The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature
Open accessAbstract
Flowering time is a key life-history trait in the plant life cycle. Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions. Here, we describe a study about the genetics of flowering time that differs from previous studies in two important ways: first, we measure flowering time in a more complex and ecologically realistic environment; and, second, we combine the advantages of genome-wide association (GWA) and traditional linkage (QTL) mapping. Our experiments involved phenotyping nearly 20,000 plants over 2 winters under field conditions, including 184 worldwide natural accessions genotyped for 216,509 SNPs and 4,366 RILs derived from 13 independent crosses chosen to maximize genetic and phenotypic diversity. Based on a photothermal time model, the flowering time variation scored in our field experiment was poorly correlated with the flowering time variation previously obtained under greenhouse conditions, reinforcing previous demonstrations of the importance of genotype by environment interactions in A. thaliana and the need to study adaptive variation under natural conditions. The use of 4,366 RILs provides great power for dissecting the genetic architecture of flowering time in A. thaliana under our specific field conditions. We describe more than 60 additive QTLs, all with relatively small to medium effects and organized in 5 major clusters. We show that QTL mapping increases our power to distinguish true from false associations in GWA mapping. QTL mapping also permits the identification of false negatives, that is, causative SNPs that are lost when applying GWA methods that control for population structure. Major genes underpinning flowering time in the greenhouse were not associated with flowering time in this study. Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes.
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Yu, J., Pressoir, G., Briggs, W. H., Vroh Bi, I., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., et al. (2006) · Nature Genetics · doi:10.1038/ng1702 · Cited by 4,133
Efficient Control of Population Structure in Model Organism Association Mapping
Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J., & Eskin, E. (2008) · Genetics · doi:10.1534/genetics.107.080101 · Cited by 1,835
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-citationPlant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage
Dodd, A. N., Salathia, N., Hall, A., Kévei, E., Tóth, R., Nagy, F., Hibberd, J. M., Millar, A. J., & Webb, A. A. R. (2005) · Science · doi:10.1126/science.1115581 · Cited by 1,487
The Genetic Architecture of Maize Flowering Time
Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., et al. (2009) · Science · doi:10.1126/science.1174276 · Cited by 1,457
Genome-wide association studies: theoretical and practical concerns
Wang, W. Y. S., Barratt, B. J., Clayton, D. G., & Todd, J. A. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1522 · Cited by 1,165
Genetic Design and Statistical Power of Nested Association Mapping in Maize
Yu, J., Holland, J. B., McMullen, M. D., & Buckler, E. S. (2008) · Genetics · doi:10.1534/genetics.107.074245 · Cited by 1,094
The effects of human population structure on large genetic association studies
Marchini, J., Cardon, L. R., Phillips, M. S., & Donnelly, P. (2004) · Nature Genetics · doi:10.1038/ng1337 · Cited by 869
Transgressive segregation, adaptation and speciation
Rieseberg, L. H., Archer, M. A., & Wayne, R. K. (1999) · Heredity · doi:10.1038/sj.hdy.6886170 · Cited by 820
Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana
Tian, D., Traw, M. B., Chen, J. Q., Kreitman, M., & Bergelson, J. (2003) · Nature · doi:10.1038/nature01588 · Cited by 788
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Cited by
The genetic basis of flowering responses to seasonal cues
Andrés, F., & Coupland, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3291 · Cited by 1,538
Adaptation genomics: the next generation
Stapley, J., Reger, J., Feulner, P. G. D., Smadja, C., Galindo, J., Ekblom, R., Bennison, C., Ball, A. D., Beckerman, A. P., & Slate, J. (2010) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.09.002 · Cited by 684
Adaptation to Climate Across the Arabidopsis thaliana Genome
Hancock, A. M., Brachi, B., Faure, N., Horton, M. W., Jarymowycz, L. B., Sperone, F. G., Toomajian, C., Roux, F., & Bergelson, J. (2011) · Science · doi:10.1126/science.1209244 · Cited by 665
Self-citationHorton, M. W., Hancock, A. M., Huang, Y. S., Toomajian, C., Atwell, S., Auton, A., Muliyati, N. W., Platt, A., Sperone, F. G., Vilhjálmsson, B. J., et al. (2012) · Nature Genetics · doi:10.1038/ng.1042 · Cited by 543
Self-citationEvolutionary genetics of plant adaptation
Anderson, J. T., Willis, J. H., & Mitchell-Olds, T. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.04.001 · Cited by 434
Metadata
- Authors
- Brachi, B., Faure, N., Horton, M., Flahauw, E., Vazquez, A., Nordborg, M., Bergelson, J., Cuguen, J., & Roux, F.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-05-06
- Volume
- 6
- Issue
- 5
- Pages
- e1000940
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W1988351368
- Cited by
- 511
- References
- 60
- FWCI
- 22.47
- Type
- journal article
- Language
- en
- Open access
- gold
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- Brachi, B., Faure, N., Horton, M., Flahauw, E., Vazquez, A., Nordborg, M., Bergelson, J., Cuguen, J., & Roux, F. (2010). Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1000940
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
