ArticleThe Plant journal : for cell and molecular biology2020
Imputation of 3 million SNPs in the Arabidopsis regional mapping population.
Article in The Plant journal : for cell and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- On the genetic origins of phenotypes in genome-wide association studies: the SAFE-hBMC bioinformatics · 2026Article
- GWAS reveal SUBER GENE1-mediated suberization via type one phosphatases.Nature plants · 2026Article
- Natural expression variation for the ArabidopsisFrontiers in plant science · 2025Article
- The benefits of permutation-based genome-wide association studies.Journal of experimental botany · 2024Article
- Article
- Population-aware permutation-based significance thresholds for genome-wide association studies.Bioinformatics advances · 2024Article
- Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation.Plant physiology · 2023Article
- Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- Analysis of dog breed diversity using a composite selection index.Scientific reports · 2023Article
- Predicting Gene Regulatory Interactions Using Natural Genetic Variation.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A genome-wide association study identifies novel players in Na and Fe homeostasis in Arabidopsis thaliana under alkaline-salinity stress.The Plant journal : for cell and molecular biology · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate inPlants (Basel, Switzerland) · 2022Article
- Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions.Bioinformatics (Oxford, England) · 2022Article
- Genome-wide association mapping within a localPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- The megabase-scale crossover landscape is largely independent of sequence divergence.Nature communications · 2022Article
- Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes.BMC genomics · 2022Article
- Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis.The Plant cell · 2022Article
- A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species.Frontiers in plant science · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural variation has become a prime resource to identify genetic variants that contribute to phenotypic variation. The regional mapping (RegMap) population is one of the most important populations for studying natural variation in Arabidopsis thaliana, and has been used in a large number of association studies and in studies on climatic adaptation. However, only 413 RegMap accessions have been completely sequenced, as part of the 1001 Genomes (1001G) Project, while the remaining 894 accessions have only been genotyped with the Affymetrix 250k chip. As a consequence, most association studies involving the RegMap are either restricted to the sequenced accessions, reducing power, or rely on a limited set of SNPs. Here we impute millions of SNPs to the 894 accessions that are exclusive to the RegMap, using the 1135 accessions of the 1001G Project as the reference panel. We assess imputation accuracy using a novel cross-validation scheme, which we show provides a more reliable measure of accuracy than existing methods. After filtering out low accuracy SNPs, we obtain high-quality genotypic information for 2029 accessions and 3 million markers. To illustrate the benefits of these imputed data, we reconducted genome-wide association studies on five stress-related traits and could identify novel candidate genes.
Indexed as
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.