The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Runs of homozygosity and population history in cattle
Open accessAbstract
Background: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring. The extent and frequency of ROHs may inform on the ancestry of an individual and its population. Here we use high density (n = 777,962) bi-allelic SNPs in a range of cattle breed samples to correlate ROH with the pedigree-based inbreeding coefficients and to validate subsequent analyses using 54,001 SNP genotypes. This study provides a first testing of the inference drawn from ROH through comparison with estimates of inbreeding from calculations based on the detailed pedigree data available for several breeds. Results: All animals genotyped on the HD panel displayed at least one ROH that was between 1–5 Mb in length with certain regions of the genome more likely to be involved in a ROH than others. Strong correlations (r = 0.75, p < 0.0001) existed between the pedigree-based inbreeding coefficient and a statistic based on sum of ROH of length > 0.5 KB and suggests that in the absence of an animal’s pedigree data, the extent of a genome under ROH may be used to infer aspects of recent population history even from relatively few samples. Conclusions: Our findings suggest that ROH are frequent across all breeds but differing patterns of ROH length and burden illustrate variations in breed origins and recent management.
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Cites
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds
The Bovine HapMap Consortium, Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., et al. (2009) · Science · doi:10.1126/science.1167936 · Cited by 868
Self-citationEvidence for Two Independent Domestications of Cattle
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812
Self-citationRecent human effective population size estimated from linkage disequilibrium
Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D. L., Clarke, G. M., Goddard, M. E., & Visscher, P. M. (2007) · Genome Research · doi:10.1101/gr.6023607 · Cited by 438
Hanotte, O., Tawah, C. L., Bradley, D. G., Okomo, M., Verjee, Y., Ochieng, J., & Rege, J. E. O. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.00858.x · Cited by 257
Self-citationGenetic and Haplotypic Structure in 14 European and African Cattle Breeds
Gautier, M., Faraut, T., Moazami-Goudarzi, K., Navratil, V., Foglio, M., Grohs, C., Boland, A., Garnier, J.-G., Boichard, D., Lathrop, G. M., et al. (2007) · Genetics · doi:10.1534/genetics.107.075804 · Cited by 158 · cited 1×
“The domestication process itself featured a limited sampling from the wild with a more recent bottleneck detectable 50–100 generations ago, presumably corresponding to breed formation [16].”
Background
Cited by
Inbreeding and runs of homozygosity: A possible solution to an old problem
Curik, I., Ferenčaković, M., & Sölkner, J. (2014) · Livestock Science · doi:10.1016/j.livsci.2014.05.034 · Cited by 419
Runs of homozygosity: current knowledge and applications in livestock
Peripolli, E., Munari, D. P., Silva, M. V. G. B., Lima, A. L. F., Irgang, R., & Baldi, F. (2017) · Animal Genetics · doi:10.1111/age.12526 · Cited by 403
Meyermans, R., Gorssen, W., Buys, N., & Janssens, S. (2020) · BMC Genomics · doi:10.1186/s12864-020-6463-x · Cited by 367
Purfield, D. C., McParland, S., Wall, E., & Berry, D. P. (2017) · PLOS ONE · doi:10.1371/journal.pone.0176780 · Cited by 308
Self-citationPryce, J. E., Haile-Mariam, M., Goddard, M. E., & Hayes, B. J. (2014) · Genetics Selection Evolution · doi:10.1186/s12711-014-0071-7 · Cited by 287
Metadata
- Authors
- Purfield, D. C., Berry, D. P., McParland, S., & Bradley, D. G.
- Venue
- BMC Genetics
- Published
- 2012-08-14
- Volume
- 13
- Issue
- 1
- Pages
- 70-70
- ISSN
- 1471-2156 (ISSN-L)
- OpenAlex
- W2138863022
- Cited by
- 653
- References
- 5
- FWCI
- 7.97
- Type
- journal article
- Language
- en
- Open access
- gold
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