Integrative population genomics and tissue-specific expression profiling in cattle using whole-genome sequence...

Area of Science:

• Genomics
• Immunology
• Livestock Science

Background:

• Large-scale genomic data facilitates the study of genetic variation and immune gene expression in livestock.
• The NF-κB signaling pathway is crucial for immune responses.

Purpose of the Study:

• To characterize genomic differentiation and gene expression patterns of NF-κB pathway genes in cattle.
• To integrate population genomics with tissue-specific transcriptomics.

Main Methods:

• Whole-genome sequence data from the 1000 Bull Genomes Project was analyzed.
• Transcriptional profiling of NF-κB pathway genes was performed across four tissues in cattle.
• Histological assessment of spleen and in silico structural annotation were utilized.

Main Results:

• Prioritized differentiated variants in NF-κB pathway genes (CD14, NF-κB1, IL-1β, BAFFR) were identified.
• Significant tissue-dependent regulation of gene expression was observed, with distinct organ-specific patterns.
• CD14 expression was higher in liver, while intestinal tissues showed lower innate immune gene expression.

Conclusions:

• Population-level genomic differentiation in cattle's NF-κB pathway genes is associated with tissue-specific transcriptional differences.
• Findings highlight functional specialization within the NF-κB signaling network across tissues.
• Breed and sex effects on gene expression were gene-dependent.