Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
Open accessAbstract
Summary: Oilseed rape (Brassica napus) was selected as an example of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7. A methodology and computational tools were developed to exploit, as a reference sequence, a publicly available set of approximately 94 000 Brassica species unigenes. Sequences transcribed in the leaves of juvenile plants were aligned to approximately 26 Mb of the reference sequences. The aligned sequences enabled the detection of 23 330–41 593 putative single nucleotide polymorphisms (SNPs) between the cultivars, depending on the read depth stringency applied. The majority of the detected polymorphisms (87.5–91.2%) were of a type indicative of transcription from homoeologous genes from the two parental genomes within oilseed rape, and are termed here ‘hemi‐SNPs’. The overall estimated polymorphism rate (~0.047%–0.084%) is consistent with that previously observed between the cultivars analysed. To demonstrate the heritability of SNPs and to assess their suitability for applications such as linkage map construction and association genetics, approximately nine million ESTs were generated, using the Solexa system, from each of four lines of a doubled haploid mapping population derived from a cross between Tapidor and Ningyou 7. Computational tools were developed to score the alleles present in these lines for each of the potential SNPs identified between their parents. For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers.
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
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?
Over the last two years, Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model and non-model organisms.
“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [12]
The Solexa sequencing and validation sections show successful Illumina transcriptome sequencing in Brassica napus, supporting its use as an example involving a non-model organism. But the Alignment of ESTs to reference sequences and SNP calling using MAQ sections say the reads were mapped to previously assembled Brassica unigenes; the paper does not demonstrate de novo assembly of the Illumina reads. Page numbers are unavailable in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredLarge collections of ESTs have proven invaluable for functional genomics and molecular marker development.
“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.
Cites
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301 · see citing works
Nuclear DNA content of some important plant species
Arumuganathan, K., & Earle, E. D. (1991) · Plant Molecular Biology Reporter · doi:10.1007/bf02672069 · Cited by 3,271 · see citing works
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638 · see citing works
Structure of Linkage Disequilibrium in Plants
Flint-Garcia, S. A., Thornsberry, J. M., & Buckler, E. S. (2003) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.54.031902.134907 · Cited by 1,700 · see citing works
Genome evolution in polyploids
Wendel, J. F. (2000) · Plant Molecular Biology · doi:10.1023/a:1006392424384 · Cited by 1,622 · see citing works
Association study designs for complex diseases
Cardon, L. R., & Bell, J. I. (2001) · Nature Reviews Genetics · doi:10.1038/35052543 · Cited by 1,380 · see citing works
Chromosome triplication found across the tribe BrassiceaePreprint
Lysák, M. A., Koch, М. A., Pečinka, A., & Schubert, I. A. (2005) · Genome Research · doi:10.1101/gr.3531105 · Cited by 670 · see citing works
Leitch, I. J., & Bennett, M. D. (1997) · Trends in Plant Science · doi:10.1016/s1360-1385(97)01154-0 · Cited by 620 · see citing works
The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes
Schranz, M. E., Lysak, M. A., & Mitchell-Olds, T. (2006) · Trends in Plant Science · doi:10.1016/j.tplants.2006.09.002 · Cited by 575 · see citing works
Town, C. D., Cheung, F., Maiti, R., Crabtree, J., Haas, B. J., Wortman, J. R., Hine, E., Althoff, R., Arbogast, T. S., Tallon, L. J., et al. (2006) · The Plant Cell · doi:10.1105/tpc.106.041665 · Cited by 422 · see citing works
Self-citationWhole-genome sequencing and variant discovery in C. elegans
Hillier, L. W., Marth, G., Quinlan, A. R., Dooling, D. J., Fewell, G. A., Barnett, D. W., Fox, P. M., Glasscock, J. I., Hickenbotham, M. T., Huang, W., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1179 · Cited by 405 · see citing works
