Functional transcriptome analysis revealed major changes in pathways affecting systems biology of Tharparkar cattle under seasonal heat stress

• Published in: 3 Biotech 2024-07, Vol.14 (7), p.177-177, Article 177
• Main Authors: Singh, Ayushi, Verma, Archana, Dutta, Gaurav, Gowane, Gopal R., Ludri, Ashutosh, Alex, Rani
• Format: Article
• Language: English
• Subjects: Adaptability; Agriculture; Annotations; Bioinformatics; Biology; Biomaterials; Biotechnology; Cancer Research; Cattle; Chemistry; Chemistry and Materials Science; Chemokines; Cluster analysis; dairy cattle; Down-regulation; gene expression regulation; Genes; Heat stress; Immune response; Immune system; insulin; Ion transport; Metal ions; mRNA processing; neoplasms; Nervous system; Original Article; potassium; Protein interaction; Proteins; reproduction; Ribonucleic acid; RNA; RNA processing; sequence analysis; Signal transduction; spring; Stem Cells; summer; Temperature effects; transcriptome; Transcriptomes; Transcriptomics; Translation initiation; Ubiquitination; zebu breeds
• ISSN: 2190-572X; 2190-5738; 2190-5738
• DOI: 10.1007/s13205-024-04018-2

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.