Genetics, Vol. 160, 683-696, February 2002, Copyright © 2002

Quantitative Trait Loci Controlling Light and Hormone Response in Two Accessions of Arabidopsis thaliana

Justin O. Borevitza,b, Julin N. Maloofa, Jason Lutesa,c, Tsegaye Dabia, Joanna L. Redferna, Gabriel T. Trainera,c, Jonathan D. Wernera,b, Tadao Asamid, Charles C. Berrye, Detlef Weigela,f, and Joanne Chorya,c
a Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037,
b Department of Biology, University of California, La Jolla, California 92037,
c Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037,
d The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama 351-0198, Japan,
e Department of Family/Preventive Medicine, University of California, La Jolla, California 92093
f Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany

Corresponding author: Joanne Chory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037., chory{at}salk.edu (E-mail)

Communicating editor: T. F. C. MACKAY

We have mapped quantitative trait loci (QTL) responsible for natural variation in light and hormone response between the Cape Verde Islands (Cvi) and Landsberg erecta (Ler) accessions of Arabidopsis thaliana using recombinant inbred lines (RILs). Hypocotyl length was measured in four light environments: white, blue, red, and far-red light and in the dark. In addition, white light plus gibberellin (GA) and dark plus the brassinosteroid biosynthesis inhibitor brassinazole (BRZ) were used to detect hormone effects. Twelve QTL were identified that map to loci not previously known to affect light response, as well as loci where candidate genes have been identified from known mutations. Some QTL act in all environments while others show genotype-by-environment interaction. A global threshold was established to identify a significant epistatic interaction between two loci that have few main effects of their own. LIGHT1, a major QTL, has been confirmed in a near isogenic line (NIL) and maps to a new locus with effects in all light environments. The erecta mutation can explain the effect of the HYP2 QTL in the blue, BRZ, and dark environments, but not in far-red. LIGHT2, also confirmed in an NIL, has effects in white and red light and shows interaction with GA. The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions.




This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
O. Loudet, T. P. Michael, B. T. Burger, C. Le Mette, T. C. Mockler, D. Weigel, and J. Chory
A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana
PNAS, November 4, 2008; 105(44): 17193 - 17198.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. L. Filiault, C. A. Wessinger, J. R. Dinneny, J. Lutes, J. O. Borevitz, D. Weigel, J. Chory, and J. N. Maloof
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light
PNAS, February 26, 2008; 105(8): 3157 - 3162.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. A. Sangster, N. Salathia, S. Undurraga, R. Milo, K. Schellenberg, S. Lindquist, and C. Queitsch
HSP90 affects the expression of genetic variation and developmental stability in quantitative traits
PNAS, February 26, 2008; 105(8): 2963 - 2968.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. M. Warpeha, S. Upadhyay, J. Yeh, J. Adamiak, S. I. Hawkins, Y. R. Lapik, M. B. Anderson, and L. S. Kaufman
The GCR1, GPA1, PRN1, NF-Y Signal Chain Mediates Both Blue Light and Abscisic Acid Responses in Arabidopsis
Plant Physiology, April 1, 2007; 143(4): 1590 - 1600.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. M. Nichols, K. W. Broman, K. Sundin, J. M. Young, P. A. Wheeler, and G. H. Thorgaard
Quantitative Trait Loci x Maternal Cytoplasmic Environment Interaction for Development Rate in Oncorhynchus mykiss
Genetics, January 1, 2007; 175(1): 335 - 347.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
G. Mouille, H. Witucka-Wall, M.-P. Bruyant, O. Loudet, S. Pelletier, C. Rihouey, O. Lerouxel, P. Lerouge, H. Hofte, and M. Pauly
Quantitative Trait Loci Analysis of Primary Cell Wall Composition in Arabidopsis
Plant Physiology, July 1, 2006; 141(3): 1035 - 1044.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
V. M. C. Luquez, Y. Sasal, M. Medrano, M. I. Martin, M. Mujica, and J. J. Guiamet
Quantitative trait loci analysis of leaf and plant longevity in Arabidopsis thaliana
J. Exp. Bot., March 1, 2006; 57(6): 1363 - 1372.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. I. Sergeeva, J. J. B. Keurentjes, L. Bentsink, J. Vonk, L. H. W. van der Plas, M. Koornneef, and D. Vreugdenhil
Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis
PNAS, February 21, 2006; 103(8): 2994 - 2999.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. L. Malmberg, S. Held, A. Waits, and R. Mauricio
Epistasis for Fitness-Related Quantitative Traits in Arabidopsis thaliana Grown in the Field and in the Greenhouse
Genetics, December 1, 2005; 171(4): 2013 - 2027.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. D. Werner, J. O. Borevitz, N. H. Uhlenhaut, J. R. Ecker, J. Chory, and D. Weigel
FRIGIDA-Independent Variation in Flowering Time of Natural Arabidopsis thaliana Accessions
Genetics, July 1, 2005; 170(3): 1197 - 1207.
[Abstract] [Full Text] [PDF]

Home page
 Integr. Comp. Biol.Home page
H. S. Callahan
Using Artificial Selection to Understand Plastic Plant Phenotypes
Integr. Comp. Biol., June 1, 2005; 45(3): 475 - 485.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
T. M. A. Magliano, J. F. Botto, A. V. Godoy, V. V. Symonds, A. M. Lloyd, and J. J. Casal
New Arabidopsis Recombinant Inbred Lines (Landsberg erecta x Nossen) Reveal Natural Variation in Phytochrome-Mediated Responses
Plant Physiology, June 1, 2005; 138(2): 1126 - 1135.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
S. Mathews
Phytochrome Evolution in Green and Nongreen Plants
J. Hered., May 1, 2005; 96(3): 197 - 204.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. D. Edwards, J. R. Lynn, P. Gyula, F. Nagy, and A. J. Millar
Natural Allelic Variation in the Temperature-Compensation Mechanisms of the Arabidopsis thaliana Circadian Clock
Genetics, May 1, 2005; 170(1): 387 - 400.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. D. Werner, J. O. Borevitz, N. Warthmann, G. T. Trainer, J. R. Ecker, J. Chory, and D. Weigel
Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation
PNAS, February 15, 2005; 102(7): 2460 - 2465.
[Abstract] [Full Text] [PDF]

