Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles

The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROM...

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Bibliographic Details
Published in:Genetics (Austin) 2004-07, Vol.167 (3), p.1361-1369
Main Authors: Olsen, K.M, Halldorsdottir, S.S, Stinchcombe, J.R, Weinig, C, Schmitt, J, Purugganan, M.D
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Arabidopsis
Arabidopsis - genetics
Arabidopsis - physiology
Arabidopsis Proteins - genetics
Arabidopsis thaliana
Base Sequence
Cryptochromes
Flowers & plants
Flowers - physiology
Gene Components
Genetics
Genetics, Population
Haplotypes - genetics
Linkage Disequilibrium
Mapping
Molecular Sequence Data
Photoperiod
Phylogeny
Polymorphism, Genetic
Sequence Analysis, DNA
Time Factors
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Summary:The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to
ISSN:0016-6731
1943-2631
DOI:10.1534/genetics.103.024950