1. Composite/ LegumeCotton wood, OakArabidopsis lyrata Miriam grass Aquilegia, Arabidopsis, Mimulus? Indiana Dunes National Lakeshore Justin Borevitz Ecology & Evolution University of Chicago http://naturalvariation.org/ Genomic Systems underlying the genetics of local adaptation

2. Talk Outline SNP/Tiling microarraysSNP/Tiling microarrays –Methylation and Transcriptional polymorphism Genetic DiversityGenetic Diversity –Population structure, migration, admixture Phenotyping in natural environmentsPhenotyping in natural environments –Seasonal nariation in the Lab Next species, AquilegiaNext species, Aquilegia Ecological Conservation GenomicsEcological Conservation Genomics

3. 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

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

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

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

7. 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,

8. Potential Deletions

9. 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

10. 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

11. 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

12. Verification of methylation polymorphisms

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

15. bp Co-methylation of pericentromere regions bp 1Mb bins 200kb sliding window

16. Genic distribution of constitutive and polymorphic methylation sites promoter 5’ CDS 3’ downstream

17. Correlation of polymorphic CG methylation and gene expression variation What’s next? How stable are these >5000 CC*GG (mSFP) sites? Do they change with development? Do they change with the environment? What is the genetic architecture? mQTL cis/trans

18. Global and Local Population Structure Olivier Loudet

20. Seasonal Variation Matt Horton Megan Dunning

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

22. 149 Non singleton SNPs >6600 accessions Global, Midwest, and UK 384 diverse haplotypes 250,000 SNPs for LD mapping Local Population Structure Yan Li

23. 80 Major Haplotypes Diversity within and between populations Google Earth Fly By

24. 17 Major Haplotypes 80 Major Haplotypes Diversity within and between populations

25. 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

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

27. 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

28. 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

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

30. Genetics of Speciation along a Hybrid Zone

32. 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)

33. 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….

34. NaturalVariation.org USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel University of Chicago Xu Zhang Yan Li Evadne Smith Megan Dunning Joy Bergelson