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

Approaches to describe the shade avoidance response genetic network 05-16-07. Sun (R/FR)=2.3. Shade (R/FR)=0.6. 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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Approaches to describe the shade avoidance response genetic network 05-16-07

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

  2. Sun (R/FR)=2.3 Shade (R/FR)=0.6 the shade avoidance response • produced by: surrounding vegetation • symptoms: elongation of stem and petioles upward orientation of leaves reduced branching early flowering

  3. the network the old way

  4. 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

  5. light light light x x x x light receptors light receptors light receptors light signaling 1 light signaling 3 light signaling 1 light signaling 3 light signaling 1 light signaling 3 light signaling 2 green color light signaling 2 green color light signaling 2 green color short stem short stem shade shade shade sun sun sun short stem the old way: reverse genetics

  6. light light x light light receptors light receptors light receptors light signaling 1 light signaling 3 light signaling 1 light signaling 1 light signaling 3 light signaling 3 light signaling 2 green color light signaling 2 light signaling 2 green color green color short stem shade sun short stem short stem the old way: reverse genetics x x x x shade shade sun sun

  7. classic shade avoidance response networks

  8. the shade avoidance response has an adaptive value…

  9. Who is the responsible for the variation in the shade avoidance response

  10. Arabidopsis as a model organism to study natural variation

  11. resources for the study of natural variation in the shade avoidance response

  12. alternative ways of building networks: quantitative trait locus analysis (QTL analysis)

  13. 14428 genes 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

  14. how do i make sense out of 14000 genes?

  15. Sun (R/FR)=2.3 Shade (R/FR)=0.6 549!!! 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

  16. my first network

  17. 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.

  18. I II III IV V eQTL analysis

  19. 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.

  20. 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.

  21. I II III IV V so how about the shade avoidance response network?

  22. eQTL analysis

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