In Africa, livestock forms a critical part of the livelihoods of most rural households, with approximately 162 million low-income livestock keepers (Kruska et al., 2003). In most African countries, livestock is managed under small- to large-scale systems, with small-scale production systems predominating and including pastoral, agro-pastoral, and mixed smallholder farming (Ibeagha-Awemu et al., 2019). They represent approximately 70% of livestock productivity and serve as household assets with multiple livelihood functions, providing food, income, and important non-market services (Ruto et al., 2008). These small-scale systems are characterised by small animal population sizes and low inputs and outputs, which make it difficult to set up programmes aiming at increasing livestock productivity for food production and income generation (Ibeagha-Awemu et al., 2019). However, given the importance of livestock to the diets and incomes of poor farming households and the predicted increase in demand for livestock products throughout the low- and middle-income world over the next few decades, understanding how livestock fits into these systems and how these systems may evolve in the future is critical (Kruska et al., 2003).

The main factors limiting cattle performance under extensive range management in tropical environments are feed resource availability and quality (Hernández-Castellano et al., 2019) and health-related issues, with ticks being among the most important vectors of disease pathogens in livestock and companion animals (Ghosh et al., 2006). Direct effects of tick infestation on cattle include the consumption of blood, causing anaemia and damage to the skin or hide, with downstream effects resulting in reductions in fertility, body weight, and milk production, as well as toxicoses, paralysis, and mortality (Jongejan and Uilenberg, 2004). The economic losses due to ticks and tick-borne diseases (TBDs) have been estimated at more than 3 billion dollars per year in Brazil alone (Grisi et al., 2014). No estimates of economic losses were found for the African continent; however, in Tanzania alone, for example, the total annual national loss due to TBDs was estimated to be 364 million dollars, including the estimated mortality of 1.3 million cattle, mainly attributed to the tick-borne disease East Coast fever, caused by Theileria parva (Kivaria, 2006).

The economically most important TBDs of cattle on a global scale are bovine babesiosis, caused by protozoa of the genus Babesia (Babesia bovis and Babesia bigemina), bovine anaplasmosis (Anaplasma marginale), bovine theileriosis, caused by Theileria annulata, East Coast fever, caused by Theileria parva, and ehrlichiosis or heartwater of cattle (Ehrlichia ruminantium) (Uilenberg, 1995). Both babesiosis and anaplasmosis can cause severe anaemia, while heartwater, especially in its acute form, can cause a sudden high fever, loss of appetite, depression, and breathing problems. All these diseases have a significant negative economic impact on livestock in tropical countries, due to the expense of vector control, treatment of the disease, effect on animal productivity, and the death of susceptible animals (Mukhebi et al., 1999; Kocan et al., 2003).

In addition to the relatively limited use of live vaccines against a small number of tick-borne pathogens, the strategy most commonly adopted to control tick-borne parasitic diseases is the application of acaricides. The widespread and large-scale use of these acaricides has increased the incidence of acaricide-resistant ticks and exacerbated the occurrence of environmental and food contamination (Parizi et al., 2009; Abbas et al., 2014; Githaka et al., 2022). This has led to an economic and social demand for alternative approaches to reduce tick infestation and thereby enhance the contribution of cattle to the world economy. Natural immunity to the tick vector, which is observed in cattle in environments where ticks are endemic, shows promise for genetic tick control strategies that can reduce expenditure on acaricides and other chemical control methods (Mapholi et al., 2014). Across Africa, it has been common to crossbreed indicine (Bos taurus indicus) with taurine (Bos taurus taurus) cattle (Jonsson et al., 2008; Cardoso et al., 2021), one reason being that indicine animals are known to be more resistant to ticks as well as TBDs (Silva et al., 2002; Wragg et al., 2022), and this has resulted in generally admixed populations across the continent (Gebrehiwot et al., 2020).

There is precedent for genetic tolerance to vector-borne pathogens proving tractable and potentially applicable as a practical aid in disease control in cattle (Bahbahani and Hanotte, 2015). A very well-defined example is trypanosomiasis, caused by tsetse fly-transmitted protozoan parasites of the Trypanosoma genus, where the tolerance of some African taurine breeds has been long recognised and characterised, and loci underpinning this trait have been identified (Murray et al., 1984; Hanotte et al., 2003; Kim et al., 2020). With respect to TBDs, natural tolerance among certain African cattle populations to the Theileria parva pathogen has been known for some time. T. parva infection is responsible for East Coast fever (ECF), a TBD that causes significant mortality in infected, susceptible cattle in East and Southern Africa. Ndungu et al. (2005) demonstrated that East African Shorthorn Zebu (EASZ) originating from ECF endemic areas showed significantly higher tolerance to T. parva challenges than exotic breeds and EASZ from non-endemic areas. Likewise, a notable recent study by Wragg et al. (2022) highlighted that certain lineages of Boran cattle also show elevated tolerance to T. parva infection and identified a locus associated with tolerance to ECF. The identification of this locus by Wragg et al. (2022) raises the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva. However, in general, only a few studies have reported naturally occurring loci with large effects that confer resistance to disease in livestock (White et al., 2014; Chen et al., 2015; Matika et al., 2019), and studies of natural tolerance to most African cattle pathogens remain limited.

Resistance to diseases is usually a physiologically complex trait that develops over time, with the mechanisms underlying genetic differences in resistance being poorly understood. Traditionally, the genetic control of complex traits in livestock has been based on estimating breeding values from phenotypic and pedigree information, without identifying the genes or gene variants underlying the observed variation (Goddard and Hayes, 2009), which can be a challenge in most African husbandry systems. However, current molecular tools allow animal geneticists to investigate the nature of genetic variation underlying complex traits, without requiring pedigree information, making selection a possibility.

While several genome-wide association studies (GWAS) have already reported quantitative trait loci for resistance to ticks (see Mapholi et al., 2014 for a review) in cattle, very few studies investigating loci underlying variation in resistance to tick-borne haemoparasites are reported in the literature.

Although a variety of arrays are currently available for genotyping in cattle, they are mostly designed for European breeds and are, therefore, biased toward variants common to these breeds. This can make it difficult to map the genetic loci that underlie important traits in African cattle, which are a mixture of African taurine and indicine backgrounds (Gebrehiwot et al., 2020). A recent study demonstrated that the Illumina HD (https://www.illumina.com/ documents/products/datasheets/datasheet_bovine HD.pdf) and the Axiom Genome-Wide BOS1 (https://www.thermofisher.com/order/catalog/product/901791#/901791) arrays are the best at capturing the diversity across African breeds/populations, even if compared with Bos t. indicus-specific arrays (Riggio et al., 2022). Another limitation to performing GWAS on African cattle is the small size of most herds, which limits the power to detect significant associations. In this case, a meta-analysis, combining results across independent studies, could help boost statistical power (Munafò and Flint, 2004). This study aimed to investigate the potential of breeding for cattle resistant or tolerant to particular TBDs by characterising the heritability of relevant traits and investigating the potential of identifying loci underlying the variation in the presence of tick-borne haemoparasites, as well as important traits such as body weight and body condition score (BCS), in African cattle from four different countries (Burkina Faso, Ghana, Nigeria, and Tanzania).

To estimate the heritability of the presence of tick-borne haemoparasites, body weight, and body condition score in African cattle, we analysed four independent datasets from Burkina Faso, Ghana, Nigeria, and Tanzania, for a total of 1,694 cattle. Heritability estimates were then used to calculate the weighted mean of heritability estimates (h² _m ) across countries. The same data were also used to carry out GWAS to identify potential loci underlying genetic variation in the traits of interest, with a meta-analysis across countries being conducted.

Means, standard deviations, coefficients of variation, and ranges of the continuous traits considered in this study (i.e., body weight and BCS) are presented per country in Table 1. Body weight values over three standard deviations from the mean were removed. Although there is some variation across countries for body weight, coefficients of variation (CVs) are similar for all countries, ranging between 30 and 39, with Nigeria having the highest value. This is confirmed by the histogram in Supplementary Figure S1, which shows higher variability in the body weight distribution for Nigeria. More variability was observed for the BCS, with CVs ranging between 18 for Ghana and 34 for Burkina Faso (see also Supplementary Figure S2, showing the distribution of BCS categories across the four countries).

Table 2 shows the prevalence of different haemoparasites as assayed by species-specific qPCR across the four countries. The prevalence of Theileria is not presented as it was not detected in any sample. The highest prevalence was observed for A. marginale across all countries (ranging between 43% and 97%), with Ghana presenting the highest prevalence. In general, prevalence was lower in Burkina Faso than in other countries for all parasites considered. This might have an impact on the estimation of the heritabilities and analyses of GWAS, as there is insufficient information to generate reliable results. Similarly, the analyses for A. marginale in Ghana may be affected by the very high prevalence.

