Document Detail


Genetic and haplotypic structure in 14 European and African cattle breeds.
MedLine Citation:
PMID:  17720924     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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:
Mathieu Gautier; Thomas Faraut; Katayoun Moazami-Goudarzi; Vincent Navratil; Mario Foglio; Cécile Grohs; Anne Boland; Jean-Guillaume Garnier; Didier Boichard; G Mark Lathrop; Ivo G Gut; André Eggen
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Publication Detail:
Type:  Journal Article     Date:  2007-08-24
Journal Detail:
Title:  Genetics     Volume:  177     ISSN:  0016-6731     ISO Abbreviation:  Genetics     Publication Date:  2007 Oct 
Date Detail:
Created Date:  2007-10-23     Completed Date:  2008-04-30     Revised Date:  2010-09-15    
Medline Journal Info:
Nlm Unique ID:  0374636     Medline TA:  Genetics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1059-70     Citation Subset:  IM    
Affiliation:
INRA, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France. mathieu.gautier@jouy.inra.fr
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MeSH Terms
Descriptor/Qualifier:
Africa
Animals
Breeding
Cattle / genetics*
Chromosome Mapping / methods*
Computational Biology
Europe
Genotype
Haplotypes*
Linkage Disequilibrium*
Microsatellite Repeats
Polymorphism, Single Nucleotide*
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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