Genomic diversity of East African shorthorn Zebu of western Kenya

Abstract

Indigenous zebu cattle in Kenya are predominant across the country owing to their tropical adapted physiology. These breeds have been embraced by most small-scale farmers, who are the drivers of the low-input sustainable agricultural sector within the country. Though autosomal microsatellites revealed ancient taurine and zebu admixture in East African sh0l1horn zebu (EASZ) cattle, the extent of this admixture and the effect of modern European taurine introgression through indiscriminate breed improvement programmes in these populations remains unclear. The population structure and ancestral origin of the EASZ a pre-requisite to genome-wide association studies has also not been documented yet. In this study, 548 East African shorthorn zebu (EASZ) calves were randomly sampled from 20 sub-locations across 4 agro-ecological zones in Western Kenya and monitored from bi11h to I year of age, with no veterinary intervention allowed. Data included reports of calf clinical episodes, post-mortem examination and selected sets of phenotypic parameters associated with infectious parasitic disease (Packed Cell Volume (PCV), parasiteamia load and body weight). Phenotypic data also included detailed information on coat color, coat patterns, hair texture, calf body stature measures, horn size, hump size and dewlap size. A total of 460 calves survived the one year period follow-up and diseases challenges, while 88 died across the one year period, succumbing to various infectious and non-infectious causes. The leading cause of death at 38% was attributed to East Coast Fever (ECF) infections. The main objectives of the study were to : (i) Evaluate the informativeness of the Illumina® BovineSNP50 beadchip, a genetic tool primarily developed for European commercial breed, on an indigenous African cattle population, (ii) unravel the genetic architecture and origin of EASZ of Western Kenya and (iii) identify imprints of genetic selection through phenotype-genotype associations. Out of the 56,947 SNPs genotyped using the IIIumina® BovineSNP50 beadchip, 55,777 were successfully mapped on the University of Maryland genome assembly (3 .0) 1 and only 6,151 failed the quality control criteria. An average genome spacing of 46 kbp was observed with less than 5% of the gaps between informative SNPs being larger than 100 kbp. The ancestral origin of the study cohort was established, with 83%, 15% and 2% of the genetic background being of Asiatic zebu, African taurine and European taurine ancestry respectively. Most importantly, we identified the main taurine ancestral source as African and established the degrees of admixture within this indigenous breed. In addition, a North-South genetic cline in the amount of European taurine introgression was observed \ ) I I VI with two localized hotspots in the Northern and central studied regions. The dissemination of the European blood was attributed to rampant breed improvement programmes and animal markets as main entry points. A three-tier categorization associated with the amount of European taurine introgression was revealed, namely pure (:S 1.56%), moderate (> 1.56 - < 12.5%) and substantial (~ 12.5%). Excluding the moderate and substantial calf categories, revealed an EASZ population that was genetically homogenous with closer genetic relatedness been observed within sub-locations than between sub-locations. However, genetic differentiation, between sub-locations was not significant and the population may be considered as "panmictic" for the purpose of genetic mapping. The effective population size (N) analysis, revealed a short stint of increasing population size but was generally characterized by a major population decline over-time. A rich diversity of coat colours and patterns was observed across the study site with a characteristic spatial distribution of some ofthese phenotypic traits. Significant SNPs were identified within or neighbouring genomic loci that control for selected non-disease (coat color) and disease traits (survival). Our findings provide valuable new insights in the understanding of the genetic landscape, genetic admixture and demographic history of an African indigenous breed. The genotype-phenotype association outcomes call for fU11her analysis aiming to unravel the genotype control of adaptations using more " powerful" approaches (e .g. High Density SNPs genotyping or next generation sequencing). We advocate for an urgent move towards understanding these unique adaptations of African indigenous cattle breeds before the ultimate loss of these ecologically important traits to unsustainable economic traits via indiscriminate crossbreeding.EThOS - Electronic Theses Online ServiceGBUnited Kingdo