Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs.

Area of Science:

• Genomics
• Evolutionary Biology
• Animal Science

Background:

• The CD163 gene is essential for porcine reproductive and respiratory syndrome virus (PRRSV) infection.
• PRRSV is a significant pathogen impacting global pig production.
• Understanding CD163's genetic variation and evolutionary pressures is vital for swine health.

Purpose of the Study:

• To investigate sequence variation, evolutionary constraint, and selection at the pig CD163 gene.
• To identify potential loss-of-function variants in CD163.
• To assess the impact of evolutionary and breeding selection on CD163.

Main Methods:

• Targeted pooled sequencing of CD163 exons in 35,000 pigs.
• Analysis of whole-genome sequence data from three pig lines.
• Calculation of variant intolerance scores, evolutionary selection estimates, and haplotype diversity.

Main Results:

• No potential knockout variants (stop-gain or frameshift indels) were detected in the CD163 gene.
• The CD163 gene demonstrated moderate intolerance to protein-coding variation.
• Evidence of positive selection was observed in the pig lineage, but no recent selective sweeps during breeding were identified.

Conclusions:

• The CD163 gene is functionally conserved in domestic pigs, with no identified knockout variants.
• Evolutionary processes have selected for specific CD163 variations in pigs.
• Recent artificial selection during pig breeding has not significantly impacted CD163 variation.