The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
SNP discovery via 454 transcriptome sequencing
Open accessAbstract
Summary: A massively parallel pyro‐sequencing technology commercialized by 454 Life Sciences Corporation was used to sequence the transcriptomes of shoot apical meristems isolated from two inbred lines of maize using laser capture microdissection (LCM). A computational pipeline that uses the POLYBAYES polymorphism detection system was adapted for 454 ESTs and used to detect SNPs (single nucleotide polymorphisms) between the two inbred lines. Putative SNPs were computationally identified using 260 000 and 280 000 454 ESTs from the B73 and Mo17 inbred lines, respectively. Over 36 000 putative SNPs were detected within 9980 unique B73 genomic anchor sequences (MAGIs). Stringent post‐processing reduced this number to > 7000 putative SNPs. Over 85% (94/110) of a sample of these putative SNPs were successfully validated by Sanger sequencing. Based on this validation rate, this pilot experiment conservatively identified > 4900 valid SNPs within > 2400 maize genes. These results demonstrate that 454‐based transcriptome sequencing is an excellent method for the high‐throughput acquisition of gene‐associated SNPs.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Furthermore, large collections of ESTs have proven invaluable for functional genomics and molecular marker development [9-13].”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
The International SNP Map Working Group, Laboratories:, C. S. H., Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., National Center for Biotechnology Information:, Marth, G., Sherry, S., et al. (2001) · Nature · doi:10.1038/35057149 · Cited by 2,977
Nested Retrotransposons in the Intergenic Regions of the Maize Genome
SanMiguel, P. J., Tikhonov, A. P., Jin, Y., Motchoulskaia, N., Zakharov, D., Melake‐Berhan, A., Springer, P. S., Edwards, K. J., Lee, M., AVRAMOVA, Z. V., et al. (1996) · Science · doi:10.1126/science.274.5288.765 · Cited by 1,402
Nickerson, D. A. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.14.2745 · Cited by 929
The Effects of Artificial Selection on the Maize Genome
Wright, S., Bi, I. V., Schroeder, S., Yamasaki, M., Doebley, J., McMullen, M. D., & Gaut, B. S. (2005) · Science · doi:10.1126/science.1107891 · Cited by 844
The limits of selection during maize domestication
Wang, R.-L., Stec, A., Hey, J., Lukens, L., & Doebley, J. (1999) · Nature · doi:10.1038/18435 · Cited by 740
Patterns of DNA sequence polymorphism along chromosome 1 of maize ( Zea mays ssp. mays L.)
Tenaillon, M. I., Sawkins, M. C., Long, A. D., Gaut, R. L., Doebley, J., & Gaut, B. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.151244298 · Cited by 698
Arabidopsis Map-Based Cloning in the Post-Genome Era
Jander, G., Norris, S. R., Rounsley, S. D., Bush, D. F., Levin, I. M., & Last, R. L. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.003533 · Cited by 653
Methods for Genotyping Single Nucleotide Polymorphisms
Kwok, P. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.235 · Cited by 582
A general approach to single-nucleotide polymorphism discovery
Marth, G., Korf, I. F., Yandell, M. D., Yeh, R. T., Gu, Z., Zakeri, H., Stitziel, N. O., Hillier, L., Kwok, P., & Gish, W. R. (1999) · Nature Genetics · doi:10.1038/70570 · Cited by 573
Cited by
Sorted by citations
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Status and Prospects of Association Mapping in Plants
Zhu, C., Gore, M. A., Buckler, E. S., & Yu, J. (2008) · The Plant Genome · doi:10.3835/plantgenome2008.02.0089 · Cited by 1,395
Applications of next-generation sequencing technologies in functional genomics
Morozova, O., & Marra, M. A. (2008) · Genomics · doi:10.1016/j.ygeno.2008.07.001 · Cited by 1,222
Zwenger, S. R., & Basu, C. (2010) · Science Publishers eBooks · doi:10.1201/9781439845523-14 · Cited by 951
Next-generation sequencing technologies and their implications for crop genetics and breeding
Varshney, R. K., Nayak, S. N., May, G. D., & Jackson, S. A. (2009) · Trends in biotechnology · doi:10.1016/j.tibtech.2009.05.006 · Cited by 953
Metadata
- Authors
- Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., & Schnable, P. S.
- Affiliations
- Donald Danforth Plant Science Center (US)
- Iowa State University (US)
- Corresponding author
- Schnable, Patrick S.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2007-07-27
- Volume
- 51
- Issue
- 5
- Pages
- 910-918
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- PMC
- PMC2169515
- OpenAlex
- W2114475493
- Cited by
- 405
- References
- 44
- Citations by year
- 2026: 2 · 2025: 3 · 2023: 1 · 2022: 3 · 2021: 16 · 2020: 15 · 2019: 4 · 2018: 11 · 2017: 14 · 2016: 9 · 2015: 27 · 2014: 37 · 2013: 38 · 2012: 60
- FWCI
- 20.25
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The Plant Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0321595, 0527192, 0321711)
- Iowa State University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Keywords
- single nucleotide polymorphisms, SNP discovery, maize, shoot apical meristem, 454 pyrosequencing, expressed sequence tags, laser capture microdissection, B73, Mo17, inbred lines, SNP validation
- MeSH terms
- Base Sequence, Zea mays, Molecular Sequence Data, Software, Sequence Analysis, DNA, Meristem, Genome, Plant, Expressed Sequence Tags, Polymorphism, Single Nucleotide
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
