Characterization of genes for beef marbling based on applying gene coexpression network

Abstract

Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large degree and BC values in the global network. We performed gene expression analysis to detect candidate genes in M. longissimus with divergent marbling phenotype (marbling scores 2 to 7) using qRT-PCR. The results demonstrate that transmembrane protein 60 (TMEM60) and dihydropyrimidine dehydrogenase (DPYD) are associated with increasing marbling fat. We suggest that the network-based approach in livestock may be an important method for analyzing the complex effects of candidate genes associated with complex traits like marbling or tenderness.

Figure 1

Comparison of weighted and unweighted networks associated with marbling score. (a) The scale-free plot for unweighted network (τ = 0.7). (b) The scale-free plot for weighted network (β = 7). Two types of network approximately follow power-law distribution. (c) The scatter plot of clustering coefficient (y-axis) and connectivity (x-axis) in unweighted network. Genes are colored by module membership. (d) The scatter plot of clustering coefficient (y-axis) and connectivity (x-axis) in weighted network.

Figure 2

(a) Hierarchical clustering of marbling score-related genes and visualization of gene modules. The colored bars (below) one directly consistent with the module (color) for the clusters of genes. Distance between genes is shown as height on the y-axis. (b) Multidimensional scaling plot of the weighted network. Genes are represented by a dot and colored by module membership. The distance between each gene is indicated by their topological overlap. This representation explains how the module is related to the rest of the network and how closely two modules are linked.

Figure 3

Analysis results of gene expression data by regression model and PCA. (a) Biplot of the first two principal components. The symbols of L (left) and H (right) represent low- and high-marbled samples in the plot, respectively. (b) Regression analysis between expression level (x-axis) and intramuscular fat content (%, y-axis) for each sample. CEBPa and PPARG were used as indicators of marbling (intramuscular fat).