Whole-genome sequencing of Landim pigs of Mozambique reveals a close relationship with Angolan native pigs and suggests selection for immune response

Abstract

Landim pigs, a population of native pigs from Mozambique are currently threatened by the recent introduction of European exotic breeds. Like most African pig populations, Landim pigs have never been characterized at the genome level and are well adapted to harsh conditions which include adaptation to endemic diseases. In this study, we provide a comprehensive genetic characterization of Landim pigs using whole-genome sequencing (WGS). We generated genomes from Landim pigs (n = 6) and compared these genomes to local pigs from Angola and European and Asian domestic pigs and wild boars currently in the public domain (n = 78). Analyses of population structure showed that Angola local and Landim pigs are closely related, and both are more closely related to European than Asian breeds. Preliminary results suggest that Landim pigs display a duplication in Chr4 that has been reported only in Chinese domestic pigs, overlapping the TBX19 gene that is associated with development and growth. The functional analysis of missense SNPs in Landim pigs shows that these occur in genes related to immune system response. The integrated haplotype score (iHS) analysis revealed candidate regions under selection overlapping genes also related to immune response. This study represents the first assessment of the genetic background of native pigs from Mozambique and opens the path to understanding the dynamic and interlinked history of African pig populations. The present study further reports unique genetic attributes related to an immune response that should be further explored