Mining genomes of African and Portuguese local breeds to study host/pathogen adaptation

Abstract

This work explores the genetic and molecular mechanisms underlying host–pathogen adaptation and environmental resilience in African and Portuguese livestock, with emphasis on sheep and pig populations. In Portuguese Merino sheep, genome-wide analyses were conducted to identify genetic determinants of resistance to coccidial infection, a disease that causes significant production losses in young lambs. Genotyping of nearly 400 lambs using high-density SNP arrays identified 19 significant variants, including loci within genes associated with protease inhibition pathways. Functional enrichment indicated that peptidase inhibitors and regulators play a key role in limiting Eimeria sporozoite invasion, suggesting natural selection has increased tolerance-associated genotypes in this breed.Complementary analyses of livestock across diverse Angolan biomes examined genetic diversity, relatedness, selective sweeps, and epigenetic differentiation to identify mutations linked to environmental adaptation. Whole-genome sequencing of Angolan pigs revealed high genetic diversity and signatures of selection associated with metabolism, tissue remodeling, and feed efficiency, while comparative analyses indicated close ancestry between Angolan, Landim, and Iberian pigs. Additional evidence suggests selective pressure on loci involved in neural circuitry and the neuroimmune axis, potentially enhancing survival behaviors and innate immune responses.Together, these findings demonstrate how genomic variation, natural selection, and ecological pressures shape disease resistance and adaptive traits in locally adapted breeds, providing insights to support sustainable breeding strategies and resilience to pathogens and environmental stressors.