Identification of the key genes in Sanhe cattle for health and milk composition traits based on the weighted gene co-expression network analysis

Sanhe cattle are domestically bred dual-purpose (i.e., milk and meat) cattle in northeast China that exhibit exceptional adaptability, resilience, and milk composition traits. Nevertheless, few studies that have analyzed the transcriptome of Sanhe cattle and elucidated the key pathways and genes accountable for its immune and production traits. Weighted gene co-expression network analysis is effective for cattle genetic studies. In this study, with Holstein cattle (n = 82) serving as the dairy breed, we aimed to investigate the manifestations and regulatory pathways of the health and milk composition traits for the Sanhe cattle population (n = 61). We employed principal composition analysis and pathway scoring to compare the distinct characteristics between the 2 cattle breeds using transcriptome, routine blood examination, milk composition, and dairy herd improvement data. We then identified 20 hub genes and potentially crucial pathways that were specifically and significantly correlated with the health and milk composition traits of Sanhe cattle by weighted co-expression network analysis and enrichment analysis. We discovered 56 hub genes that might give rise to commonalities and differences in health and milk composition between Sanhe cattle and Holstein cattle. Finally, we examined the differences in hub gene expression in health and milk composition traits between Sanhe cattle and Holstein cattle using correlation analysis. Overall, this study establishes a foundation for further exploration of the molecular markers related to the health and milk composition traits of Sanhe cattle.