1. Ecological Genomics Underlying Plant Evolution Deer mouse burrowBirds/insects in a cotton woodFresh water and marine invasives Aquilegia, Arabidopsis, Mimulus? Indiana Dunes National Lakeshore Justin Borevitz Ecology & Evolution University of Chicago http://naturalvariation.org/ Ecological Genomics Underlying Plant Evolution

2. Talk Outline Genetic Diversity ~ biodiverisity –Population structure, migration, admixture Phenotyping in Natural environments –Seasonal Variation in the Lab Next Species, Aquilegia SNP/Tiling microarrays –Methylation –Deletions Ecological Conservation Genomics Genetic Diversity ~ biodiverisity –Population structure, migration, admixture Phenotyping in Natural environments –Seasonal Variation in the Lab Next Species, Aquilegia SNP/Tiling microarrays –Methylation –Deletions Ecological Conservation Genomics

3. Global and Local Population Structure Olivier Loudet

4. Local adaptation under strong selection

6. Seasonal Variation Matt Horton Megan Dunning

7. 149 Non singleton SNPs >6000 accessions Global, Midwest, and UK common haplotypes Local Population Structure Megan Dunning, Yan Li

8. 80 Major Haplotypes Diversity within and between populations Google Earth Fly By

9. 17 Major Haplotypes 80 Major Haplotypes Diversity within and between populations

10. Variation within a field http://naturalvariation.org/hapmap

11. Begin with regions spanning the Native Geographic range Nordborg et al PLoS Biology 2005 Li et al PLoS ONE 2007 Tossa Del Mar Spain Lund Sweden

12. 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

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

14. Seasonal Flowering Time Response Kas/Col RILs Van/Col RILs 384 diverse Accessions Spain/Sweden Spring (early late) Fall (early late) Kas/Col RILs Van/Col RILs 384 diverse Accessions Spain/Sweden Spring (early late) Fall (early late) ******** ******** 10 Days 1000X

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

16. Genetics of Speciation along a Hybrid Zone

18. Aquilegia (Columbine) NSF Genome Complexity Microarray floral development –QTL candidates Physical Map (BAC tiling path) –Physical assignment of ESTs QTL for pollinator preference –~400 RILs, map abiotic stress –QTL fine mapping/ LD mapping Develop transformation techniques –VIGS Whole Genome Sequencing (JGI 2007) Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus Nordborg (USC) Justin Borevitz (U Chicago) Jeff Tompkins (Clemson)

19. SNP SFP MMMMMM MMMMMM Chromosome (bp) conservation SNP ORFa start AAAAA Transcriptome Atlas ORFb deletion The Genomic Response Mediating the Environment

20. Which arrays should be used? cDNA array Long oligo array BAC array

21. Which arrays should be used? Gene array Exon array Tiling array 35bp tile, 25mers 10bp gaps

22. Which arrays should be used? Tiling/SNP array 2007 250k SNPs, 1.6M tiling probes SNP array Ressequencing array How about multiple species? Microbial communities? Pst,Psm,Psy,Psx, Agro, Xanthomonas, H parasitica, 15 virus,

23. RNA DNA Universal Whole Genome Array Transcriptome Atlas Expression levels Tissues specificity Transcriptome Atlas Expression levels Tissues specificity Gene/Exon Discovery Gene model correction Non-coding/ micro-RNA Gene/Exon Discovery Gene model correction Non-coding/ micro-RNA Alternative Splicing Comparative Genome Hybridization (CGH) Insertion/Deletions Copy Number Polymorphisms Comparative Genome Hybridization (CGH) Insertion/Deletions Copy Number Polymorphisms Methylation Chromatin Immunoprecipitation ChIP chip Chromatin Immunoprecipitation ChIP chip Polymorphism SFPs Discovery/Genotyping Polymorphism SFPs Discovery/Genotyping Control for hybridization/genetic polymorphisms to understand TRUE expression variation RNA Immunoprecipitation RIP chip RNA Immunoprecipitation RIP chip Antisense transcription Allele Specific Expression

