ArticleInternational journal of plant genomics2012
SNP Discovery through Next-Generation Sequencing and Its Applications.
Article in International journal of plant genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
132 citing papers in PubMed.
- Exploring the Role of Single Nucleotide Polymorphisms in Modern Plant Genomic Research.Methods in molecular biology (Clifton, N.J.) · 2027Review
- An Assessment of Allelic and SNP Bias in a Genome-Wide SNP Enrichment Kit for Killer Whales.Ecology and evolution · 2026Article
- Decoding Complex Traits in Goats Through Genome-Wide Association Studies: Progress, Challenges, and Perspectives.International journal of molecular sciences · 2026Review
- Article
- High-Resolution Chloroplast SNV Profiling of 409 Grapevine (International journal of molecular sciences · 2026Article
- Article
- Comparative genetic diversity of the endangered, narrowly endemic Chinese orchidFrontiers in plant science · 2026Article
- Development of KASP molecular markers and construction of fingerprinting for cowpea (Vigna unguiculata (L.) Walp.) based on ddRAD-Seq.PloS one · 2026Article
- Genome-wide association study of the reproductive, body size, and carcass-related latent and directly measured traits in admixed beef heifers.Frontiers in genetics · 2026Article
- Missing genotype imputation in non-model species using self-organizing maps.Molecular ecology resources · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- The application of DNA markers in population genetics of mosquitoes: a comprehensive review.Frontiers in insect science · 2025Review
- Pan-Chloroplast Genomes Reveal the Accession-Specific Marker forInternational journal of molecular sciences · 2024Article
- Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS).BMC plant biology · 2024Article
- Genotypic and phenotypic spectrum of maple syrup urine disease in Zhejiang of China.QJM : monthly journal of the Association of Physicians · 2024Article
- Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings.The plant genome · 2024Article
- Exploring Disease Resistance in Pepper (Plants (Basel, Switzerland) · 2024Article
- DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.Breeding science · 2024Article
- A comparative study of 11 non-linear regression models highlighting autoencoder, DBN, and SVR, enhanced by SHAP importance analysis in soybean branching prediction.Scientific reports · 2024Article
- Article
72 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.