Cited by 405Genetic Mapping and Diversity in Plants and AnimalsGenomics and Phylogenetic StudiesPlant Genetic and Mutation Studies

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 access

Barbazuk, W. Brad, Emrich, Scott J., Chen, Hsin D., Li, Li, Schnable, Patrick S.·2007·The Plant Journal

DOI 10.1111/j.1365-313x.2007.03193.xPMC PMC2169515

Open this paper in CoChat — free account Open PDF

Abstract

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.

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

Crossref · 10.1111/j.1365-313x.2007.03193.x

Cites

44 of 44 references verified0 citation errors · 0 not checkable

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
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

Show all 44 references

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
Transcriptional Profiling
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
Genome-wide mapping of alternative splicing in Arabidopsis thalianaPreprint
Filichkin, S. A., Priest, H. D., Givan, S. A., Shen, R., Bryant, D. W., Fox, S. E., Wong, W., & Mockler, T. C. (2009) · Genome Research · doi:10.1101/gr.093302.109 · Cited by 917
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
Tassell, C. P. V., Smith, T. P. L., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C., Haudenschild, C. D., Moore, S. S., Warren, W. C., & Sonstegard, T. S. (2008) · Nature Methods · doi:10.1038/nmeth.1185 · Cited by 648
Metabolomics-assisted breeding: a viable option for crop improvement?
Fernie, A. R., & Schauer, N. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.10.010 · Cited by 550
Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C., Jia, Y., Wu, W., Richmond, T., Kitzman, J. O., Rosenbaum, H., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000734 · Cited by 557
Self-citation
Transcriptome analysis using next-generation sequencing
Mutz, K.-O., Heilkenbrinker, A., Lönne, M., Walter, J., & Stahl, F. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.09.004 · Cited by 547
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03666.x · Cited by 714
RNA-seq: from technology to biology
Marguerat, S., & Bähler, J. (2009) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-009-0180-6 · Cited by 566
The development and impact of 454 sequencing
Rothberg, J. M., & Leamon, J. H. (2008) · Nature Biotechnology · doi:10.1038/nbt1485 · Cited by 561
SNP Markers and Their Impact on Plant Breeding
Mammadov, J., Aggarwal, R., Buyyarapu, R., & Kumpatla, S. P. (2012) · International Journal of Plant Genomics · doi:10.1155/2012/728398 · Cited by 559
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
Novaes, E., Drost, D. R., Farmerie, W. G., Pappas, G. J., Grattapaglia, D., Sederoff, R. R., & Kirst, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-312 · Cited by 493
Genomic Selection in Plant Breeding
Lorenz, A. J., Chao, S., Asoro, F. G., Heffner, E. L., Hayashi, T., Iwata, H., Smith, K. P., Sorrells, M. E., & Jannink, J. (2011) · Advances in agronomy · doi:10.1016/b978-0-12-385531-2.00002-5 · Cited by 487
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479
SNP identification in crop plants
Ganal, M. W., Altmann, T., & Röder, M. S. (2009) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.12.009 · Cited by 473
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)
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
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-180 · Cited by 446
Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers
Wei, W., Qi, X., Wang, L., Zhang, Y., Hua, W., Li, D., Lv, H., & Zhang, X. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-451 · Cited by 426
Genomic Selection in Plant Breeding
Newell, M. A., & Jannink, J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0446-4_10 · Cited by 413
Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)
Liu, S., Yeh, C., Tang, H. M., Nettleton, D. S., & Schnable, P. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036406 · Cited by 379
Self-citation
A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds
Kijas, J., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. F., McGrath, A., Wilson, P. J., Ingersoll, R., McCulloch, R. J., McWilliam, S. M., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004668 · Cited by 388
Plant genome sequencing: applications for crop improvement
