Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Area of Science:

• Comparative genomics
• Animal genetics
• Transcriptomics

Background:

• Global gene expression in the liver transcriptome varies significantly among cattle breeds.
• Understanding these variations is crucial for optimizing cattle breeding programs and improving livestock traits.
• Previous studies have not comprehensively analyzed the liver transcriptome differences across dairy, beef, and dual-purpose cattle breeds.

Purpose of the Study:

• To identify differentially expressed genes (DEGs), metabolic gene networks, and pathways in the bovine liver transcriptome of young bulls from three distinct cattle breeds.
• To compare the liver gene expression profiles of Polish Holstein Friesian (dairy), Hereford (beef), and Polish-Red (dual-purpose) cattle breeds.
• To provide genetic markers for trait-associated studies and genomics selection in cattle breeding.

Main Methods:

• Comparative analysis of bovine liver transcriptome data from Polish Holstein Friesian (n=6), Hereford (n=6), and Polish-Red (n=6) cattle breeds using RNA-sequencing.
• Identification of significant differentially expressed genes (DEGs) (p < 0.01) across pairwise breed comparisons.
• Gene Ontology (GO) analysis and gene network analysis to identify enriched functional groups and metabolic pathways.

Main Results:

• A substantial number of DEGs were identified across all pairwise breed comparisons, with 75 DEGs commonly shared among all three.
• Gene Ontology analysis revealed significant enrichment of functional groups related to amino acid metabolism, lipid synthesis, gluconeogenesis, and signaling pathways.
• Network analysis highlighted key metabolic pathways including glutamine family amino-acid metabolism, triglyceride synthesis, cholesterol biosynthesis, and IGF-receptor signaling, varying by breed comparison.
• Validation using quantitative reverse transcription PCR (RT-qPCR) confirmed the RNA-seq results with high correlation (Pearson's r > 0.90).

Conclusions:

• The study identified a large set of DEGs and associated metabolic pathways in the liver transcriptome of different cattle breeds.
• These DEGs serve as potential genetic markers for trait-associated studies and can be utilized in genomics selection (GS) for cattle breeding programs in Poland.
• The findings provide novel insights into the genetic basis of liver gene expression variation among dairy, beef, and dual-purpose cattle breeds.