title: Genetic and haplotypic structure in 14 European and African cattle breeds.
abstract: 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.
authors.affiliation: INRA, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France. mathieu.gautier@jouy.inra.fr
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gautier
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.forename: Katayoun
authors.initials: K
authors.lastname: Moazami-Goudarzi
authors.forename: Vincent
authors.initials: V
authors.lastname: Navratil
authors.forename: Mario
authors.initials: M
authors.lastname: Foglio
authors.forename: Cécile
authors.initials: C
authors.lastname: Grohs
authors.forename: Anne
authors.initials: A
authors.lastname: Boland
authors.forename: Jean-Guillaume
authors.initials: JG
authors.lastname: Garnier
authors.forename: Didier
authors.initials: D
authors.lastname: Boichard
authors.forename: G Mark
authors.initials: GM
authors.lastname: Lathrop
authors.forename: Ivo G
authors.initials: IG
authors.lastname: Gut
authors.forename: André
authors.initials: A
authors.lastname: Eggen
mesh_terms: D000349:Africa; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology; D005060:Europe; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide