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

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SNP discovery via 454 transcriptome sequencing

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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

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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.

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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

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