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Rapid array mapping of circadian clock and developmental mutations in Arabidopsis

Academic Article
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Overview

authors

  • Hazen, S. P.
  • Borevitz, J. O.
  • Harmon, F. G.
  • Pruneda-Paz, J. L.
  • Schultz, T. F.
  • Yanovsky, M. J.
  • Liljegren, S. J.
  • Ecker, J. R.
  • Kay, Steve A.

publication date

  • June 2005

journal

  • Plant Physiology  Journal

abstract

  • Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits were mapped. The mapping accuracy using bulk pools of 26 to 100 F(2) individuals ranged from 0.22 to 1.96 Mb of the mutations revealing mutant alleles of EARLY FLOWERING 3, EARLY FLOWERING 4, TIMING OF CAB EXPRESSION 1, and ASYMMETRIC LEAVES 1. While direct detection of small mutations, such as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sensitivity, large deletions such as those that can be caused by fast neutrons are easily detected. We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays.

subject areas

  • Arabidopsis
  • Chromosome Mapping
  • Chromosomes, Plant
  • Circadian Rhythm
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Genotype
  • Mutation
  • Oligonucleotide Array Sequence Analysis
  • Phenotype
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Identity

PubMed Central ID

  • PMC1150413

International Standard Serial Number (ISSN)

  • 0032-0889

Digital Object Identifier (DOI)

  • 10.1104/pp.105.061408

PubMed ID

  • 15908595
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Additional Document Info

start page

  • 990

end page

  • 997

volume

  • 138

issue

  • 2

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