Transcriptomic insights into heat tolerance in Vechur cattle: RNA-Seq profiling, gene ontology and pathway analysis
Cattle farming, a cornerstone of global agriculture, delivers critical resources such as milk, meat and labor, which are indispensable for human sustenance and economic activity. Despite its importance, the productivity and health of cattle are significantly influenced by environmental conditions, particularly in regions characterised by extreme climates. Wayand, a tropical highland district in northern Kerala, India, exemplifies such challenging environment with its regular hot and partially dry summer season. This climate imposes substantial stress on livestock, making the identification and breeding of heat-tolerant cattle imperative. Such efforts are crucial not only for maintaining and enhancing livestock production but also for ensuring the overall welfare of the animals in these demanding conditions.Within the spectrum of Indigenous cattle breeds, Vechur cattle, the only cattle breed from Kerala, are distinguished by their adaptability to local environmental conditions, including notable heat tolerance. Conversely, crossbred cattle, which often result from decades of crossbreeding of indigenous and exotic breeds, may not exhibit the same degree of resilience to heat. Elucidating the genetic, physiological, and biochemical mechanisms underpinning heat tolerance can yield invaluable insights for the formulation of breeding programs aimed at cultivating heat-resilient livestock.The negative effects of heat stress on cattle, including decreased feed intake, lower milk production, impaired reproductive performance and increased susceptibility to diseases, can result in substantial economic losses for farmers and the wider agricultural sector. Overall, the economic burden of heat stress encompasses both reduced output and increased costs. Therefore, enhancing heat tolerance in cattle is a crucial goal for improving productivity and animal welfare in areas frequently subjected to high temperatures.RNA sequencing (RNA-Seq), a formidable tool for analysing gene expression profiles, not only provides a high-resolution perspective on gene activity but also helps in identifying candidate genes implicated in heat tolerance. One of the key advantages of whole blood RNA-Seq is its ability to capture a holistic picture of systemic responses to heat stress. Unlike tissue-specific RNA-Seq, which focuses on individual organs or tissues, whole-blood RNA-Seq provides insights into the coordinated responses of various cell types throughout the body. This comprehensive perspective is crucial for understanding how different physiological systems, such as immune function, metabolism, and stress response mechanisms, interact and adapt to heat stress conditions in cattle. By sequencing cDNA derived from total RNA, the RNA-Seq facilitates the detection of both well-characterised and novel transcripts, including alternative splicing variants and non-coding RNAs. Its broader dynamic range enhances its sensitivity to low-abundance transcripts and improves accuracy in measuring gene expression levels. Furthermore, it can identify differential gene expression, detect gene fusions and reveal mutations within transcripts. This capability to provide a comprehensive analysis of the entire transcriptome with exceptional throughput and precision makes RNA-seq an exceptionally powerful tool for in-depth understanding of gene expression and regulation.The identification of candidate genes for heat tolerance holds the potential to facilitate the development of genetic markers that can be employed in breeding programs to select for heat-tolerant individuals, thereby significantly enhancing the productivity and welfare of cattle in tropical regions and contributing to the sustainability of livestock farming in Kerala.