The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies

Thevenon Sophie, Dayo Guiguigbaza-Kossigan, Sylla Souleymane, Sidibé I., Berthier David, Legros H., Boichard D., Eggen André, Gautier Mathieu. 2007. The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Animal Genetics, 38 (3) : 277-286.

https://doi.org/10.1111/j.1365-2052.2007.01601.x

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Résumé : Several previous studies concluded that linkage disequilibrium (LD) in livestock populations from developed countries originated from the impact of strong selection. Here, we assessed the extent of LD in a cattle population from western Africa that was bred in an extensive farming system. The analyses were performed on 363 individuals in a Bos indicus x Bos taurus population using 42 microsatellite markers on BTA04, BTA07 and BTA13. A high level of expected heterozygosity (0.71), a high mean number of alleles per locus (9.7) and a mild shift in Hardy-Weinberg equilibrium were found. Linkage disequilibrium extended over shorter distances than what has been observed in cattle from developed countries. Effective population size was assessed using two methods; both methods produced large values: 1388 when considering heterozygosity (assuming a mutation rate of 10-3) and 2344 when considering LD on whole linkage groups (assuming a constant population size over generations). However, analysing the decay of LD as a function of marker spacing indicated a decreasing trend in effective population size over generations. This decrease could be explained by increasing selective pressure and/or by an admixture process. Finally, LD extended over small distances, which suggested that whole-genome scans will require a large number of markers. However, association studies using such populations will be effective.

Classification Agris : L10 - Génétique et amélioration des animaux

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

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