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The Pattern of Polymorphism in Arabidopsis thaliana
Open accessAbstract
We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
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Golub, G. (2012) · doi:10.56021/9781421407944 · Cited by 34,505
The hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (1974) · Genetical Research · doi:10.1017/s0016672300014634 · Cited by 3,415
Linkage disequilibrium in finite populations
Hill, W. G., & Robertson, A. (1968) · Theoretical and Applied Genetics · doi:10.1007/bf01245622 · Cited by 2,035
Hudson, R. R., & Kaplan, N. L. (1985) · Genetics · doi:10.1093/genetics/111.1.147 · Cited by 1,555
Cited by
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., et al. (2010) · Nature · doi:10.1038/nature08800 · Cited by 1,780
Self-citationLinkage disequilibrium--understanding the evolutionary past and mapping the medical future.
Slatkin, M. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2361 · Cited by 1,614
Determinants of genetic diversity
Ellegren, H., & Galtier, N. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.58 · Cited by 874
Association mapping: critical considerations shift from genotyping to experimental design
Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., & Buckler, E. S. (2009) · The Plant Cell · doi:10.1105/tpc.109.068437 · Cited by 857
Natural selection on protein-coding genes in the human genome
Bustamante, C. D., Fledel-Alon, A., Williamson, S., Nielsen, R., Todd Hubisz, M., Glanowski, S., Tanenbaum, D. M., White, T. J., Sninsky, J. J., Hernandez, R. D., et al. (2005) · Nature · doi:10.1038/nature04240 · Cited by 788
Metadata
- Authors
- Nordborg, M., Hu, T. T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N. A., Shah, C., Wall, J. D., Wang, J., Zhao, K., Kalbfleisch, T., Schulz, V., Kreitman, M., & Bergelson, J.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2005-05-24
- Volume
- 3
- Issue
- 7
- Pages
- e196
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2008147924
- Cited by
- 968
- References
- 4
- FWCI
- 40.00
- Type
- journal article
- Language
- en
- Open access
- gold
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- Nordborg, M., Hu, T. T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N. A., Shah, C., Wall, J. D., Wang, J., . . . Bergelson, J. (2005). The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biology. https://doi.org/10.1371/journal.pbio.0030196
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