The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Open accessAbstract
Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F(2) individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.
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Cites
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., & Kingsley, D. M. (2005) · Science · doi:10.1126/science.1107239 · Cited by 1,448
The genetic architecture of parallel armor plate reduction in threespine sticklebacks.
Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., & Kingsley, D. M. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020109 · Cited by 390
Cited by
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2727 · Cited by 1,470
Cruickshank, T. E., & Hahn, M. W. (2014) · Molecular Ecology · doi:10.1111/mec.12796 · Cited by 1,061
Genotyping‐by‐Sequencing for Plant Breeding and Genetics
Poland, J. A., & Rife, T. W. (2012) · The Plant Genome · doi:10.3835/plantgenome2012.05.0005 · Cited by 892
Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016) · The American Naturalist · doi:10.1086/688018 · Cited by 876
Accelerating crop genetic gains with genomic selection
Voss-Fels, K. P., Cooper, M., & Hayes, B. J. (2019) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3270-8 · Cited by 381
Metadata
- Authors
- Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-10-13
- Volume
- 3
- Issue
- 10
- Pages
- e3376
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2169773990
- Cited by
- 3,356
- References
- 2
- FWCI
- 21.80
- Type
- journal article
- Language
- en
- Open access
- gold
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- Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A. (2008). Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE. https://doi.org/10.1371/journal.pone.0003376
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