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Previous studies have shown that host genetic heterogeneity in the response to infectious challenge can affect the emergence risk and the severity of diseases transmitted through direct contact between individuals. However, there is substantial uncertainty about the degree and direction of influence owing to different definitions of genetic variation, most of which are not in line with the current understanding of the genetic architecture of disease traits. Also, the relevance of previous results for diseases transmitted through environmental sources is unclear. In this article a compartmental genetic-epidemiological model was developed to quantify the impact of host genetic diversity on epidemiological characteristics of diseases transmitted through a contaminated environment. The model was parameterized for footrot in sheep. Genetic variation was defined through continuous distributions with varying shape and degree of dispersion for different disease traits. The model predicts a strong impact of genetic heterogeneity on the disease risk and its progression and severity, as well as on observable host phenotypes, when dispersion in key epidemiological parameters is high. The impact of host variation depends on the disease trait for which variation occurs and on environmental conditions affecting pathogen survival. In particular, compared to homogeneous populations with the same average susceptibility, disease risk and severity are substantially higher in populations containing a large proportion of highly susceptible individuals, and the differences are strongest when environmental contamination is low. The implications of our results for the recording and analysis of disease data and for predicting response to selection are discussed. © 2011 by the Genetics Society of America.

In 2002, Parties to the UN Convention on Biological Diversity made a commitment to "achieve by 2010 a significant reduction of the current rate of biodiversity loss at the global, regional and national level". In order to assess progress towards the 2010 target a limited number of indicators of biodiversity need to be developed using existing data. The objectives of this study were i) to produce an indicator of genetic diversity for livestock species; and ii) to evaluate the proposed indicator in UK sheep and cattle. The indicator proposed is the species average effective population size (Ne) for the lower tail of the distribution of Ne across breeds within the species. It is sensitive to i) genetic variation within breeds, as it is based on the Ne of individual breeds, and ii) what is happening to breeds most at risk of disappearing. A total of 31 sheep and 20 cattle UK breed societies provided the information required for estimating Ne. This represents 53% of sheep and 58% of cattle breeds native to the UK. For breeds with pedigrees available, Ne was estimated from rates of change in inbreeding. For breeds with no pedigree information, Ne was estimated from predictive equations assuming mass selection on a trait with a heritability of 0.4. For each species, the indicator was calculated by i) estimating Ne for each breed; ii) calculating the distribution of Ne; iii) finding the average Ne for the lower 20% tail of the distribution. In step iii), 20% was chosen because, given the number of breeds with available information, it provides a good compromise between giving high weight to the breeds most at risk, without being too sensitive to events surrounding a single breed. For sheep, the indicator values were 36 and 41 animals for years 2001 and 2007, respectively. Equivalent values for cattle were 26 and 34. Bootstrapping was used to assess if these changes over time would have been observed with data from all native breeds. There was no evidence that the small incr

Gene banks are usually used for storing general genetic variability of endangered living populations but can be also used for storing alleles of a particular locus that are being eradicated through artificial selection programmes. In such scenarios gene banks would allow future re-introduction of one or more of the alleles being eradicated (and the associated diversity) into living populations. Frequencies within the bank for the locus of interest should have predetermined target values. In this study, an algorithm is derived to obtain the optimal contributions of all candidate donors to achieve the target frequencies of the removed alleles in the bank while maintaining at the same time genetic variability in other loci unlinked to those targeted in the eradication programme. The efficiency of the algorithm is tested using the case of gene banks storing prion protein alleles currently disfavoured in scrapie eradication programmes (i.e.;the AHQ, ARH, ARQ and VRQ alleles). Results showed that the algorithm was able to find the combinations of candidate contributions fulfilling different objectives regarding target frequencies and restrictions on coancestry. The most important factors influencing the optimal contributions were the allelic frequencies and the levels of diversity (coancestry) of the living population. Heterozygotes were favoured over homozygous individuals as, for a given number of animals contributing to the bank, the use of heterozygotes leads to lower levels of coancestry. Notwithstanding, almost all donors were sampled when restrictions on the global genetic diversity to be stored were severe.