Edwards, D., & Batley, J. (2009) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2009.00459.x · Cited by 364
Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
Trick, M., Long, Y., Meng, J., & Bancroft, I. (2009) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2008.00396.x · Cited by 338
Optimization of de novo transcriptome assembly from next-generation sequencing data
Surget-Groba, Y., & Montoya-Burgos, J. I. (2010) · Genome Research · doi:10.1101/gr.103846.109 · Cited by 339
Genotyping-by-Sequencing in Plants
Deschamps, S., Llaca, V., & May, G. D. (2012) · Biology · doi:10.3390/biology1030460 · Cited by 348
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
Sim, S., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Deynze, A. V., Hamilton, J. P., Buell, C. R., Causse, M., Wijeratne, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040563 · Cited by 316
SNP Discovery through Next-Generation Sequencing and Its Applications
Kumar, S. D., Banks, T. W., & Cloutier, S. (2012) · International Journal of Plant Genomics · doi:10.1155/2012/831460 · Cited by 337
Monitoring adaptive genetic responses to environmental change
Hansen, M. M., Olivieri, I., Waller, D. M., Nielsen, E. E., & The GeM Working Group (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05463.x · Cited by 307
Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay
Akhunov, E., Nicolet, C. M., & Dvořák, J. (2009) · Theoretical and Applied Genetics · doi:10.1007/s00122-009-1059-5 · Cited by 301
Accessing complex crop genomes with next-generation sequencing
Edwards, D., Batley, J., & Snowdon, R. J. (2012) · Theoretical and Applied Genetics · doi:10.1007/s00122-012-1964-x · Cited by 292
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence
Hyten, D. L., Cannon, S. B., Song, Q., Weeks, N. T., Fickus, E., Shoemaker, R. C., Specht, J. E., Farmer, A. D., May, G. D., & Cregan, P. B. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-38 · Cited by 281
Application of Genomic Tools in Plant Breeding
Pérez-de-Castro, A. M., Vilanova, S., Cañizares, J., Pascual, L., Blanca, J., Díez, M. J., Prohens, J., & Belén Picó, M. (2012) · Current Genomics · doi:10.2174/138920212800543084 · Cited by 293
Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development
Alagna, F., D'Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., Chiusano, M. L., Baldoni, L., & Perrotta, G. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-399 · Cited by 263
On the origin of species: insights from the ecological genomics of lake whitefish
Bernatchez, L., Renaut, S., Whiteley, A. R., Derôme, N., Jeukens, J., LANDRY, L., Lu, G., Nolte, A. W., Østbye, K., Rogers, S. M., et al. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0274 · Cited by 248
An improved allele-specific PCR primer design method for SNP marker analysis and its application
Liu, J., Huang, S., Sun, M., Liu, S., Liu, Y., Wang, W., Zhang, X., Wang, H., & Hua, W. (2012) · Plant Methods · doi:10.1186/1746-4811-8-34 · Cited by 245
Rapid Genomic Characterization of the Genus Vitis
Myles, S., Chia, J.-M., Hurwitz, B. L., Simon, C. J., Zhong, G. Y., Buckler, E. S., & Ware, D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008219 · Cited by 249
Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala)
Gao, Z., Luo, W., Liu, H., Zeng, C., Liu, X., Yi, S., & Wang, W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042637 · Cited by 237
Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX
Hou, R., Bao, Z., Wang, S., Su, H., Li, Y., Du, H., Hu, J., Wang, S., & Hu, X. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021560 · Cited by 230
Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
van Orsouw, N. J., Hogers, R. C. J., Janssen, A., Yalçin, F., Snoeijers, S. S., Verstege, E., Schneiders, H., van der Poel, H. J. A., van Oeveren, J., Verstegen, H., et al. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001172 · Cited by 227
Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
Blanca, J., Cañizares, J., Roig, C., Ziarsolo, P., Nuez, F., & Belén Picó, M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-104 · Cited by 228
Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1
Strickler, S. R., Bombarely, A., & Mueller, L. A. (2012) · American Journal of Botany · doi:10.3732/ajb.1100292 · Cited by 232
Application of single nucleotide polymorphisms to non‐model species: a technical review
