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Research Article: Bioinformatics analysis of key genes and biological pathways in rainbow trout (Oncorhynchus mykiss) affected by proliferative kidney disease (PKD)
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R. Pasandideh *1   , M. Pasandideh2 |
1- Shrimp Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran , Rezapasandideh63@gmail.com
2- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran |
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Abstract: (16 Views) |
| Proliferative kidney disease (PKD), caused by Tetracapsuloides bryosalmonae, is a major challenge in rainbow trout (Oncorhynchus mykiss) aquaculture. To better understand the host response at the molecular level, eight microarray datasets from erythrocytes of healthy and infected fish (GSE198859) were analyzed to identify differentially expressed genes (DEGs) using the GEO2R tool. The results revealed that upregulated genes such as SNRPE, miR-301b, TNFRSF10B, Bckdha, and Aqp1 are associated with RNA processing, post-transcriptional regulation, osmoregulation, energy metabolism, and apoptosis, highlighting their essential roles in compensatory responses to kidney damage. Conversely, downregulated genes including Degs1, Flt1, BATF3, and RALY suggested suppression of angiogenesis, inhibition of dendritic cell responses, disruption of immune signaling, and impairment of lipid metabolism and RNA processing, which may represent part of the parasite’s strategy to evade host immunity. GO analysis showed significant enrichment in cellular components such as the nucleus, nucleosome, plasma membrane, exosomes, and extracellular regions. In parallel, molecular functions related to kinase activity and protein binding emphasized the importance of signaling and intercellular communication during infection. Overall, these findings suggest that the rainbow trout response to PKD involves a combination of activated defense pathways and simultaneous suppression of some critical immune components by the parasite, which contributes to its survival. The identified genes and pathways may serve as potential molecular markers and support future efforts in selective breeding to improve resistance against PKD. |
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| Keywords: Differentially expressed genes (DEGs), Gene network analysis, Microarray, Proliferative kidney disease (PKD), Rainbow trout (Oncorhynchus mykiss) |
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Full-Text [PDF 889 kb]
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Type of Study: Orginal research papers |
Subject:
Genetics
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