Genome-wide association study for tick resistance in South African Nguni cattle

Ticks and tick-borne diseases are major constraints on beef cattle production in tropical and subtropical countries. South African Nguni cattle are adapted to harsh environments and are tolerant to tick and tick-borne diseases. The objective of this study was to explore variation in genetic resistance to ticks in Nguni cattle genotyped with the Illumina BovineSNP50 assay. Tick counts were collected for several endemic species (Amblyomma hebraeum, Hyalomma marginatum, Rhipicephalus appendiculatus, Rhipicephalus Boophilus (decoloratus and microplus), and Rhipicephalus evertsi evertsi), under natural challenge conditions, over a period of twelve months from 400 Nguni cattle in three provinces of South Africa. After quality control, 41,522 SNPs were used for the genome-wide association study (GWAS), fitting the fixed effects of sex, ranch, year of birth and the first three principal components. Relationships between animals was accounted for by using the G matrix in a univariate mixed model analysis. Several SNPs were identified as being associated with tick resistance, some of which were significant across different sampling times throughout the year. One SNP (on chromosome 12, rs 60527567) was significant at the Bonferroni genome-wide (p<0.05) threshold, whereas seven SNPs (on chromosomes 3, 8, 9, 10, 14, 20 and 27) were significant at the suggestive threshold (i.e., one false positive in a genome scan). Further analyses will be needed to confirm these results.