Document Type : Research Paper
Authors
1 Animal science research institute of Iran (ASRI), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
2 Department of animal science, faculaty of Agriculture, Jiroft university, Jiroft,Iran
Abstract
Milk production is one of the most important economic traits in dairy cattle and plays a crucial role in the profitability of livestock production systems. The aim of the present study was to identify differentially expressed genes associated with milk production between two dairy cattle breeds and to characterize the biological pathways and functional activities involved in this trait. The transcriptomic data used in this study were obtained from the GEO database under accession number GSE54790. Differentially expressed genes (DEGs) were identified using the limma package in R, and the shared DEGs between the two breeds were determined. To investigate protein–protein interactions, the shared genes were analyzed in the STRING database, and network visualization, module detection, and hub gene identification were performed using Cytoscape. Furthermore, functional enrichment and pathway analysis of genes within significant modules were conducted using DAVID. In total, 440 DEGs were identified in Holstein–Friesian cattle and 248 DEGs in Polish Red cattle (p-value<0.05). The results revealed three significant modules, containing the hub genes HP, THBS1, PTX3, and CAV1. The most important pathways and biological processes associated with milk production in these modules included extracellular matrix organization, calcium ion response, tissue development, proteolysis, focal adhesion, and ECM–receptor interaction. The information obtained from the identified hub genes and key biological pathways can be directly applied in breeding programs by supporting the development of genetic markers and improving the accuracy of genomic selection, thereby facilitating the identification of animals with higher milk production potential.
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