1. Linkage disequilibrium and past effective population size in native Tunisian cattle
- Author
-
Mekki Boussaha, Slim Ben Jemaa, Emmanuelle Rebours, Sofiane Mnara, Nejia Thamri, Dominique Rocha, Institut National Agronomique de Tunisie (INAT), Ministry of Agriculture, Water Resources and Fishing, Partenaires INRAE, Banque Nationale de Gènes, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), INRA, International Foundation for Science (IFS) [B/5478], and Basic Science Research Program through the National Research Foundation of Korea (NRF) - Ministry of Science, ICT & Future Planning [2013K2A4A1044519]
- Subjects
0106 biological sciences ,0301 basic medicine ,Linkage disequilibrium ,lcsh:QH426-470 ,[SDV]Life Sciences [q-bio] ,Population ,Tunisian cattle ,Runs of Homozygosity ,Biology ,01 natural sciences ,03 medical and health sciences ,Effective population size ,single nucleotide polymorphism ,Genetics ,conservation ,linkage disequilibrium ,effective population size ,Association mapping ,education ,Molecular Biology ,Genetic association ,education.field_of_study ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,SNP genotyping ,lcsh:Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,030104 developmental biology ,Animal Genetics ,Inbreeding ,010606 plant biology & botany ,Demography - Abstract
International audience; 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 r(2) 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.
- Published
- 2019