Genotyping of an intensively monitored cohort of Bos indicus cattle in western Kenya for the FAF1B allele associated with resistance to East Coast fever (Theileria parva infection) with a real-time PCR assay

A single nucleotide polymorphism (SNP) on bovine chromosome 15 has been shown previously to be highly associated with resistance to disease caused by <i>Theileria parva</i>. The SNP comprises a CT mutation in a paralogue of the FAF1 gene. Disease caused by <i>T. parva</i> is of major economic importance in eastern to southern Africa and better control methods are urgently required. Genotyping cattle for this snp will aid epidemiological studies to understand the origins and dissemination of resistance to <i>T. parva</i> and will facilitate marker-assisted breeding for resistant cattle. The current study reports the development of a simple and economic genotyping assay based on real-time, Fluorescence Resonance Energy Transfer (FRET)-based PCR. The assay was optimized to ensure reliable, automatic calling of the three genotypes and was validated by comparing the assay results to sequencing analyses on different sample types including extracted DNA, whole blood without extracting DNA and serum. The assay was used to genotype East African Shorthorn Zebu (EASZ) cattle from an intensively studied calf cohort from western Kenya. The results confirmed the protective effect associated with the T allele, and showed that it had no deleterious effect on the growth rate of this calf population. The assay was also used to determine variation in the frequency of the T allele in Boran cattle populations from different regions of eastern Africa. The assay will make a useful breeding selection tool especially in studies involving prevalence and evolution of the protective haplotype in different cattle populations.