Identification of Key Gene Co-expression Modules and Genes Associated with Pork Quality Based on WGCNA Method

PurposeTo explore and identify the key gene co-expression modules and genes associated with meat quality trait in pigs.

MethodsThe key gene co-expression modules and genes were investigated using gene expression data GSE119368 of longissimus dorsi muscles including eight Dapulian and eight Landrace pigs from NCBI GEO database by weighted gene co-expression network analysis (WGCNA), gene interaction network and centrality methods. Some key genes associated with pork quality trait were identified by qPCR on three Saba and three Large White pigs.

ResultsTwo gene co-expression modules including the blue and the red modules related to pork quality trait were identified, which the r values were 0.89 (P=5E−6) and 0.91 (P=7E−7), respectively. The genes in the blue module were mainly associated with transition between fast and slow fiber and extracellular matrix and so on. Among the identified genes, 10 genes were identified as the key genes associated with pork quality, including COL3A1, COL5A1, COL1A2, COL14A1, CRTAP, COL5A3, LEPREL1, DEPTOR, COL4A2 and COL6A2. The genes in the red module were mainly related to skeletal muscle and fat cell differentiation. Among these genes, 11 genes were identified as the key genes associated with pork quality, including FBXL4, RNF115, FBXO40, ASB4, ASB15, UBE2L6, RNF41, ASB5, HERC5, SOCS1 and ASB11. The expression levels of the top three genes in the blue module had extremely significant differences in longissimus dorsi muscles between Saba and Large white pig breeds (P<0.01), while the top three genes in the red module had no significant differences (P>0.05).

ConclusionThe results preliminarily identified the co-expression modules and key genes of meat quality between different types of pig breeds, but the key genes associated with meat quality trait and their effects between the pig breeds with the same meat type may be significantly different.