Abstract
To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D’, decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with the absence of strong selective pressure within the Tunisian population and suggests that, in order to be effective, any potential genome-wide association mapping studies will need to use chips with higher marker density. An analysis of effective population size (Ne) based on LD data showed a decline in past Ne, with a sudden drop starting about eight generations ago. This finding, combined with the high levels of recent inbreeding revealed by runs of homozygosity (ROH) analysis, indicate that this population is endangered and may be in urgent need of a conservation plan that includes a well-designed genetic management program.
Highlights
Native Tunisian cattle are small animals that are well adapted to the harsh environmental conditions that characterize their rearing area, such as reduced food resources, elevated temperatures during the hot season, and an abundance of parasites and pathogens
A total of 3,313 runs of homozygosity (ROH) were identified in the 87 Tunisian cattle individuals
5.4%, on average, of the entire genome of Tunisian cattle was covered by ROH segments
Summary
Native Tunisian cattle are small animals that are well adapted to the harsh environmental conditions that characterize their rearing area, such as reduced food resources, elevated temperatures during the hot season, and an abundance of parasites and pathogens They are currently endangered by the result of extensive crossbreeding with imported breeds (Djemali and Kayouli, 2003). The availability of highthroughput genotyping technologies makes it possible to use genetic markers to map genes that are responsible for economically important traits. Such information can be incorporated into breeding programs. To get an overview of population inbreeding, we present a genome-wide characterization of runs of homozygosity (ROH) in the Tunisian individuals
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