POPULATION STRUCTURE OF NIGERIAN INDIGENOUS CATTLE BREEDS BASED ON ILLUMINA BOVINE50K SNP PANEL

Abstract

In this study, the genetic structure of Nigerian indigenous cattle breeds using the Illumina Bovine50K SNP array was investigated. A total of 96 DNA samples including White Fulani (n = 20), Red Bororo (n = 20), Sokoto Gudali (n = 20), Muturu (n = 20) and Bornu Kuri (n = 16) were genotyped. Statistical analysis was performed using PLINK version 2.0. Genetic diversity, measured as expected heterozygosity, was estimated at 0.502, 0.499, 0.510, 0.506 and 0.499 for White Fulani (WF), Red Bororo (RB), Sokoto Gudali (SG), Bornu Kuri (BK) and Muturu (MU) cattle breeds, respectively. The individual inbreeding coefficient varied from 0.013 ± 0.05, 0.008 ± 0.07, 0.014 ± 0.06, 0.017 ± 0.08 and 0.012 ± 0.04 for WF, RB, SG, BK and MU cattle breeds, respectively. The Principal component analysis clustered the populations according to agro-ecological zones and breed types. Linkage disequilibrium (LD) for shorter intervals (0–10 kb) ranged from 0.44 to 0.56 and WF had highest values. The cattle populations exhibited high level of genetic variation which holds potential for improved production in the agro-ecological zones. The results of this study demonstrated that 54,609 SNPs were polymorphic (MAF >0.05) in these breeds and indicate potential for application in Nigerian indigenous cattle populations. Genomic information generated from the BovineSNP50K can now be applied in genetic prediction; genetic characterization and genome-wide association studies. In addition,a national strategy is required to maintain genetic diversity in the cattle production systems through well-structured breeding and conservation programs.