title: 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.
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Jenny
authors.initials: J
authors.lastname: Hagenblad
authors.forename: Chunlao
authors.initials: C
authors.lastname: Tang
authors.forename: John
authors.initials: J
authors.lastname: Molitor
authors.forename: Jonathan
authors.initials: J
authors.lastname: Werner
authors.forename: Keyan
authors.initials: K
authors.lastname: Zhao
authors.forename: Honggang
authors.initials: H
authors.lastname: Zheng
authors.forename: Paul
authors.initials: P
authors.lastname: Marjoram
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping; D002875:Chromosomes; D035264:Flowers / Q000235:genetics* / Q000502:physiology; D008040:Genetic Linkage; D005819:Genetic Markers; D006239:Haplotypes; D008969:Molecular Sequence Data; D010641:Phenotype; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers