ArticleThe Plant journal : for cell and molecular biology2007
SNP discovery via 454 transcriptome sequencing.
Article in The Plant journal : for cell and molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
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Who cites it
170 citing papers in PubMed.
- Si-Miao-Yong-An decoction suppresses necroptosis by regulating the p53 pathway in myocardial ischemia/reperfusion injury.Scientific reports · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Cell Biological Analyses of Anther Morphogenesis and Pollen Viability in Arabidopsis and Rice.Methods in molecular biology (Clifton, N.J.) · 2023Article
- De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.Genetica · 2022Article
- Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes.Molecular biology reports · 2021Article
- Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean).Genomics & informatics · 2021Article
- Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map.Scientific reports · 2020Article
- deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.Genome biology · 2019Article
- Development of EST-based SSR and SNP markers in3 Biotech · 2019Article
- Analysis of genome-wide variants through bulked segregant RNA sequencing reveals a major gene for resistance to Plasmodiophora brassicae in Brassica oleracea.Scientific reports · 2018Article
- Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.Molecular biology and evolution · 2018Article
- The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.PloS one · 2018Article
- Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array.Frontiers in plant science · 2018Review
- Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing.PloS one · 2018Article
- Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper.BioMed research international · 2018Review
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement.Scientific reports · 2017Article
- Effects of TiO2 nanoparticles on nutrition metabolism in silkworm fat body.Biology open · 2016Article
110 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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