Evolutionary Adaptation Genomics of Nigerian Indigenous Livestock Breeds to Tropical Disease and Climate Stressors

This study applies evolutionary adaptation genomics approaches to identify selection signatures and adaptive genetic variants in Nigerian indigenous livestock breeds associated with resistance to tropical diseases and climate stress, contributing original insights into the genetic architecture of local adaptation. Nigerian indigenous livestock breeds have evolved under intense selection pressure from trypanosomiasis, haemorrhagic septicaemia, tick-borne diseases, and heat and drought stress over millennia, resulting in adaptive genomic signatures that differ from exotic imported breeds. Identifying these signatures is essential for conservation, utilisation in improvement programmes, and understanding evolutionary adaptation mechanisms. This study generates 50K SNP genotyping data from 2,400 individuals representing 12 indigenous cattle, 6 sheep, and 4 goat breeds sampled from across Nigeria's six geopolitical zones. Selective sweep analysis using XP-EHH, iHS, and FST statistics identifies genomic regions under positive selection. GWAS using disease challenge and heat stress phenotype data from controlled experiments identifies specific variants associated with adaptive traits. Functional annotation links signatures to candidate genes. Cross-species comparison with African cattle, sheep, and goat genomes identifies convergent adaptive evolution. Findings reveal 47 significant selective sweep regions in indigenous Nigerian cattle, with enrichment for immune function, thermotolerance, and metabolic efficiency gene categories. Novel trypanosome resistance-associated variants distinct from known N'Dama resistance loci are identified in northern ecotypes. The study contributes an original Nigerian livestock adaptation genomics dataset and recommends targeted conservation of breeds showing the richest adaptive genetic diversity.

Keywords: adaptation genomics, selective sweep, Nigerian indigenous breeds, tropical disease resistance, evolution.