Garvin, M. R., Saitoh, K., & Gharrett, A. J. (2010) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2010.02891.x · Cited by 223
Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery
Kaur, S., Cogan, N. O. I., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., & Forster, J. W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-265 · Cited by 202
Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history
Vos, P. G., Uitdewilligen, J. G. A. M. L., Voorrips, R. E., Visser, R. G. F., & van Eck, H. J. (2015) · Theoretical and Applied Genetics · doi:10.1007/s00122-015-2593-y · Cited by 194
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data
Li, P., Piao, Y., Shon, H. S., & Ryu, K. H. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0778-7 · Cited by 188
Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers
Kaur, S., Pembleton, L. W., Cogan, N. O. I., Savin, K. W., Leonforte, T., Paull, J. G., Materne, M., & Forster, J. W. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-104 · Cited by 187
Herbaceous energy crop development: recent progress and future prospects
Heaton, E. A., Flavell, R. B., Mascia, P. N., Thomas, S. R., Dohleman, F. G., & Long, S. P. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.05.001 · Cited by 173
Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
Renaut, S., Nolte, A. W., & Bernatchez, L. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04477.x · Cited by 173
Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery
Hale, M. C., McCormick, C. R., Jackson, J. R., & DeWoody, J. A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-203 · Cited by 163
Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing
Bundock, P. C., Eliott, F. G., Ablett, G. A., Benson, A. D., Casu, R. E., Aitken, K. S., & Henry, R. J. (2009) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2009.00401.x · Cited by 157
High-throughput SNP discovery and assay development in common bean
Hyten, D. L., Song, Q., Fickus, E., Quigley, C., Lim, J.-S., Choi, I., Hwang, E. Y., Pastor-Corrales, M. A., & Cregan, P. B. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-475 · Cited by 157
De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
Cardoso-Silva, C. B., Costa, E. A., Mancini, M. C., Balsalobre, T. W. A., Canesin, L. E. C., Pinto, L. R., Carneiro, M. S., Garcia, A. A. F., de Souza, A. P., & Vicentini, R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088462 · Cited by 159
Insertion-deletion polymorphisms (indels) as genetic markers in natural populations
Väli, Ü., Durling, M. B., Johansson, M., & Ellegren, H. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-8 · Cited by 156
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
Deschamps, S., & Campbell, M. A. (2009) · Molecular Breeding · doi:10.1007/s11032-009-9357-9 · Cited by 153
Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation
Duran, C., Appleby, N., Edwards, D., & Batley, J. (2009) · Current Bioinformatics · doi:10.2174/157489309787158198 · Cited by 153
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
You, F. M., Huo, N., Deal, K. R., Gu, Y., Luo, M., McGuire, P. E., Dvořák, J., & Anderson, O. D. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-59 · Cited by 155
Single-Molecule DNA Amplification and Analysis Using Microfluidics
Zhang, C., & Xing, D. (2010) · Chemical Reviews · doi:10.1021/cr900081z · Cited by 148
Quantification of rare allelic variants from pooled genomic DNA
Druley, T. E., Vallania, F., Wegner, D., Varley, K. E., Knowles, O. L., Bonds, J. A., Robison, S. W., Doniger, S. W., Hamvas, A., Cole, F. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1307 · Cited by 148
Global gene expression analysis of the shoot apical meristem of maize ( Zea mays L.)
Ohtsu, K., Smith, M. B., Emrich, S., Borsuk, L. A., Zhou, R., Chen, T., Zhang, X., Timmermans, M. C. P., Beck, J., Buckner, B., et al. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03244.x · Cited by 144
Self-citation
Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array
You, Q., Yang, X., Peng, Z., Xu, L., & Wang, J. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00104 · Cited by 156
Targeted sequence capture as a powerful tool for evolutionary analysis1
Grover, C. E., Salmon, A., & Wendel, J. F. (2012) · American Journal of Botany · doi:10.3732/ajb.1100323 · Cited by 141
Development and mapping of SNP assays in allotetraploid cotton
