Physiochemical and transcriptomics of exotic holstein friesian cattle in Pakistani subtropics

The Holstein Friesian (HF) cows are raised in diverse agroecological zones of Pakistan, where they face diverse agro-climatic effects, which consequently affect their productive and reproductive potential. This environmental stress impacts gene expression and influences molecular pathways, which needs exploration. Therefore, the current study was performed to evaluate environmental effects on biochemical, antioxidant, and genetic effects in HF dairy cows managed in three different agroecological zones of Pakistan. Biochemical parameters and antioxidant enzymes were analyzed through ELISA kits. Deep RNA Sequencing was performed to explore DGE, GO terms, and their KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. The mRNA expression was quantified through qRT-PCR. Different agroecological zones significantly (p < 005) affected biochemical stress markers (SOD, GPX, cortisol, glucose) and heat shock protein 70 (HSP70) in HF cows during early and late summer. The highest SOD levels were found in early and late summer, and the highest GPX level was found in late summer (p < 0.05) in the Abbottabad zone. Additionally, the lowest cortisol levels in early and late summer were found in Abbottabad, and the highest in Okara (p < 0.05). The HSP70 level exhibited a significant (p < 0.05) increase in Okara in the early and late summer. In total, 265 DEGs were explored, of which 76 were downregulated and 189 were upregulated. The top GO terms of DEGs were positive regulations of biological processes, axons and protein binding, cytokine-mediated signalling, acyltransferase activity, and lipid binding. The important KEGG pathways regulated by the DEGs are linoleic acid metabolism, alpha-linoleic acid metabolism, cell cycle, aminoacyl-tRNA biosynthesis, TNF signalling pathway, citrate cycle (TCA cycle), and apoptosis. The relative mRNA levels of the HSP90 AB1, CD19, CYBB, HSPAB, IL2RG, LYN, MAPK7, MSN, and PRDX2 were significantly (p < 0.05) enriched in the Abbottabad zone as compared with the Okara and Quetta zones. These findings will deepen our understanding regarding the molecular adaptation of Holstein Friesian cows to their particular ecological contexts and their adaption to Pakistan's tropical climate.