SNP discovery via 454 transcriptome sequencing
Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., & Schnable, P. S. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03193.x · Cited by 405 · see citing works
Yang, Y.-W., Lai, K.-N., Tai, P.-Y., & Li, W. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006502 · Cited by 392 · see citing works
Comparative Genome Mapping in Brassica
Lagercrantz, U., & Lydiate, D. J. (1996) · Genetics · doi:10.1093/genetics/144.4.1903 · Cited by 378 · see citing works
Identification of the A and C genomes of amphidiploidBrassica napus(oilseed rape)
Parkin, I. A. P., Sharpe, A., Keith, D. J., et al. (1995) · Genome · doi:10.1139/g95-149 · Cited by 365 · see citing works
Warwick, S. I., & Black, L. D. (1991) · Theoretical and Applied Genetics · doi:10.1007/bf00231281 · Cited by 308 · see citing works
Qiu, D., Morgan, C., Shi, J., et al. (2006) · Theoretical and Applied Genetics · doi:10.1007/s00122-006-0411-2 · Cited by 297 · see citing works
Goldberg, S. M. D., Johnson, J. H., Busam, D., Feldblyum, T. V., Ferriera, S., Friedman, R., Halpern, A. L., Khouri, H. M., Kravitz, S. A., Lauro, F. M., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604351103 · Cited by 285 · see citing works
Yang, T., Kim, J. S., Kwon, S.-J., Lim, K., Choi, B., Kim, J., Jin, M., Park, J. Y., Lim, M.-H., Kim, H.-I., et al. (2006) · The Plant Cell · doi:10.1105/tpc.105.040535 · Cited by 243 · see citing works
Self-citationConservation of the microstructure of genome segments in Brassica napus and its diploid relatives
Rana, D., van den Boogaart, T., O’Neill, C. M., et al. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02244.x · Cited by 234 · see citing works
Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
Whitelaw, C. A., Barbazuk, W. B., Pertea, G. M., Chan, A. P.-Y., Cheung, F., Lee, Y. R., Zheng, L., van Heeringen, S. J., Karamycheva, S. A., Bennetzen, J. L., et al. (2003) · Science · doi:10.1126/science.1090047 · Cited by 208 · see citing works
O’Neill, C. M., & Bancroft, I. (2000) · The Plant Journal · doi:10.1046/j.1365-313x.2000.00781.x · Cited by 206 · see citing works
Self-citationInaba, R., & Nishio, T. (2002) · Theoretical and Applied Genetics · doi:10.1007/s00122-002-0968-3 · Cited by 121 · see citing works
Park, J. Y., Koo, D., Hong, C. P., et al. (2005) · Molecular Genetics and Genomics · doi:10.1007/s00438-005-0041-4 · Cited by 87 · see citing works
Fu, Y., Emrich, S., Guo, L., Wen, T., Ashlock, D., Aluru, S., & Schnable, P. S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503394102 · Cited by 68 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., & Li, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-726 · Cited by 433 · see citing works
- Authors
- Trick, M., Long, Y., Meng, J., & Bancroft, I.
- Affiliations
- John Innes Centre (GB)
- Huazhong Agricultural University (CN)
- Corresponding author
- Bancroft, Ian
- Venue
- Plant Biotechnology Journal
- Publisher
- Wiley
- Published
- 2009-04-13
- Volume
- 7
- Issue
- 4
- Pages
- 334-346
- ISSN
- 1467-7644 (ISSN-L)
- 1467-7652
- OpenAlex
- W2086338036
- Cited by
- 338
- References
- 26
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 6 · 2023: 6 · 2022: 8 · 2021: 10 · 2020: 20 · 2019: 11 · 2018: 16 · 2017: 22 · 2016: 27 · 2015: 34 · 2014: 44 · 2013: 31 · 2012: 44
- FWCI
- 18.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- onlinelibrary.wiley.com/termsAndConditions#vor (vor)
- Locations
- Plant Biotechnology Journal (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/E017363, BB/E017363/1)
- 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 › Chromosomal and Genetic Variations
- Keywords
- single nucleotide polymorphisms, Brassica napus, oilseed rape, polyploidy, homoeologous genes, expressed sequence tags, Illumina sequencing, SNP discovery, doubled haploid mapping population, allele segregation, linkage mapping, genetic association studies, polymorphism rate
- MeSH terms
- Alleles, Chromosome Mapping, Polyploidy, Software, Sequence Alignment, Sequence Analysis, DNA, Plant Leaves, Genome, Plant, RNA, Plant, Computational Biology, Expressed Sequence Tags, Polymorphism, Single Nucleotide, Gene Expression Profiling, Brassica napus
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
