Cited by 159Genetic and phenotypic traits in livestockGenetic Mapping and Diversity in Plants and AnimalsGenetic Associations and Epidemiology

Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

Open access
Gautier, Mathieu, Faraut, Thomas, Moazami-Goudarzi, Katayoun, Navratil, Vincent, Foglio, Mario, Grohs, Cécile, Boland, Anne, Garnier, Jean-Guillaume +4 more·2007·Genetics

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.

Integrity signals

Registry

Crossref · 10.1534/genetics.107.075804

Cites

52 of 52 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Cites

Flagged first, then by citations

1 of the 53 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Authors
Gautier, M., Faraut, T., Moazami-Goudarzi, K., Navratil, V., Foglio, M., Grohs, C., Boland, A., Garnier, J.-G., Boichard, D., Lathrop, G. M., Gut, I. G., & Eggen, A.
Affiliations
  • Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
  • Laboratoire de Génétique Cellulaire (FR)
  • INRA , UR339 Laboratoire de Génétique Biochimique et Cytogénétique, F-78350 Jouy-en-Josas, France
  • Centre National de la Recherche Scientifique (FR)
  • Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
  • CEA , Institut de Génomique, Centre National de Génotypage, F-91057 Evry, France and
Corresponding author
Gautier, Mathieu
Venue
Genetics
Published
2007-10-01
Volume
177
Issue
2
Pages
1059-1070
ISSN
  • 0016-6731 (ISSN-L)
  • 1943-2631
OpenAlex
W2099232387
Cited by
158
References
53
Citations by year
2026: 4 · 2025: 5 · 2024: 4 · 2023: 9 · 2022: 5 · 2021: 3 · 2020: 8 · 2019: 7 · 2018: 4 · 2017: 3 · 2016: 12 · 2015: 11 · 2014: 13 · 2013: 11 · 2012: 12
FWCI
5.91
Type
journal article
Language
en
Open access
Locations
  • Genetics (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
cattle breeds, linkage disequilibrium, haplotype structure, haplotype blocks, single nucleotide polymorphisms, genetic structure, African cattle breeds, European cattle breeds, SNP genotyping
MeSH terms
Africa, Animals, Breeding, Cattle, Chromosome Mapping, Europe, Genotype, Haplotypes, Linkage Disequilibrium, Microsatellite Repeats, Computational Biology, Polymorphism, Single Nucleotide

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review