Ancestry and genome-wide association study of domestic pigs that survive African swine fever in Uganda.

Abstract

African swine fever (ASF) is endemic to Uganda and causes annual outbreaks. Some pigs survive these outbreaks and remain asymptomatic but are African swine fever virus (ASFV) positive. The potential heritability and genetic disparities in disease susceptibility among Ugandan pigs are not fully understood. In a 12-year study, whole blood and tissue samples were collected from 212 pigs across 19 districts in Uganda. Polymerase chain reaction (PCR) assays were used to determine ASFV infection status and genotyping was completed using a commercial porcine array. The point prevalence of ASF was calculated for each district, and breed composition origins were quantified for the sampled pigs by implementing established ancestry analyses. Genome-wide associated studies (GWAS) were conducted using all available domestic swine samples (full study population; n = 206) as well as a reduced dataset (farm-level study population; n = 129). This study revealed a greater number of ASFV-positive pigs in border districts than in non-border districts, a high level of admixture among domestic pigs sampled from Ugandan smallholder farms, and 48 loci that were associated with ASFV infection status. The discovery of 48 significant SNPs and 28 putative candidate genes may imply the possibility of heritability for resistance to ASFV. However, additional investigations in ASFV-endemic regions are required to fully elucidate the heritability of ASFV susceptibility among surviving pigs in Uganda.