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Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle

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Abstract

Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change’s impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.

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Acknowledgements

The authors acknowledge the Director, ICAR-National Dairy Research Institute (NDRI), Karnal, and, Incharge NICRA, ICAR-NDRI for providing the necessary facilities to carry out the research work.

Funding

This research was carried out under a project funded by National Innovations in Climate Resilient Agriculture (NICRA). The author received financial aid under the ICAR-NDRI Institute Fellowship program.

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  1. Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India

    Gaurav Dutta, Rani Alex, Ayushi Singh, Gopal R. Gowane, Vikas Vohra, Sachidanandan De, Archana Verma & Ashutosh Ludri

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  1. Gaurav Dutta
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Contributions

Conceptualization: S.D. and R.A.; Methodology: G.D. and A.V.; Formal analysis and investigation: G.D., A.S. and R.A.; Writing original draft preparation: G.D. and R.A. and: Writing—review and editing: G.R.G. and V.V.; Funding acquisition and resources: A

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Correspondence to Rani Alex.

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The experiment was carried out as per the guidelines and approval of the Institutional Animals Ethics Committee.

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Authors declare no conflict of interest.

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Dutta, G., Alex, R., Singh, A. et al. Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle. Int J Biometeorol (2024). https://doi.org/10.1007/s00484-024-02672-y

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