Seasonal regulation of mRNAs and lncRNAs under cold exposure favours metabolic and immune-related pathways in Sahiwal Cattle

Seasonal fluctuations in environmental conditions impose physiological challenges on livestock, necessitating adaptive molecular responses. While heat-stress biology in cattle is well studied, responses to cold exposure remain largely unexplored in indigenous Indian breeds such as Sahiwal, one of the country’s best milch cattle. To investigate seasonal adaptation mechanisms, we conducted transcriptome profiling of peripheral blood mononuclear cells (PBMCs) collected from Sahiwal cattle during winter and spring. RNA-Seq analysis identified 7,659 differentially expressed mRNAs (DE-mRNAs; 1,332 upregulated and 6,327 downregulated) and 2,369 differentially expressed long non-coding RNAs (DE-lncRNAs; 106 upregulated and 2,263 downregulated), using thresholds of |log₂(fold change)| > 2 and false discovery rate < 0.05. Functional enrichment analysis of DE-mRNAs and cis-mRNAs of DE-lncRNAs using Gene Ontology, KEGG, Reactome pathways, and STRING networks showed that genes involved in cellular metabolism, immune responses, translation, and oxidative stress, such as MYC , CD4 , PTPRC , MTSS1 , CYBB , TLR10 , THAP12 , AIFM1 , COX6A2 , and SOD1 , were upregulated during cold exposure. Conversely, genes associated with cell proliferation, response to external stimuli, tissue development, and angiogenesis, including IGF1 , BDNF , SRC , YES1 , CTTN , G0S2 , CDK15 , CCNA1 , TLCD1 , and BCL2L1 , were downregulated. These patterns suggest an energy trade-off favouring thermoregulation and immune function over tissue development in winter. This study provides new molecular insights into seasonal physiological trade-offs in Sahiwal cattle, highlighting adaptive gene-expression changes that support cold resilience. The findings enhance our understanding of environmental adaptability in indigenous breeds and may aid in breeding climate-resilient livestock.