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Originally published as Genetics Published Articles Ahead of Print on August 24, 2007.
Genetics, Vol. 177, 1059-1070, October 2007, Copyright © 2007
doi:10.1534/genetics.107.075804
Genetic and Haplotypic Structure in 14 European and African Cattle Breeds
Mathieu Gautier*,1,
Thomas Faraut
,
Katayoun Moazami-Goudarzi*,
Vincent Navratil
,
Mario Foglio
,
Cécile Grohs*,
Anne Boland,
Jean-Guillaume Garnier,
Didier Boichard**,
G. Mark Lathrop,
Ivo G. Gut and
André Eggen*
* INRA, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France, INRA, UMR444 Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France, CNRS, UMR5558 Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France, CEA, Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and ** INRA, UR337 Station de Génétique Quantitative et Appliquée, F-78350 Jouy-en-Josas, France
1 Corresponding author: Laboratoire de Génétique Biochimique et de Cytogénétique Département de Génétique Animale, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
E-mail: mathieu.gautier{at}jouy.inra.fr
To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances (<10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of <300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds.
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