Byers, R. L., Harker, D. B., Yourstone, S., Maughan, P. J., & Udall, J. A. (2012) · Theoretical and Applied Genetics · doi:10.1007/s00122-011-1780-8 · Cited by 140
Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea
Duarte, J., Rivière, N., Baranger, A., Aubert, G., Burstin, J., Cornet, L., Lavaud, C., Lejeune-Hénaut, I., Martinant, J., Pichon, J.-P., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-126 · Cited by 139
Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery
Jung, H., Lyons, R. E., Dinh, H., Hurwood, D. A., McWilliam, S. M., & Mather, P. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027938 · Cited by 140
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
Saintenac, C., Jiang, D., & Akhunov, E. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r88 · Cited by 146
High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)
Trebbi, D., Maccaferri, M., de Heer, P., Sørensen, A. P., Giuliani, S., Salvi, S., Sanguineti, M. C., Massi, A., van der Vossen, E. A. G., & Tuberosa, R. (2011) · Theoretical and Applied Genetics · doi:10.1007/s00122-011-1607-7 · Cited by 135
Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing
Wheat, C. W. (2008) · Genetica · doi:10.1007/s10709-008-9326-y · Cited by 136
Large SNP arrays for genotyping in crop plants
Ganal, M. W., Polley, A., Graner, E.-M., Plieske, J., Wieseke, R., Luerßen, H., & Durstewitz, G. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9225-3 · Cited by 141
Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next‐generation sequencing and Sequenom iPLEX MassARRAY genotyping
Buggs, R. J. A., Chamala, S., WU, W., Gao, L., May, G. D., Schnable, P. S., Soltis, P. S., Soltis, P. S., & Barbazuk, W. B. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04469.x · Cited by 137
Self-citation
High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)
Gaur, R. K., Azam, S., Jeena, G., Khan, A. W., Choudhary, S., Jain, M., Yadav, G., Tyagi, A. K., Chattopadhyay, D., & Bhatia, S. (2012) · DNA Research · doi:10.1093/dnares/dss018 · Cited by 134
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
Yang, S. S., Tu, Z. J., Cheung, F., Xu, W. W., Lamb, J. F., Jung, H. G., Vance, C. P., & Gronwald, J. W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-199 · Cited by 132
Discovering genetic polymorphisms in next‐generation sequencing data
Imelfort, M., Duran, C., Batley, J., & Edwards, D. (2009) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2009.00406.x · Cited by 129
Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes
Wang, S., Chen, J., Zhang, W., Hu, Y., Chang, L., Fang, L., Wang, Q., Lv, F., Wu, H., Si, Z., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0678-1 · Cited by 131
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
Castaño-Sánchez, C., Smith, T. P. L., Wiedmann, R. T., Vallejo, R. L., Salem, M., Yao, J., & Rexroad, C. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-559 · Cited by 128
Genetic improvement of C4 grasses as cellulosic biofuel feedstocks
Jakob, K., Zhou, F., & Paterson, A. H. (2009) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-009-9214-x · Cited by 129
Quality assessment parameters for EST-derived SNPs from catfish
Wang, S., Sha, Z., Sonstegard, T. S., Liu, H., Xu, P., Somridhivej, B., Peatman, E., Kucuktas, H., & Liu, Z. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-450 · Cited by 123
Transcriptome sequencing of wild chickpea as a rich resource for marker development
Jhanwar, S., Priya, P., Garg, R., Parida, S. K., Tyagi, A. K., & Jain, M. (2012) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2012.00712.x · Cited by 123
Shedding light on an extremophile lifestyle through transcriptomics
Dassanayake, M., Haas, J. S., Bohnert, H. J., & Cheeseman, J. M. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02913.x · Cited by 121
Sequence-based marker development in wheat: Advances and applications to breeding
Paux, E., Sourdille, P., Mackay, I., & Feuillet, C. (2011) · Biotechnology Advances · doi:10.1016/j.biotechadv.2011.09.015 · Cited by 122
Genic and nongenic contributions to natural variation of quantitative traits in maizePreprint
Li, X., Zhu, C., Yeh, C., Wu, W., Takacs, E. M., Petsch, K. A., Tian, F., Bai, G., Buckler, E. S., Muehlbauer, G. J., et al. (2012) · Genome Research · doi:10.1101/gr.140277.112 · Cited by 122
Self-citation
