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Genetics, Vol. 167, 907-917, June 2004, Copyright © 2004
doi:10.1534/genetics.103.024810
Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana
David J. Wolyn*,1,
Justin O. Borevitz
,
Olivier Loudet,
Chris Schwartz,
Julin Maloof
,
Joseph R. Ecker,
Charles C. Berry
and
Joanne Chory,**
* Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
Department of Family/Preventative Medicine, University of California, San Diego, California 92093
Section of Plant Biology, University of California, Davis, California 95616
** Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037
1 Corresponding author: Department of Plant Agriculture, Bovey Bldg., University of Guelph, Guelph, ON N1G 2W1, Canada.
E-mail: dwolyn{at}uoguelph.ca
Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis.
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