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doi:10.1534/genetics.107.075804
A more recent version of this article appeared on October 1, 2007.
REGULAR RESEARCH PAPERS |
Genetic and haplotypic structure in 14 European and African cattle breeds
Mathieu Gautier 1*, Thomas Faraut 1, Katayoun Moazami-Goudarzi 1, Vincent Navratil 2, Mario Foglio 3, Cécile Grohs 1, Anne Boland 3, Jean-Guillaume Garnier 3, Didier Boichard 1, Mark Lathrop 3, Ivo Gut 3 and André Eggen 1
1 INRA
2 CNRS
3 INSERM
* To whom correspondence should be addressed. E-mail: mathieu.gautier{at}jouy.inra.fr.
Submitted on May 10, 2007
Revised on July 27, 2007
Accepted on 16 August 2007
To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localised 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 (less than 10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kb. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of less than 300000 SNPs, which should be efficient for mapping purposes in most cattle breeds.
Key Words: BTA03, SNP, cattle, haplotype blocks, linkage disequilibrium
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