M. Tapio

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya.

The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%<X<12.5%) and non-introgressed (⩽1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n=425) show an unfluctuating zebu and taurine ancestry of 0.84±0.009 s.d. and 0.16±0.009 s.d., respectively, with significant differences in African taurine (AT) and Asian zebu backgrounds across chromosomes (P<0.0001). In contrast, no such differences are observed for the European taurine ancestry (P=0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (Fst=0.0033, P=0.09; r=0.155, P=0.07). Following a short population expansion, a major reduction in effective population size (Ne) is observed from approximately 240 years ago to present time. Our results support ancient zebu × AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.

Co-infections determine patterns of mortality in a population exposed to parasite infection.

Highly protective effect of co-infections on mortality due to East Coast fever and consequences for disease epidemiology and control. Many individual hosts are infected with multiple parasite species, and this may increase or decrease the pathogenicity of the infections. This phenomenon is termed heterologous reactivity and is potentially an important determinant of both patterns of morbidity and mortality and of the impact of disease control measures at the population level. Using infections with Theileria parva (a tick-borne protozoan, related to Plasmodium) in indigenous African cattle [where it causes East Coast fever (ECF)] as a model system, we obtain the first quantitative estimate of the effects of heterologous reactivity for any parasitic disease. In individual calves, concurrent co-infection with less pathogenic species of Theileria resulted in an 89% reduction in mortality associated with T. parva infection. Across our study population, this corresponds to a net reduction in mortality due to ECF of greater than 40%. Using a mathematical model, we demonstrate that this degree of heterologous protection provides a unifying explanation for apparently disparate epidemiological patterns: variable disease-induced mortality rates, age-mortality profiles, weak correlations between the incidence of infection and disease (known as endemic stability), and poor efficacy of interventions that reduce exposure to multiple parasite species. These findings can be generalized to many other infectious diseases, including human malaria, and illustrate how co-infections can play a key role in determining population-level patterns of morbidity and mortality due to parasite infections.

Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

BackgroundPositive multi-locus heterozygosity-fitness correlations have been observed in a number of natural populations. They have been explained by the correlation between heterozygosity and inbreeding, and the negative effect of inbreeding on fitness (inbreeding depression). Exotic introgression in a locally adapted population has also been found to reduce fitness (outbreeding depression) through the breaking-up of co-adapted genes, or the introduction of non-locally adapted gene variants.In this study we examined the inter-relationships between genome-wide heterozygosity, introgression, and death or illness as a result of infectious disease in a sample of calves from an indigenous population of East African Shorthorn Zebu (crossbred Bos taurus x Bos indicus) in western Kenya. These calves were observed from birth to one year of age as part of the Infectious Disease in East African Livestock (IDEAL) project. Some of the calves were found to be genetic hybrids, resulting from the recent introgression of European cattle breed(s) into the indigenous population. European cattle are known to be less well adapted to the infectious diseases present in East Africa. If death and illness as a result of infectious disease have a genetic basis within the population, we would expect both a negative association of these outcomes with introgression and a positive association with heterozygosity.ResultsIn this indigenous livestock population we observed negative associations between heterozygosity and both death and illness as a result of infectious disease and a positive association between European taurine introgression and episodes of clinical illness.ConclusionWe observe the effects of both inbreeding and outbreeding depression in the East African Shorthorn Zebu, and therefore find evidence of a genetic component to vulnerability to infectious disease. These results indicate that the significant burden of infectious disease in this population could, in principle, be reduced by altered breeding practices.

Using body measurements to estimate live weight of dairy cattle in low-input systems in Senegal

ABSTRACT We investigated the prediction of live weight (LW) of dairy cattle in low- to medium-input systems in Senegal, based on measurements of heart girth (HG) and height at the withers (HW). A total of 459 female dairy cattle, mainly comprising indigenous Zebu and their crosses with Guzerat or Bos Taurus, were weighed (kg), and their HG (cm) and HW (cm) determined. Farmers were asked to provide their own weight estimates for each animal. The single explanatory variable that explained the most variation in LW was HG. The best model to predict LW from HG for the overall data was with an adjusted R2 of 0.85 and a root mean square error of 34.25 kg corresponding to 11.10% of the mean LW. This model predicted the LW of 91–100% of cows and 64–100% of heifers within 20% of their true-live weight, in the weight range of about 100–500 kg. In comparison, farmers could only estimate the LW of about a quarter of their animals within 20% of their true LW. This weight prediction equation, when translated into a weigh band, could provide a simple and reliable method for cattle keepers to estimate the weight of studied cattle breed types.