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Light Affects the Entire Plant Life Cycle

Genetics of Adaptation: Arabidopsis thaliana as an ecological model Justin Borevitz Ecology & Evolution University of Chicago naturalvariation.org. Light Affects the Entire Plant Life Cycle. de-etiolation. }. hypocotyl. Light Affects the Entire Plant Life Cycle.

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Light Affects the Entire Plant Life Cycle

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  1. Genetics of Adaptation: Arabidopsis thaliana as an ecological modelJustin BorevitzEcology & EvolutionUniversity of Chicagonaturalvariation.org

  2. Light Affects the Entire Plant Life Cycle de-etiolation } hypocotyl

  3. Light Affects the Entire Plant Life Cycle Light response variation can be seen under constant conditions in the lab Natural Variation != Natural Selection

  4. Widely Distributed Olivier Loudet http://www.inra.fr/qtlat/NaturalVar/NewCollection.htm

  5. Quantitative Trait Loci

  6. 6+ years ago

  7. Local Population Variation

  8. Local adaptation under strong selection

  9. Seasonal Variation Matt Horton Megan Dunning

  10. Local Population Structure in the Midwest 48 Non singleton SNPs of 87 tested Megan Dunning, poster #268

  11. Global Population Structure 120 SNPs of 149 tested including inbred lines Norman Warthmann`

  12. Collections • > 500 lines N and S Sweden (Nordborg) • > 400 Lines France and Midwest (Bergelson) • 800 Lines Midwest (Diane Byers IL state) • 400 lines Midwest (Borevitz) • 857 Accessions stock center (Randy Scholl) • Others welcome… • Will be genotyped with Sequenom 149 SNPs $0.03 per SNP, 40plex > 400SNPs available

  13. Seasons in the Growth Chamber Seasons in the Growth Chamber Developmental Plasticity == Behavior Developmental Plasticity == Behavior Sweden Spain • Changing Day length • Cycle Light Intensity • Cycle Light Colors • Cycle Temperature • Changing Day length • Cycle Light Intensity • Cycle Light Colors • Cycle Temperature Geneva Scientific/ Percival

  14. Solar Calc II • Kurt Spokas • Version 2.0a June 2006 • USDA-ARS Website Midwest Area (Morris,MN) • http://www.ars.usda.gov/mwa/ncscrl

  15. Genetic map of the Kas-1 x Col-gl1 RIL population I II III IV V 55 markers from Wolyn et al. (2004) & 64 additional SNP markers.

  16. Distribution of flowering time among 96 Kas-1/Col-gl1 RILs Col-gl1 Col-gl1 Number of RILs Sweden 2 Sweden 1 Kas1 Kas1 Col-gl1 Col-gl1 Spain 1 Spain 2 Number of RILs Kas1 Kas1

  17. Kas/Col flowering time QTL Chr4 FRI Yan Li, poster #362

  18. Kas/Col flowering time QTL GxE Chr4 FRI

  19. FLC Total Leaf Number Van no mitochondrial insertion 768 VanC AIL-RILs 149 + 87 SNPs Stock Center Release (Evadne Smith) 768 VanC AIL-RILs 149 + 87 SNPs Stock Center Release (Evadne Smith)

  20. Webcam • http://growth1-cam.bsd.uchicago.edu • Record growth

  21. With the Aid of Genomics Experimental Design Mapping population Marker Identification Genotyping Phenotyping QTL Analysis Fine Mapping Candidate gene Polymorphisms gene expression loss of function QTL gene Confirmation QTL gene Confirmation Phenotyping QTL Analysis Fine Mapping Genomics path Experimental Design Mapping population

  22. http://www.plosone.org/

  23. Aquilegia (Columbines)

  24. Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus Nordborg (USC) Justin Borevitz (U Chicago) Jeff Tompkins (Clemson)

  25. 300 F4 RILs growing (Evadne Smith) • TIGR gene index 85,000 ESTs >16,00 SNPs • Complete BAC physical map Clemson • Nimblegen arrays of 5 floral whorls Whole Genome Shotgun Sequencing 2007 JGI

  26. Aquilegia (Columbines) Recent adaptive radiation, 350Mb genome

  27. Plant lineage: crop plant coverage > 20k dbEST 11/14/2003 Animal lineage: good coverage

  28. NaturalVariation.org NaturalVariation.org USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zollner USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zollner University of Chicago Xu Zhang Yan Li Peter Roycewicz Evadne Smith Michigan State Shinhan Shui Purdue Ivan Baxter University of Chicago Xu Zhang Yan Li Peter Roycewicz Evadne Smith Michigan State Shinhan Shui Purdue Ivan Baxter

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