1. Genetics of Adaptation: Arabidopsis thaliana as an ecological model Justin Borevitz Ecology & Evolution University of Chicago naturalvariation.org

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

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

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

12. Quantitative Trait Loci

15. 6+ years ago

17. Local Population Variation

18. Local adaptation under strong selection

21. Seasonal Variation Matt Horton Megan Dunning

22. 48 Non singleton SNPs of 87 tested Megan Dunning, poster #268 Local Population Structure in the Midwest

23. 120 SNPs of 149 tested including inbred lines Norman Warthmann` Global Population Structure

24. 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

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

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

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

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

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

30. MarkerChr. LocationcM * GeneEnvironmentGene x Environment t-valuep- value t- value p- value t- value p- value 21607030chr1.2765017999.32.68<0.01-0.730.541.300.19 21607175chr3.514089414.13.19<0.010.850.49-1.160.25 GL1chr3.1036187049.5-4.94<0.011.120.38-1.890.06 MSAT4.39chr4.896590-15.94<0.013.660.07-5.82<0.01 44607955chr4.559148628.8-7.98<0.011.380.30-2.250.02 44607234chr5.15072247.7-4.11<0.012.030.18-3.66<0.01 Kas/Col flowering time QTL GxE Chr4 FRI

31. 768 VanC AIL-RILs 149 + 87 SNPs Stock Center Release (Evadne Smith) 768 VanC AIL-RILs 149 + 87 SNPs Stock Center Release (Evadne Smith) Van no mitochondrial insertion FLC Total Leaf Number

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

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

34. http://www.plosone.org/

35. Aquilegia (Columbines)

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

37. 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

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

41. > 20k dbEST 11/14/2003 Animal lineage: good coverage Plant lineage: crop plant coverage

42. 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