Approaches to describe the shade avoidance response genetic network

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Approaches to describe the shade avoidance
response genetic network 05-16-07
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the shade avoidance response

• produced by
• surrounding vegetation
• symptoms
• elongation of stem and petioles
• upward orientation of leaves
• reduced branching
• early flowering

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the network the old way
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the shade avoidance response network the old way
reverse genetics
light
Sun (R/FR)2.3
Shade (R/FR)0.6
light receptors
light signaling 1
light signaling 3
light signaling 2
green color
short stem
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the old way reverse genetics
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the old way reverse genetics
x
x
x
x
shade
shade
sun
sun
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classic shade avoidance response networks
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the shade avoidance response has an adaptive
value
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Who is the responsible for the variation in the
shade avoidance response
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Arabidopsis as a model organism to study natural
variation
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resources for the study of natural variation in
the shade avoidance response
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alternative ways of building networks
quantitative trait locus analysis (QTL analysis)
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my QTL analysis

• Traits
• leaves 4 and 6
• total length
• blade length
• blade width
• petiole length
• leaf angle

• bolting time
• rosette diameter
• flowering time
• number of leaves
• hypocotyl length
• internode length

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how do i make sense out of 14000 genes?
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how do i make sense out of 14000 genes?
Sessa, G., M. Carabelli, et al. (2005). "A
dynamic balance between gene activation and
repression regulates the shade avoidance response
in Arabidopsis." Genes Dev 19(23) 2811-5.
1176 genes differentially expressed
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my first network
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The newest approaches the eQTL analysis

• Keurentjes, J. J. B., J. Fu, et al. (2007).
  "Regulatory network construction in Arabidopsis
  by using genome-wide gene expression quantitative
  trait loci." PNAS 104(5) 1708-1713.

• West, M. A. L., K. Kim, et al. (2007). "Global
  eQTL Mapping Reveals the Complex Genetic
  Architecture of Transcript-Level Variation in
  Arabidopsis." Genetics 175(3) 1441-1450.

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eQTL analysis
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corroboration of common network motifs in yeast
by eQTL analysis

• Bing, N. and I. Hoeschele (2005). "Genetical
  Genomics Analysis of a Yeast Segregant Population
  for Transcription Network Inference." Genetics
  170(2) 533-542.

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eQTL network in yeast

• Bing, N. and I. Hoeschele (2005). "Genetical
  Genomics Analysis of a Yeast Segregant Population
  for Transcription Network Inference." Genetics
  170(2) 533-542.

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so how about the shade avoidance response network?
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eQTL analysis