Browsing by Author "AYUSHI SINGH"
Now showing 1 - 1 of 1
Results Per Page
Sort Options
ThesisItem Open Access COMPARATIVE TRANSCRIPTOME PROFILING OF THARPARKAR CATTLE IN THERMO-NEUTRAL AND HEAT STRESS CONDITIONS(ICAR-NDRI, KARNAL, 2022) AYUSHI SINGH; ARCHANA VERMAThere is a major shift in understanding of functional role of gene expression as an additional crucial layer to the understanding of thermo-adaptation. Vis-à-vis climate change, there is an urgent need to explore the more climate-resilient cattle population and decipher the seasonal transcriptomics behind it, an area that still remains relatively novel in bovine genomics. Tharparkar cattle represent the arid and semi-arid ecotypes of India. In the present investigation, Tharparkar cattle were sampled in thermo-neutral (n=2) and heat stress (n=3) conditions. Physiological and haematological parameters were found to be elevated in consonance with heat stress. Peripheral blood mononuclear cells (PBMCs) and RNA were isolated, followed by library construction and testing. Using fastp, a total of 66.65 and 94.62 percent reads were retained in spring and summer samples, respectively. Using HISAT2, the overall alignment rates of quality reads were 77.63 % in spring and 85.85 % in summer samples. The transcript quantification was performed with featureCounts. A total of 3,280 genes were found to be differentially expressed, significantly using DESeq2. Out of them, 1,207 genes were up-regulated and 2,073 genes were down-regulated in heat stress conditions, as compared to thermo-neutral conditions. The tofp up-regulated genes such as, KCNG2, DNAJB8 were related to transport and heat stress. The top down-regulated genes such as, UBB, EEF1A1 were related to ubiquitination and eukaryotic initiation factor. To generate a link between genome and phenome, ShinyGO v.0.76, iDEP v.951, gProfiler and STRING network software were used. GO terms (Biological process) identified in differentially expressed genes were found to be upregulated for axon guidance and down-regulated for mRNA processing. The KEGG pathways such as, mineral absorption pathway and Spliceosome pathway were found to be up- and down- regulated, respectively. The Reactome pathway was significantly downregulated for L13 a-mediated translational silencing of Ceruloplasmin expression and Nonsense mediated decay (NMD) independent of exon junction complex. The gene set enrichment analysis (GSEA) and gProfiler also revealed the results on the same line. The co-expression network analysis revealed genes such as, RPS17, RACK1, LYZ, SQSTM1. The protein-protein interactions using STRING database revealed genes such as, EIF4A2, UBXN7, ATP13A3. The potential candidate genes NPFRR1, KCNG2, EIF4A2 can be further explored in relation to heat stress. This study has provided a catalogue of differentially expressed genes which are likely to play a significant role in coping up with heat stress. The results from the current study can be used to prioritize SNPs in TWAS to identify the SNPs involved in adaptational traits of cattle.