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. 2023 Nov 20;14(11):2105.
doi: 10.3390/genes14112105.

Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle

Zahra Roudbari  1 , Morteza Mokhtari  1 , Abdolvahab Ebrahimpour Gorji  2 , Tomasz Sadkowski  2 , Ayeh Sadat Sadr  3 , Masoud Shirali  4   5
Affiliations

Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle

Zahra Roudbari et al. Genes (Basel). .

Abstract

Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database to understand the biological importance of milk production through gene expression and modules. In this study, we employed CytoNCA and ClusterONE plugins within Cytoscape for network analysis. Moreover, miRWalk software was utilized to detect miRNAs, and DAVID was employed to identify gene ontology and pathways. The results revealed 140 up-regulated genes and 312 down-regulated genes. In addition, we have identified 91 influential genes and 47 miRNAs that are closely associated with milk production. Through our examination of the network connecting these genes, we have found significant involvement in important biological processes such as calcium ion transit across cell membranes, the BMP signaling pathway, and the regulation of MAPK cascade. The conclusive network analysis further reveals that GAPDH, KDR, CSF1, PYGM, RET, PPP2CA, GUSB, and PRKCA are closely linked to key pathways essential for governing milk production. Various mechanisms can control these genes, making them valuable for breeding programs aiming to enhance selection indexes.

Keywords: gene ontology; miRNA identification; milk production; network analysis.

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Conflict of interest statement

The authors have not reported any potential conflicts of interest.

Figures

Figure 1
Figure 1
Protein–protein Interaction (PPI) network of genes that exhibit differential expression and are closely associated with milk production. The size of each node is drawn in proportion to its degree value, with greater dimensions indicating higher degrees. Furthermore, the color of each node is indicative of gene expression, with up-regulated genes shaded blue and downregulated genes shaded red.
Figure 2
Figure 2
Interaction among hub genes and identified miRNAs. Green diamond shape is shown for miRNA; blue and red circles are shown for up- and down-regulated genes, respectively.
Figure 3
Figure 3
The interrelation among hub genes and their connection with factors associated with milk production, including tissue, organ, cell, and biological process.
Figure 4
Figure 4
Relevance network of all identified DEGs, miRNAs, and biological processes.
See this image and copyright information in PMC

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