Exploring Genetic Architecture of Tick Resistance in South African Nguni Cattle

Tick infections have a major economic impact on livestock in South Africa. To understand the genetic basis of tick infestation levels in South African Nguni beef cattle, we conducted a heritability study and a genome-wide association study (GWAS). Tick data were collected on different body parts over a period of three years in three different Nguni populations (n=500), under natural grazing conditions, with up to 23 monthly measurements per animal. DNA was extracted from hair or blood samples and genotyped using the Illumina BovineSNP50 assay. After QC (call rate >90%, minor allele frequency > 0.02), 40,436 SNPs and 488 individuals were retained. The Bonferroni genome-wide (p<0.05) corrected threshold was 1.24x10^-6, with 2.47x10^-5 as the suggestive level (i.e. one false positive per genome scan). Fixed effects comprised location, month, year, location-month interaction, age and sex; random effects were animal or sire, and the animal permanent environmental effect. Genetic parameters were estimated using ASREML, whereas the association analysis was conducted using GenABEL. Six Ixodid ticks species were identified with Amblyomma being the dominant species. Heritability estimates ranged from 0 to 0.02, when using animal model with a repeatability of 0.03 to 0.11, and from 0 to 0.13 using the sire model. Genetic correlations ranged from 0.44 to 0.99. Two genome-wide regions (on chromosome 7 and 10) were identified for total tick count on the head and total Amblyomma ticks. Suggestive regions were identified on chromosomes 1, 6, 7, 8, 10, 12, 14, 17, and 26 for several tick traits.