ArticleScientific data2017
Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples.
Article in Scientific data, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Experimental Validation of Genome-Environment Associations in Arabidopsis.Molecular ecology · 2025Article
- Species-wide gene editing of a flowering regulator reveals hidden phenotypic variation.PLoS biology · 2025Article
- Life-history trade-offs explain local adaptation inbioRxiv : the preprint server for biology · 2025Article
- Arabidopsis as a model for translational research.The Plant cell · 2025Review
- Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana.The New phytologist · 2025Article
- Article
- SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding.Nucleic acids research · 2024Article
- DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis.International journal of molecular sciences · 2023Article
- On the causes of gene-body methylation variation in Arabidopsis thaliana.PLoS genetics · 2023Article
- CottonMD: a multi-omics database for cotton biological study.Nucleic acids research · 2023Article
- Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation.IMA fungus · 2021Article
- Reported differences in the flg22 response of the null mutation of AtRGS1 correlates with fixed genetic variation in the background of Col-0 isolates.Plant signaling & behavior · 2021Article
- Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia.Frontiers in plant science · 2021Article
- Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue.Bio-protocol · 2020Article
- The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors.Communications biology · 2020Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- In the presence of population structure: From genomics to candidate genes underlying local adaptation.Ecology and evolution · 2020Article
- Allelic Variation in the Chloroplast Division GenePlant physiology · 2019Article
- An Ultra High-DensityGenetics · 2019Article
- Article
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10 authors.
Funding
Abstract
Large-scale studies such as the Arabidopsis thaliana '1,001 Genomes' Project require routine genotyping of stocks to avoid sample contamination. To genotype samples efficiently and economically, sequencing must be inexpensive and data processing simple. Here we present SNPmatch, a tool that identifies strains (or inbred lines, or accessions) by matching them to a SNP database. We tested the tool by performing low-coverage resequencing of over 2,000 strains from our lab seed stock collection. SNPmatch correctly genotyped samples from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.
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Registered trials
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