Sympatric Speciation in the Post “Modern Synthesis” Era of Evolutionary Biology
Bird, C. E., Fernández-Silva, I., Skillings, D., & Toonen, R. J. (2012) · Evolutionary Biology · doi:10.1007/s11692-012-9183-6 · Cited by 120
Extreme‐phenotype genome‐wide association study ( XP ‐ GWAS ): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel
Yang, J., Jiang, H., Yeh, C., Yu, J., Jeddeloh, J. A., Nettleton, D. S., & Schnable, P. S. (2015) · The Plant Journal · doi:10.1111/tpj.13029 · Cited by 118
Self-citation
A set of EST-SNPs for map saturation and cultivar identification in melon
Deleu, W., Esteras, C., Roig, C., González, M., Fernández-Silva, I., González‐Ibeas, D., Blanca, J., Aranda, M. A., Arús, P., Nuez, F., et al. (2009) · BMC Plant Biology · doi:10.1186/1471-2229-9-90 · Cited by 121
Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon
O’Neil, S. T., Dzurisin, J. D. K., Carmichael, R., Lobo, N. F., Emrich, S., & Hellmann, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-310 · Cited by 120
Self-citation
De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes
Ashrafi, H., Hill, T. A., Stoffel, K. M., Kozik, A., Yao, J., Reyes-Chin-Wo, S., & Deynze, A. V. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-571 · Cited by 117
Single-Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed-Stock Analyses of Sockeye Salmon from the Copper River, Alaska
Ackerman, M. W., Habicht, C., & Seeb, L. W. (2011) · Transactions of the American Fisheries Society · doi:10.1080/00028487.2011.588137 · Cited by 117
Advances in molecular technology and their impact on fisheries genetics
Hauser, L., & Seeb, J. E. (2008) · Fish and Fisheries · doi:10.1111/j.1467-2979.2008.00306.x · Cited by 115
Genetic control of morphometric diversity in the maize shoot apical meristem
Leiboff, S., Li, X., Hu, H.-C., Todt, N. R., Yang, J., Li, X., Yu, X., Muehlbauer, G. J., Timmermans, M. C. P., Yu, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms9974 · Cited by 109
Self-citation
Genomics of Fungal Disease Resistance in Tomato
Panthee, D. R., & Chen, F. (2009) · Current Genomics · doi:10.2174/138920210790217927 · Cited by 111
Next‐generation sequencing applications for wheat crop improvement
Berkman, P. J., Lai, K., Lorenc, M. T., & Edwards, D. (2012) · American Journal of Botany · doi:10.3732/ajb.1100309 · Cited by 110
Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families
Eveland, A. L., McCarty, D. R., & Koch, K. E. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.108597 · Cited by 108
Characterizing the mouse ES cell transcriptome with Illumina sequencing
Rosenkranz, R., Borodina, T., Lehrach, H., & Himmelbauer, H. (2008) · Genomics · doi:10.1016/j.ygeno.2008.05.011 · Cited by 106
Transcriptomic, Proteomic, Metabolomic and Functional Genomic Approaches for the Study of Abiotic Stress in Vegetable Crops
Zhuang, J., Zhang, J., Hou, X., Wang, F., & Xiong, A. (2014) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2014.870420 · Cited by 106
Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato
Kim, J.-E., Oh, S., Lee, J.-H., Lee, B.-M., & Jo, S. (2014) · Molecules and Cells · doi:10.14348/molcells.2014.2241 · Cited by 104
Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics
Nabholz, B., Künstner, A., Wang, R., Jarvis, E. D., & Ellegren, H. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr047 · Cited by 107
Single nucleotide polymorphism discovery from wheat next‐generation sequence data
Lai, K., Duran, C., Berkman, P. J., Lorenc, M. T., Stiller, J., Manoli, S., Hayden, M., Forrest, K., Fleury, D., Baumann, U., et al. (2012) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2012.00718.x · Cited by 107
High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species
Grattapaglia, D., Silva‐Junior, O. B., Kirst, M., de Lima, B. M., de Faria, D. A., & Pappas, G. J., Jr. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-65 · Cited by 112

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.
ORCID: Barbazuk, W. Brad
Emrich, Scott J.
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
DOI: 10.1111/j.1365-313x.2007.03193.x
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
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
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

SNP discovery via 454 transcriptome sequencing

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks