GENETIC ANALYSIS OF HYBRIDISATION, MUTATION LOAD AND RUNS OF HOMOZYGOSITY OF GOATS FROM KENYA AND UGANDA

Abstract

Increase in human movements, improvement in reproductive technologies, and diversity of livestock management systems coupled with climate change determine the genetic structure and diversity within or between populations. However, little is known about different genetic parameters in most African goat populations, making it difficult to plan and implement genetic improvement and conservation programmes. This study focused on joint genome-wide SNP genetic analysis of goat populations from Uganda and Kenya to characterize the hybridization pattern of goats from the two nations, mutation load, Runs of Homozygosity and effective population sizes of goats from Kenya. A total of ten local and exotic goat genotypes sampled from different agro-ecological regions of Kenya (n = 94) and Uganda (n = 144) were used. Principal component, phylogenetic and admixture analysis were applied on the hybridization analysis. Results revealed that the studied populations are genetically distinct according to country of origin. This suggests that the transfer of genetic materials across the studied populations is possible for genetic improvement programs. For the mutational load (deleterious mutations), four Kenyan goat genotypes were used (Alpine, Saanen, Galla and Toggenburg). Gene annotation was done on ENSEMBLE (Capra hircus) using the Variant Effect Predictor (VEP) and the Biomart tool was adopted for gene ontology. Mutation load calculated through the ratio of missense to synonymous mutations was similar (0.37). Five genes were obtained from the highly deleterious mutations (SIFT score > 0.01) which include PROS1, EHBP1, LTN1, LRRN4, and FNDC3A. These results can be used as a base to predict the future rate of mutation load for future genetic improvement and conservation. Finally, Runs of Homozygosity (RoHs), effective population size, and prediction of future trends were estimated for the four goat genotypes from Kenya. Across the genotypes, 348 RoHs were detected and their distribution per chromosome was breed-specific. Higher inbreeding coefficients were observed for the Toggenburg, Saanen, and Alpine with values of 0.68, 0.35, and 0.23 respectively. Galla recorded a FROHS value of 0.09, suggesting that the genetic material for this genotype is well managed at the government station. Effective population size decreased over time across the genotypes indicating reduced genetic diversity, this will continue to decrease if recommended measures are not implemented to improve the Ne. In conclusion, goats from Uganda and Kenya are genetically distinct and can be used for cross-border genetic improvement. Furthermore, within breed selection and introduction of new exotic genetic lines must be promoted in any goat population to improve the genetic diversity.