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LiteratureArticle Details
PMID: 15579712
Published · ppublish
English
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci.
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.
MeSH Terms
Arabidopsis/genetics,physiology
Chromosome Mapping
Chromosomes
Flowers/genetics,physiology
Genetic Linkage
Genetic Markers
Haplotypes
Molecular Sequence Data
Phenotype
Polymorphism, Genetic
Chemicals
Genetic Markers
References (35)
35 references, click to expand
-
Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.Genetics. 2000 Feb;154(2):923-9 PMID: 10655241
-
Analysis of flowering time in ecotypes of Arabidopsis thaliana.J Hered. 1997 Jan-Feb;88(1):69-72 PMID: 9048445
-
Association mapping in structured populations.Am J Hum Genet. 2000 Jul;67(1):170-81 PMID: 10827107
-
Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time.Science. 2000 Oct 13;290(5490):344-7 PMID: 11030654
-
Genomic control for association studies.Biometrics. 1999 Dec;55(4):997-1004 PMID: 11315092
-
High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence.Am J Hum Genet. 2001 Jul;69(1):159-78 PMID: 11410841
-
Bayesian analysis of haplotypes for linkage disequilibrium mapping.Genome Res. 2001 Oct;11(10):1716-24 PMID: 11591648
-
Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.Science. 2001 Nov 23;294(5547):1719-23 PMID: 11721056
-
Linkage disequilibrium and the mapping of complex human traits.Trends Genet. 2002 Jan;18(1):19-24 PMID: 11750696
-
The extent of linkage disequilibrium in Arabidopsis thaliana.Nat Genet. 2002 Feb;30(2):190-3 PMID: 11780140
-
Linkage disequilibrium: what history has to tell us.Trends Genet. 2002 Feb;18(2):83-90 PMID: 11818140
-
Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana.Genetics. 2002 May;161(1):289-98 PMID: 12019242
-
DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time.Mol Biol Evol. 2002 Aug;19(8):1261-71 PMID: 12140238
-
Evidence for population growth in humans is confounded by fine-scale population structure.Trends Genet. 2002 Nov;18(11):559-63 PMID: 12414185
-
Using haplotype blocks to map human complex trait loci.Trends Genet. 2003 Mar;19(3):135-40 PMID: 12615007
-
The impact of genomics on the study of natural variation in Arabidopsis.Plant Physiol. 2003 Jun;132(2):718-25 PMID: 12805600
-
Analysis of the molecular basis of flowering time variation in Arabidopsis accessions.Plant Physiol. 2003 Jun;132(2):1107-14 PMID: 12805638
-
Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster.Genetics. 1998 Jun;149(2):999-1017 PMID: 9611209
-
The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation.Plant Cell. 1999 Mar;11(3):445-58 PMID: 10072403
-
Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations.Am J Hum Genet. 1999 Jun;64(6):1728-38 PMID: 10330361
-
FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering.Plant Cell. 1999 May;11(5):949-56 PMID: 10330478
-
Use of unlinked genetic markers to detect population stratification in association studies.Am J Hum Genet. 1999 Jul;65(1):220-8 PMID: 10364535
-
Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping.Am J Hum Genet. 1999 Sep;65(3):858-75 PMID: 10445904
-
The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits.Genome Res. 1999 Aug;9(8):720-31 PMID: 10447507
-
Haplotype fine mapping by evolutionary trees.Am J Hum Genet. 2000 Feb;66(2):659-73 PMID: 10677324
-
Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping.Genet Epidemiol. 2003 Sep;25(2):95-105 PMID: 12916018
-
Dopa decarboxylase (Ddc) affects variation in Drosophila longevity.Nat Genet. 2003 Aug;34(4):429-33 PMID: 12881721
-
Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis.Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):10102-7 PMID: 12904584
-
Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms.Genome Res. 2003 Sep;13(9):2112-7 PMID: 12952879
-
Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity.Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13442-6 PMID: 14597696
-
Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques.Am J Hum Genet. 2003 Dec;73(6):1368-84 PMID: 14631555
-
The International HapMap Project.Nature. 2003 Dec 18;426(6968):789-96 PMID: 14685227
-
The complex interplay among factors that influence allelic association.Nat Rev Genet. 2004 Feb;5(2):89-100 PMID: 14735120
-
The transmission/disequilibrium test: history, subdivision, and admixture.Am J Hum Genet. 1995 Aug;57(2):455-64 PMID: 7668272
-
Data mining applied to linkage disequilibrium mapping.Am J Hum Genet. 2000 Jul;67(1):133-45 PMID: 10848493
Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
Published
2004-11-00
Pages
1627-38
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1448803
Subset
IM
Databases
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