based on co-expression network analysis of weighted genes

Journal of Animal Science and Biotechnology

Kai Xing¹  Chuduan Wang²  Huatao Liu²  Fengxia Zhang²  Yibing Liu²  Xiangdong Ding²  Yong Shi² 

[1] Animal Science and Technology College, Beijing University of Agriculture, Beijing, China;Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China;

关键词: Fat deposition;    Pigs;    RNA-seq;    WGCNA;   

DOI  :  10.1186/s40104-021-00616-9

来源: Springer

【 摘 要 】

BackgroundFat deposition is an important economic consideration in pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers’ choice of pork. Weighted gene co-expression network analysis (WGCNA) is effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low) and to identify the core genes in each of these modules.ResultsWe used RNA sequences generated in different pig tissues to construct a gene expression matrix consisting of 12,862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA and the number of genes in these modules ranged from 39 to 3,363. Four co-expression modules were significantly correlated with backfat thickness. A total of 16 genes (RAD9A, IGF2R, SCAP, TCAP, SMYD1, PFKM, DGAT1, GPS2, IGF1, MAPK8, FABP, FABP5, LEPR, UCP3, APOF, and FASN) were associated with fat deposition.ConclusionsRAD9A, TCAP, SMYD1, PFKM, GPS2, and APOF were the key genes in the four modules based on the degree of gene connectivity. Combining these results with those from differential gene analysis, SMYD1 and PFKM were proposed as strong candidate genes for body size traits. This study explored the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms underlying porcine fat deposition.

【 授权许可】

CC BY