The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
Open accessAbstract
The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via "SNP chip" microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.
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Cites
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Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
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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
Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change
Lopes, M. S., El-Basyoni, I., Baenziger, P. S., Singh, S., Royo, C., Ozbek, K., Aktas, H., Ozer, E., Ozdemir, F., Manickavelu, A., et al. (2015) · Journal of Experimental Botany · doi:10.1093/jxb/erv122 · Cited by 535
The genetic basis of parental care evolution in monogamous mice
Bendesky, A., Kwon, Y.-M., Lassance, J.-M., Lewarch, C. L., Yao, S., Peterson, B. K., He, M. X., Dulac, C., & Hoekstra, H. E. (2017) · Nature · doi:10.1038/nature22074 · Cited by 268
Self-citationThe Value of Reference Genomes in the Conservation of Threatened Species
Brandies, P., Peel, E., Hogg, C. J., & Belov, K. (2019) · Genes · doi:10.3390/genes10110846 · Cited by 158
Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution
Todd, R. T., Forche, A., & Selmecki, A. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.funk-0051-2016 · Cited by 121
Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species
Khan, S., Nabi, G., Ullah, M. W., Yousaf, M., Manan, S., Siddique, R., & Hou, H. (2016) · International Journal of Genomics · doi:10.1155/2016/3460416 · Cited by 63
Anderson, M. Z., Saha, A., Haseeb, A., & Bennett, R. J. (2017) · Microbiology · doi:10.1099/mic.0.000478 · Cited by 53
Bangs, M. R., Douglas, M. R., Mussmann, S. M., & Douglas, M. E. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1197-y · Cited by 32
Chang, J.-T., Chao, C.-T., Nakamura, K., Liu, H.-L., Luo, M.-X., & Liao, P.-C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.824158 · Cited by 20
McCluskey, B. M., Uji, S., Mancusi, J. L., Postlethwait, J. H., & Parichy, D. M. (2021) · PLOS Genetics · doi:10.1371/journal.pgen.1009364 · Cited by 19
Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses
Goulet‐Scott, B. E., Garner, A. G., & Hopkins, R. (2021) · Evolution · doi:10.1111/evo.14279 · Cited by 14
Budding off: bringing functional genomics to Candida albicans
Anderson, M. Z., & Bennett, R. J. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv035 · Cited by 11
Metadata
- Authors
- Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-05-31
- Volume
- 7
- Issue
- 5
- Pages
- e37135
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2161184021
- Cited by
- 3,646
- References
- 6
- FWCI
- 46.95
- Type
- journal article
- Language
- en
- Open access
- gold
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