Home page
 DevelopmentHome page
L. Dolan and J. A. Langdale
New insights into plant development in New England
Development, November 1, 2004; 131(21): 5215 - 5220.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
D. H. Hobbs, J. E. Flintham, and M. J. Hills
Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis
Plant Physiology, October 1, 2004; 136(2): 3341 - 3349.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
D. J. Wolyn, J. O. Borevitz, O. Loudet, C. Schwartz, J. Maloof, J. R. Ecker, C. C. Berry, and J. Chory
Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana
Genetics, June 1, 2004; 167(2): 907 - 917.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. E. El-Lithy, E. J.M. Clerkx, G. J. Ruys, M. Koornneef, and D. Vreugdenhil
Quantitative Trait Locus Analysis of Growth-Related Traits in a New Arabidopsis Recombinant Inbred Population
Plant Physiology, May 1, 2004; 135(1): 444 - 458.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
S. Hake and T. Rocheford
Exploiting quantitative trait loci in gene discovery
Genes & Dev., March 15, 2004; 18(6): 597 - 601.
[Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. F. Botto, C. Alonso-Blanco, I. Garzaron, R. A. Sanchez, and J. J. Casal
The Cape Verde Islands Allele of Cryptochrome 2 Enhances Cotyledon Unfolding in the Absence of Blue Light in Arabidopsis
Plant Physiology, December 1, 2003; 133(4): 1547 - 1556.
[Abstract] [Full Text]

Home page
 ScienceHome page
T. P. Michael, P. A. Salome, H. J. Yu, T. R. Spencer, E. L. Sharp, M. A. McPeek, J. M. Alonso, J. R. Ecker, and C. R. McClung
Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock
Science, November 7, 2003; 302(5647): 1049 - 1053.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. D. Jermstad, D. L. Bassoni, K. S. Jech, G. A. Ritchie, N. C. Wheeler, and D. B. Neale
Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions
Genetics, November 1, 2003; 165(3): 1489 - 1506.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
J. Kim, H. Yi, G. Choi, B. Shin, P.-S. Song, and G. Choi
Functional Characterization of Phytochrome Interacting Factor 3 in Phytochrome-Mediated Light Signal Transduction
PLANT CELL, October 1, 2003; 15(10): 2399 - 2407.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Weinig, L. A. Dorn, N. C. Kane, Z. M. German, S. S. Halldorsdottir, M. C. Ungerer, Y. Toyonaga, T. F. C. Mackay, M. D. Purugganan, and J. Schmitt
Heterogeneous Selection at Specific Loci in Natural Environments in Arabidopsis thaliana
Genetics, September 1, 2003; 165(1): 321 - 329.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. C. Ungerer, S. S. Halldorsdottir, M. D. Purugganan, and T. F. C. Mackay
Genotype-Environment Interactions at Quantitative Trait Loci Affecting Inflorescence Development in Arabidopsis thaliana
Genetics, September 1, 2003; 165(1): 353 - 365.
[Abstract] [Full Text] [PDF]

Home page
 Integr. Comp. Biol.Home page
J. Schmitt, J. R. Stinchcombe, M. S. Heschel, and H. Huber
The Adaptive Evolution of Plasticity: Phytochrome-Mediated Shade Avoidance Responses
Integr. Comp. Biol., July 1, 2003; 43(3): 459 - 469.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Alonso-Blanco, L. Bentsink, C. J. Hanhart, H. Blankestijn-de Vries, and M. Koornneef
Analysis of Natural Allelic Variation at Seed Dormancy Loci of Arabidopsis thaliana
Genetics, June 1, 2003; 164(2): 711 - 729.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. O. Borevitz and M. Nordborg
The Impact of Genomics on the Study of Natural Variation in Arabidopsis
Plant Physiology, June 1, 2003; 132(2): 718 - 725.
[Full Text] [PDF]

Home page
 GeneticsHome page
O. Loudet, S. Chaillou, A. Krapp, and F. Daniel-Vedele
Quantitative Trait Loci Analysis of Water and Anion Contents in Interaction With Nitrogen Availability in Arabidopsis thaliana
Genetics, February 1, 2003; 163(2): 711 - 722.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
O. Loudet, S. Chaillou, P. Merigout, J. Talbotec, and F. Daniel-Vedele
Quantitative Trait Loci Analysis of Nitrogen Use Efficiency in Arabidopsis
Plant Physiology, January 1, 2003; 131(1): 345 - 358.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Weinig, M. C. Ungerer, L. A. Dorn, N. C. Kane, Y. Toyonaga, S. S. Halldorsdottir, T. F. C. Mackay, M. D. Purugganan, and J. Schmitt
Novel Loci Control Variation in Reproductive Timing in Arabidopsis thaliana in Natural Environments
Genetics, December 1, 2002; 162(4): 1875 - 1884.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. M. Perez-Perez, J. Serrano-Cartagena, and J. L. Micol
Genetic Analysis of Natural Variations in the Architecture of Arabidopsis thaliana Vegetative Leaves
Genetics, October 1, 2002; 162(2): 893 - 915.
[Abstract] [Full Text] [PDF]