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

Abstract

Background: In this work, we investigated sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. A functional CD163 protein is required for infection by porcine reproductive and respiratory syndrome virus, which is a serious pathogen with major impacts on pig production. Results: We used targeted pooled sequencing of the exons of CD163 to detect sequence variants in 35,000 pigs of diverse genetic backgrounds and to search for potential stop-gain and frameshift indel variants. Then, we used whole- genome sequence data from three pig lines to calculate: a variant intolerance score that measures the tolerance of genes to protein coding variation; an estimate of selection on protein-coding variation over evolutionary time; and haplotype diversity statistics to detect recent selective sweeps during breeding. Conclusions: Using a deep survey of sequence variation in the CD163 gene in domestic pigs, we found no potential knockout variants. The CD163 gene was moderately intolerant to variation and showed evidence of positive selection in the pig lineage, but no evidence of recent selective sweeps during breeding.

The authors acknowledge the financial support from the BBSRC ISPG to The Roslin Institute BBS/E/D/30002275, from Grant Nos. BB/N015339/1, BB/L020467/1, BB/M009254/1, from Genus PLC, Innovate UK, and from the Swedish Research Council Formas Dnr 2016-01386.