title: The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies.
abstract: 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.
authors: UMR Trypanosomes, CIRAD, Montpellier, F-34398 France. sophie.thevenon@cirad.fr
authors: S
authors: S
authors: Thévenon
authors: G K
authors: GK
authors: Dayo
authors: S
authors: S
authors: Sylla
authors: I
authors: I
authors: Sidibe
authors: D
authors: D
authors: Berthier
authors: H
authors: H
authors: Legros
authors: D
authors: D
authors: Boichard
authors: A
authors: A
authors: Eggen
authors: M
authors: M
authors: Gautier
mesh_terms: D000354:Africa, Western; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005787:Gene Frequency; D006580:Genetic Carrier Screening; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats / Q000235:genetics; D011157:Population Dynamics