Genetic and Haplotypic Structure in 14 European and African Cattle Breeds
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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.
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The isolation of strains and breeds in mouse, rat, cow, and dog results in much longer block lengths than are found in humans.
“The isolation of strains and breeds in these species results in much longer block lengths than are found in humans.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [23]
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- 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
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-10-01
- Volume
- 177
- Issue
- 2
- Pages
- 1059-1070
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC2034613
- 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
- green
- www.ncbi.nlm.nih.gov
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- 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
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