Abstract
Heat stress significantly disturbs the production, reproduction, and systems biology of dairy cattle. A complex interaction among biological systems helps to combat and overcome heat stress. Indicine cattle breed Tharparkar has been well known for its thermal adaptability. Therefore, present investigation considered RNA-seq technology to explore the functional transcriptomics of Tharparkar cattle with the help of samples collected in spring and summer season. Among differentially expressed genes, about 3280 genes were highly dysregulated, in which 1207 gene were upregulated and 2073 genes were downregulated (|log2fold change|≥ 1 and p ≤ 0.05). Upregulated genes were related to insulin activation, interferons, and potassium ion transport. In contrast, downregulated genes were related to RNA processing, translation, and ubiquitination. Functional annotation revealed that the pathways associated with nervous system (NPFFR1, ROBO3) and metal ion transport (KCNG2, ATP1A2) were highly activated while mRNA processing and translation (EIF4A, EIF4B) and protein processing pathway (VPS4B, PEX13) were highly downregulated. Protein–protein interactions identified hub genes such as ATP13A3, IFNGR2, UBXN7, EIF4A2, SLC12A8 found to play an important role in immune, ubiquitination, translation and transport function. Co-expression network includes LYZ, PNRC1, SQSTM1, EIF4AB and DDX17 genes which are involved in lysosomal activity, tumor inhibition, ubiquitination, and translation initiation. Chemokine signaling pathway associated with immune response was highly upregulated in cluster analysis. The findings of this study provide insights into transcriptome expression and regulation which may better explain complex thermal resilience mechanism of Tharparkar cattle in heat stress under natural conditions.
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Acknowledgements
The authors are thankful to the Director, National Dairy Research Institute (NDRI) for providing necessary infrastructure and facilities for the successful completion of research work. The authors are also thankful to the Incharge, NICRA, ICAR-NDRI, Karnal for allotment of animals and laboratory facilities.
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The authors acknowledge ICAR-National Innovations in Climate Resilient Agriculture, NDRI, Karnal for providing funding for the study.
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Ayushi Singh: conceptualization, methodology, software, data curation, investigation, writing—original draft. Archana Verma: conceptualization, writing—reviewing and editing. Gaurav Dutta: assisting in data analysis. Rani Alex: conceptualization, funding acquisition, project administration, supervision, writing—review and editing. Gopal Gowane: supervision, guidance. Ashutosh Ludri: funding and project coordinator, research facilities.
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Singh, A., Verma, A., Dutta, G. et al. Functional transcriptome analysis revealed major changes in pathways affecting systems biology of Tharparkar cattle under seasonal heat stress. 3 Biotech 14, 177 (2024). https://doi.org/10.1007/s13205-024-04018-2
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DOI: https://doi.org/10.1007/s13205-024-04018-2