24. Potential Deletions

25. Deltap0FALSECalledFDR 1.000.951886516014511.2% 1.250.95104771323907.5% 1.500.9565451150425.4% 1.750.9544841023854.2% 2.000.953298920273.4% SFP detection on tiling arrays

26. SFPs and CC*GG Methylome HpaII digestion Random labeling MspI digestion Col Genomic DNA HpaII digestion Random labeling MspI digestion Van Genomic DNA SFP Hpa msp Intensity Col Hpa msp Van * SFP * * * Hpa msp Col Hpa msp Van mSFP * * * Hpa msp Col Hpa msp Van * Full model: Intensity ~ genotype + enzyme + genotype x enzyme

27. EnzymeGenotype x enzyme p-valueHpaII > MspI a p-valueCol-specific b Van-specific c <0.012373<0.011062407 <0.054522<0.032389944 <0.16324<0.0537001515 Gene d 3628 (20%)Gene d 3498 (20%) Total gene e 17760Total gene e 17760 Promoter f 305 (6%)Promoter f 455 (9%) Total promoter g 5041Total promoter g 5041 Intergenic h 1298 (16%)Intergenic h 782 (9%) Total intergenic i 8264Total intergenic i 8264 Methylation polymorphisms are extensive a Features of constitutive CG methylation bc Features of Col- or Van-specific methylation df cDNAs or promoters with feature(s) of enzyme effect (p < 0.1) or genotype × enzyme interaction (p < 0.05) eg cDNAs or promoters containing CCGG feature(s) h Intergenic features (excluding cDNAs or promoters) of enzyme effect (p < 0.1) or genotype × enzyme interaction (p < 0.05) i Intergenic (excluding cDNAs or promoters) CCGG-containing features

28. Verification of methylation polymorphisms

30. Col Van Col♂ x Van♀ Van♂ x Col♀ CC*GG chromomethylase 2 (CMT2) exon19 epiTyper

31. Genic distribution of constitutive and polymorphic methylation sites

32. bp Co-methylation of pericentromere regions

33. Natural Copy Variation on Tiling Arrays Segregating self seed from wild ME isolate (Early – Late)

34. Potential Deletions Suggest Candidate Genes FLOWERING1 QTL Chr1 (bp) Flowering Time QTL caused by a natural deletion in FLM FLM FLM natural deletion (Werner et al PNAS 2005)

35. Chip genotyping of a Recombinant Inbred Line Van x Col RIL 23 logLK 20 AA20198 AB587 BB13064

36. Next Species…. Eco region diversity plant community population genomics. Genetic variation within and between species and locations Remnant, restored, reconstructed, prairies savannahs Comparative population structure, in species assemblages Differential effects on annuals, perennials, selfers, outcrossers Categorize existing genetic diversity- Conservation Genetics Restore with maximal regional diversity samples to allow natural selection breeding. Eco region diversity plant community population genomics. Genetic variation within and between species and locations Remnant, restored, reconstructed, prairies savannahs Comparative population structure, in species assemblages Differential effects on annuals, perennials, selfers, outcrossers Categorize existing genetic diversity- Conservation Genetics Restore with maximal regional diversity samples to allow natural selection breeding. Next Species….

38. Nielsen and Hole, 1963

39. Are Biofuels the Answer?...

40. The Next Generation of Biofuels: Greenhouse-Neutral Biofuels from High-Diversity Low-Input Prairie Ecosystems by David Tilman University of Minnesota

41. http://www.plosone.org/

42. NaturalVariation.org USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zoellner USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zoellner University of Chicago Xu Zhang Yan Li Peter Roycewicz Evadne Smith Megan Dunning Joy Bergelson Michigan State Shinhan Shiu Purdue Ivan Baxter University of Chicago Xu Zhang Yan Li Peter Roycewicz Evadne Smith Megan Dunning Joy Bergelson Michigan State Shinhan Shiu Purdue Ivan Baxter