Toward the Ecological Genomics Underlying Plant Adaptation

1. Toward the Ecological GenomicsUnderlying Plant Adaptation Toward the Ecological GenomicsUnderlying Plant Adaptation Deer mouse burrow Birds/insects in a cotton wood Fresh water and marine invasives Aquilegia, Arabidopsis, Mimulus? Justin BorevitzEcology & EvolutionUniversity of Chicagohttp://naturalvariation.org/ Indiana Dunes National Lakeshore

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

3. Global and Local Population Structure Olivier Loudet

4. Local adaptation under strong selection

6. Seasonal Variation Matt Horton Megan Dunning

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

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

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

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

12. Migration of Clonal Lines Cluster 2 Cluster 20 Cluster 26 Cluster 10 PopName: CS LAK LR MAP MDN MNFPIN MNFPOT MNFRIV MSGA MUSKSP PAW PENT RIV YNG NumLines: 14 13 1 15 12 19 9 13 26 14 26 29 33 2 Cluster2: 128 lines from diff pops; Cluster10: 16/17 lines are MNFPIN; Cluster20: all 13 lines from MNFRIV; Cl`uster 26: all 18 lines from PENT

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

14. Seasons in the Growth Chamber Seasons in the Growth Chamber 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

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

16. * * * * * * * * 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 10 Days 1000X Seasonal Flowering Time Response Seasonal Flowering Time Response

17. Kas/Col floweringtime QTL FLM FRI

18. Next Species…. 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.

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

20. Genetics of Speciationalong a Hybrid Zone

22. 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)

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

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

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

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

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

28. Potential Deletions

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

30. SFP detection on tiling arrays Delta p0 FALSE Called FDR 1.00 0.95 18865 160145 11.2% 1.25 0.95 10477 132390 7.5% 1.50 0.95 6545 115042 5.4% 1.75 0.95 4484 102385 4.2% 2.00 0.95 3298 92027 3.4%

31. 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

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

33. FLM natural deletion Potential Deletions Suggest Candidate Genes FLOWERING1 QTL Chr1 (bp) MAF1 Flowering Time QTL caused by a natural deletion in FLM (Werner et al PNAS 2005)

34. Chip genotyping of a Recombinant Inbred Line Van x Col RIL 23

35. Chip genotyping of a Recombinant Inbred Line Van x Col RIL 23

36. NaturalVariation.org 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

37. http://www.plosone.org/