Table 3 shows the heritability (h²) estimates for body weight and BCS as well as the haemoparasite traits for each country. For most traits, the standard errors of the heritability estimates were large, making the estimated h² not significant. While these estimates are not significant and there is little consistency across countries, there is evidence of genetic variation. These results are probably a reflection of the challenges of collecting consistent phenotypes in the settings concerned, as well as the limitations associated with issues such as small herd sizes.

Table 4 presents the weighted mean of heritability estimates (h² _m) and Q statistics for each trait. The h² _m was moderate and significant (p < 0.05) for both body weight and BCS (0.40 and 0.49, respectively), with significant Q statistics for BCS. When looking at the haemoparasite traits, although the h² _m estimates are low, ranging between 0.10 for B. bigemina and 0.19 for E. ruminantium, the estimates for A. marginale and E. ruminantium are both significant, suggesting a genetic component to the presence of these parasites in African cattle.

Within-country GWAS analyses did not generally show any regions associated with the traits of interest, reflecting the low sample numbers. To overcome this limitation, we performed meta-analyses across countries for the two quantitative and four haemoparasite phenotypes. When the prevalence of a phenotype was ≥0.05 or ≤0.95 within a country, the corresponding results were excluded from these meta-analyses. Across these six phenotypes, two peaks reached suggestive significance (p < 1.91 × 10⁻⁷ and p < 1.89 × 10⁻⁷, respectively). The first peak (lead variant: chr24:24760549:A:G; p = 1.2 × 10⁻⁷) was observed for the body condition score on chromosome 24 (Figure 2), with this peak overlapping the GAREM1 gene (Figure 4A) that has previously been linked to body mass in mice and humans (Nishino et al., 2022). The second peak (lead variant: chr8:62534748:T:C; p = 4.5 × 10⁻⁸) was identified for the E. ruminantium infection status on chromosome 8 (Figure 3), which overlaps seven genes (Figure 4B). Of these, the Tudor domain-containing protein 7 (TDRD7) gene has previously been associated with immune responses.

Selection programmes for the improvement of host resistance against ticks and tick-borne diseases could be considered an important strategy for reducing the expenses associated with treatment and prophylaxis management. However, the implementation of genetic improvement programmes has always been difficult in low- and middle-income country settings, due to many factors, including cost, lack of or poor infrastructure, and small herds, which hinder the estimation of population-specific parameters (i.e., heritability and genetic correlations) for traits of economic importance. Moreover, traditionally, the implementation of a breeding programme required an accurate pedigree. In smallholder properties in tropical and subtropical environments, there is often no pedigree recording and no phenotype data recording, rendering conventional breeding practices impossible to implement. Current molecular tools allow for investigating the genetics of complex traits without requiring pedigree information, making selection based on the genome a possibility. One of the key shortcomings of using these technologies in low- and middle-income countries is the cost associated with them. Genotyping arrays are currently the most commonly used tool in GWAS. However, the current commercial genotyping arrays are often biased toward variants common to European breeds, and we have recently shown that they poorly tag variants segregating in indicine breeds, with implications for performing GWAS in African breeds (Riggio et al., 2022). Further limitations associated with performing GWAS in African cattle are the generally small sample size and large variability in farming practices as well as the extensive admixture of these populations (Gebrehiwot et al., 2020). Combining results across independent studies via meta-analysis could help partly overcome these issues, boosting the power to detect significant associations.

To investigate the genetic architecture of the presence of haemoparasites, as well as body weight and BCS, in African cattle, we estimated heritabilities and carried out GWAS using 1,694 cattle from four different countries (Burkina Faso, Ghana, Nigeria, and Tanzania) with genotypes imputed from HD to the whole-genome level, both independently and via meta-analysis. We have shown evidence of genetic variation for most traits, with the weighted mean of heritability estimates being moderate for body weight and BCS and low for haemoparasites, and we have identified two peaks reaching the suggestive significance threshold (i.e., one false positive per genome scan) in the meta-analysis. We could not include Theileria parva in the analysis as we did not detect any infections in our sample set. This was expected for Ghana, Burkina Faso, and Nigeria but was surprising for Tanzania, where both the tick vector and Theileria parva are endemic (Kerario et al., 2017; Allan et al., 2021). The explanation for the lack of detection is either lack of sensitivity based on the substrate (DNA from FTA cards is less effective than DNA purified from blood (Hailemariam et al., 2017)), the assay used (only primers suitable for use in qPCR were considered for this study, which may have compromised sensitivity), or lack of detectable infection in the target animals (it is probable that any infected animals would be carriers, meaning low parasite numbers). However, the lack of detectable infections meant that we were not able to assess heritability for this important pathogen, although numbers and, therefore, power would have been very low in any case given the restriction to one country.

