De Novo Assembly and Comparative Genomics of Indigenous Nigerian Cattle Breeds: Implications for Livestock Adaptation and Improvement

Indigenous Nigerian cattle breeds, particularly the White Fulani (Bunaji), Muturu, and Keteku, have undergone millennia of natural selection for adaptation to tropical diseases, heat stress, and trypanotolerance. Their genomes encode adaptive variants of immense value for livestock improvement and conservation genetics. Despite their agricultural importance, reference genome assemblies are unavailable for any indigenous Nigerian cattle breed. This dissertation conducted de novo chromosome-level genome assembly and comparative genomic analysis of three Nigerian indigenous cattle breeds. One representative individual per breed was selected based on pedigree verification and phenotypic characterisation. High-molecular-weight DNA was extracted and sequenced using Pacific Biosciences HiFi long reads (60x coverage), Oxford Nanopore ultra-long reads (30x), and Hi-C chromatin conformation data for scaffolding. Assembly was performed using hifiasm with Hi-C scaffolding in YAHS. Functional annotation was performed using MAKER2 and Ensembl protein homology. Comparative genomic analysis against the Hereford reference genome (ARS-UCD1.2) and the indicine (Bos indicus) genome identified breed-specific structural variants, CNV regions, and positively selected genes. Trypanotolerance-related genes in the Muturu breed showed signatures of positive selection distinct from Bunaji. These chromosome-level genomes establish a transformative resource for Nigerian livestock genomics and breeding programmes. Keywords: de novo genome assembly, indigenous cattle breeds, comparative genomics, trypanotolerance, Nigeria