ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2004
What proportion of declared QTL in plants are false?
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed.
- Crop wild relative populations of Beta vulgaris as source for genome-wide association mapping of complex traits.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Complex traits and candidate genes: estimation of genetic variance components across multiple genetic architectures.G3 (Bethesda, Md.) · 2023Article
- Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From WildFrontiers in plant science · 2022Article
- Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses.PLoS genetics · 2021Article
- Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.).BMC plant biology · 2020Article
- Identification and Validation of Aerobic Adaptation QTLs in Upland Rice.Life (Basel, Switzerland) · 2020Article
- Identification of Loci and Candidate Genes Responsible for Fiber Length in Upland Cotton (Frontiers in plant science · 2019Article
- Genome-wide association mapping of quantitative traits in a breeding population of sugarcane.BMC plant biology · 2016Article
- Ensemble Learning of QTL Models Improves Prediction of Complex Traits.G3 (Bethesda, Md.) · 2015Article
- Quantitative Variation in Responses to Root Spatial Constraint within Arabidopsis thaliana.The Plant cell · 2015Article
- Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Mapping three new interspecific hybrid sterile loci between Oryza sativa and O. glaberrima.Breeding science · 2014Article
- Genomewide markers as cofactors for precision mapping of quantitative trait loci.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Phenotyping for drought tolerance of crops in the genomics era.Frontiers in physiology · 2012Article
- Wheat kernel dimensions: how do they contribute to kernel weight at an individual QTL level?Journal of genetics · 2011Article
- Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.).BMC plant biology · 2010Article
- Molecular detection of genomic regions associated with grain yield and yield-related components in an elite bread wheat cross evaluated under irrigated and rainfed conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- A quantitative genetic study for elucidating the contribution of glutamine synthetase, glutamate dehydrogenase and other nitrogen-related physiological traits to the agronomic performance of common wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Mapping multiple quantitative trait loci under Bayes error control.Genetics research · 2009Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The false discovery rate (FDR) is the probability that a quantitative trait locus (QTL) is false, given that a QTL has been declared. A misconception in QTL mapping is that the FDR is equal to the comparison-wise significance level, alpha(C). The objective of this simulation study was to determine the FDR in an F(2) mapping population, given different numbers of QTL, population sizes, and trait heritabilities. Markers linked to QTL were detected by multiple regression of phenotype on marker genotype. Phenotypic selection and marker-based recurrent selection were compared. The FDR increased as alpha(C) increased. Notably, the FDR was often 10-30 times higher than the alpha(C) level used. Regardless of the number of QTL, heritability, or size of the genome, the FDR was < or =0.01 when alpha(C) was 0.0001. The FDR increased to 0.82 when alpha(C) was 0.05, heritability was low, and only one QTL controlled the trait. An alpha(C) of 0.05 led to a low FDR when many QTL (30 or 100) controlled the trait, but this lower FDR was accompanied by a diminished power to detect QTL. Larger mapping populations led to both lower a FDR and increased power. Relaxed significance levels of alpha(C)=0.1 or 0.2 led to the largest responses to marker-based recurrent selection, despite the high FDR. To prevent false QTL from confusing the literature and databases, a detected QTL should, in general, be reported as a QTL only if it was identified at a stringent significance level, e.g., alpha(C) congruent with 0.0001.
Indexed as
Identifiers
15085262What 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.