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

Abstract

Ticks and tick-borne diseases are among the main causes of economic loss in the South African cattle industry through high morbidity and mortality rates. Concerns of the general public regarding chemical residues may tarnish their perceptions of food safety and environmental health when the husbandry of cattle includes frequent use of acaricides to manage ticks. The primary objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with host resistance to ticks in South African Nguni cattle. Tick count data were collected monthly from 586 Nguni cattle reared in four herds under natural grazing conditions over a period of two years. The counts were recorded for six species of ticks attached in eight anatomical locations on the animals and were summed by species and anatomical location. This gave rise to 63 measured phenotypes or traits, with results for 12 of these traits being reported here. Tick count (x) data were transformed using log10(x+1) and the resulting values were examined for normality. DNA was extracted from hair and blood samples and was genotyped using the Illumina BovineSNP50 assay. After quality control (call rate >90%, minor allele frequency >0.02), 40,436 SNPs were retained for analysis. Genetic parameters were estimated and association analysis for tick resistance was carried out using two approaches: a genome-wide association (GWA) analysis using the GenABEL package and a regional heritability mapping (RHM) analysis. The Bonferroni genome-wide (P<0.05) corrected significance threshold was 1.24×10(-6), with 2.47×10(-5) as the suggestive significance threshold (P<0.10) (i.e., one false positive per genome scan) in the GWA analysis. Likelihood ratio test (LRT) thresholds for genome-wide and suggestive significance were 13.5 and 9.15 for the RHM analysis. Six ixodid tick species were identified, with Amblyomma hebraeum (the vector for Heartwater disease) being the dominant species. Heritability estimates (h(2)) from the fitted animal and sire models ranged from 0.02±0.00 to 0.17±0.04 for the transformed tick count data. Several genomic regions harbouring quantitative trait loci (QTL) were identified for different tick count traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total body A. hebraeum tick count and total A. hebraeum on the perineum region, respectively. Additional regions significant at the suggestive level were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the traits. The GWA approach identified more genomic regions than did the RHM approach. The chromosomal regions identified here as harbouring QTL underlying variation in tick burden form the basis for further analyses to identify specific candidate genes and polymorphisms related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni cattle.

Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods

“…Using π = 0.9999 in a BayesB analysis resulted in a very low estimated heritability ( h 2  = 0.02), which corresponded to a small fraction of the pedigree-based heritability ( h 2  = 0.19) obtained with the same dataset [18], and was similar to the lower-bound heritability estimates recently reported for cattle tick resistance [14] in a GWAS that analyzed A. hebraeum tick counts on the tail of South African Nguni cattle (0.02). Some cycles contained no fitted SNPs when an extremely high value of π (0.9999) was used in BayesB, which resulted in the absence of any predictive SNPs, and thus this model contributed mostly to the estimated residual variance.…”

“…Other genomic regions on BTA17 at 7 Mb flanked by SNPs ARS-BFGL-NGS-5880 and BTA-122662-no-rs (top window 1758, Table 2) also include two SNPs (rs43499108 and rs29011077), which have been reported to be associated with R. evertsi evertsi tick count in African cattle [14]. The top SNP in this window (rs109822497) was mapped to the double cortin - like kinase 2 ( DCLK2 ) gene, near the LRBA gene, which is suggested by these authors to be associated with protein kinase A that supports the secretion and/or membrane deposition of immune effector molecules.…”

“…To date, several genomic regions associated with tick burden in dairy and/or beef cattle have been identified through association studies based on different regression methods [2, 8–14]. However, to estimate a greater proportion of the genetic variance explained by SNPs and to identify more complex relationships between SNPs, a shift to models that fit multiple SNPs simultaneously was proposed [15].…”

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

“…Although the ecotypes tend to have specific phenotypes with regard to colour and body and or head conformation, genetic differentiation has not been confirmed. Studies to date has confirmed adaptability traits (Marufu et al 2011(Marufu et al , 2014 of the Nguni and identified genomic regions underlying tick resistance (Mapholi et al 2015). In this study the focus was on the genetic diversity and population structure of the known and unknown ecotypes based on microsatellite markers.…”

Genetic parameters for tick counts across months for different tick species and anatomical locations in South African Nguni cattle

“…The most economically important tick genera affecting livestock production in Southern Africa are Rhipicephalus (includes the genus formerly known as Boophilus ), Amblyomma and Hyalomma (Marufu et al 2011; Nyangiwe et al 2013; Mapholi et al 2013, 2016). These tick genera have an impact on animal productivity directly through heavy infestation and indirectly through transmission of tick-borne diseases (Dold and Cocks 2001; Ghosh et al 2006).…”