ArticleGenetics2004
Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- A Single-Nucleotide Polymorphism in the Promoter of PorcineFrontiers in cell and developmental biology · 2022Article
- Single Nucleotide Polymorphisms ofGenes · 2019Article
- Identification of single nucleotide polymorphisms ofJournal of animal science and biotechnology · 2019Article
- GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data.G3 (Bethesda, Md.) · 2018Article
- Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population.BMC genetics · 2017Article
- "Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.PLoS genetics · 2015Article
- Functional analysis of the Landsberg erecta allele of FRIGIDA.BMC plant biology · 2014Article
- Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a.Journal of experimental botany · 2011Article
- Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley.PloS one · 2010Article
- The diverse applications of cladistic analysis of molecular evolution, with special reference to nested clade analysis.International journal of molecular sciences · 2010Review
- Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize.Plant physiology · 2009Article
- Local patterns of nucleotide polymorphism are highly variable in the selfing species Arabidopsis thaliana.Journal of molecular evolution · 2008Article
- Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2007Article
- Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology.Annals of botany · 2007Review
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- An Arabidopsis example of association mapping in structured samples.PLoS genetics · 2007Article
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- Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2006Article
- Association mapping with single-feature polymorphisms.Genetics · 2006Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The feasibility of using linkage disequilbrium (LD) to fine-map loci underlying natural variation in Arabidopsis thaliana was investigated by looking for associations between flowering time and marker polymorphism in the genomic regions containing two candidate genes, FRI and FLC, both of which are known to contribute to natural variation in flowering. A sample of 196 accessions was used, and polymorphism was assessed by sequencing a total of 17 roughly 500-bp fragments. Using a novel Bayesian algorithm based on haplotype similarity, we demonstrate that LD could have been used to fine-map the FRI gene to a roughly 30-kb region and to identify two common loss-of-function alleles. Interestingly, because of genetic heterogeneity, simple single-marker associations would not have been able to map FRI with nearly the same precision. No clear evidence for previously unknown alleles at either locus was found, but the effect of population structure in causing false positives was evident.
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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.