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Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

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Mathieu Gautier,
Mathieu Gautier
INRA
, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France
Corresponding author: Laboratoire de Génétique Biochimique et de Cytogénétique Département de Génétique Animale, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France. E-mail:[email protected]
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Thomas Faraut,
Thomas Faraut
INRA
, UMR444 Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France
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Katayoun Moazami-Goudarzi,
Katayoun Moazami-Goudarzi
INRA
, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France
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Vincent Navratil,
Vincent Navratil
CNRS
, UMR5558 Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
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Mario Foglio,
Mario Foglio
CEA
, Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and
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Cécile Grohs,
Cécile Grohs
INRA
, UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France
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Anne Boland,
Anne Boland
CEA
, Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and
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Jean-Guillaume Garnier,
Jean-Guillaume Garnier
CEA
, Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and
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Didier Boichard,
Didier Boichard
INRA
, UR337 Station de Génétique Quantitative et Appliquée, F-78350 Jouy-en-Josas, France
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G Mark Lathrop,
G Mark Lathrop
CEA
, Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and
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Genetics, Volume 177, Issue 2, 1 October 2007, Pages 1059–1070,https://doi.org/10.1534/genetics.107.075804
Published:
01 October 2007
Article history
Received:
10 May 2007
Accepted:
16 August 2007
Published:
01 October 2007
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Abstract

To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detectedin 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 thein 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.

© Genetics 2007
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