Although heritability estimates for body weight and BCS within the country were mostly not significant, the weighted means of heritability estimates (h² _m) were moderate and significant (i.e., 0.40 for body weight and 0.49 for BCS). This estimate of the heritability of body weight is consistent with that previously estimated within European cattle, where values generally fall between 0.4 and 0.7 (Mehtiö et al., 2021). Likewise, heritability estimates for BCS in European cattle breeds have generally fallen within the range of 0.2–0.5 (Bastin and Gengler, 2013). Consequently, our heritability estimates for these traits are consistent with previous findings.

Estimates for haemoparasites were lower, ranging between 0.10 and 0.19. Low heritability estimates for the infection levels of B. bigemina and B. bovis (i.e., 0.09 and 0.1, respectively) were also previously reported by Romero (2021). Although we use a different definition of the trait, as we are only considering the presence/absence of the pathogen, both results seem to be consistent in showing a high environmental influence on such traits. Romero (2021) also reported a heritability estimate of 0.09 for the infection level of A. marginale.

Previous studies have identified a region on chromosome 5 associated with BCS in tropical cattle (Porto-Neto et al., 2014), but there was little evidence of an association with this locus in our analyses. However, the authors in that study visually assessed body condition at an average of 30 months of age and subjectively scored at 1/3rd score increments from 1 to 5 and subsequently converted it to a continuous 15-point scale (Porto-Neto et al., 2014), whereas we used a classification scale of nine points. In this study, we identified a region reaching the suggestive significance level on chromosome 24, which overlaps the GAREM1 gene. In a study on body mass in humans and mice, Nishino et al. (2022) found that GAREM1 is required for normal growth and for maintaining average body size in these species. This gene is consequently a potentially interesting candidate for follow-up work further exploring its potential link to BCS in African cattle.

Considerable work has been carried out to address the genetic control of resistance to ticks [see Mapholi et al. (2014) for a review]. To the best of our knowledge, few studies have been published so far for TBDs (Romero, 2021; Wragg et al., 2022). Comparisons across studies are not easy, given the complexity of the traits and the differences among populations and in tick/pathogen prevalence, as well as the approaches used. Moreover, in contrast to association studies in humans, where in general largely unrelated individuals are used, livestock populations are often characterised by high levels of relatedness (i.e., closely related animals with a complex population structure) and an a priori unbalanced distribution of allele frequencies, which is likely to inflate the rate of false-positive associations between the traits and the markers, making true associations harder to detect. However, our meta-analysis showed evidence of a peak on chromosome 8 for the E. ruminantium infection status. This region overlaps several genes, though TDRD7 is potentially the strongest candidate for being linked to the infection status. Given that E. ruminantium is an intracellular bacterium, this gene could be relevant as it is an important factor involved in cellular responses to viral infection (Thakur et al., 2019; Subramanian et al., 2020; Forst et al., 2022). A previous study from Romero (2021) in a similar number of South American cattle, using predominantly low-density arrays, prioritised several regions across the genome potentially affecting the infection level of B. bigemina (chromosomes 5, 7, 10, 20, and 27) and A. marginale (chromosomes 2, 5, 8, 10, 13, 15, 17, 20, 24, and 29). However, none of these regions were significant in our analyses.

In conclusion, in this study, we aimed at estimating heritabilities and identifying loci underlying genetic variations for important haemoparasites, as well as body weight and body condition score, in African cattle. Despite the relatively modest heritability estimates in the within-country analysis, our meta-analysis results have indicated the possibility of improving these traits. Moreover, our meta-analyses have identified two regions associated with body condition score and presence/absence of E. ruminantium, which should be further explored. These data suggest that future larger-scale studies to explore the genetic basis of resistance/tolerance to tick-borne pathogens have merit, as improving the resolution by increasing animal numbers has the potential to identify genetic traits that may contribute in the future to reducing the disease burdens on smallholder farmers in Africa.