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Composite/ Legume

Composite/ Legume. Cotton wood, Oak. Arabidopsis lyrata Miriam grass. Aquilegia, Arabidopsis, Mimulus?. Genomic Systems underlying the genetics of local adaptation. Genomic Systems underlying the genetics of local adaptation.

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Composite/ Legume

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  1. Composite/ Legume Cotton wood, Oak Arabidopsis lyrata Miriam grass Aquilegia, Arabidopsis, Mimulus? Genomic Systems underlyingthe genetics of local adaptation Genomic Systems underlyingthe genetics of local adaptation Justin BorevitzEcology & EvolutionUniversity of Chicagohttp://naturalvariation.org/ Indiana Dunes National Lakeshore

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

  3. 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

  4. 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)

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

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

  7. 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

  8. Potential Deletions

  9. * * * * 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

  10. 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%

  11. 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

  13. Verification of methylation polymorphisms

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

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

  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

  19. Seasonal Variation Matt Horton Megan Dunning

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

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

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

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

  24. 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

  25. Solar Calc II • Kurt Spokas • Version 2.0a June 2006 • USDA-ARS Website Midwest Area http://www.ars.usda.gov/mwa/ncscrl

  26. 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

  27. * * * * * * * * 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

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

  29. Genetics of Speciationalong a Hybrid Zone

  30. 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)

  31. 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.

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

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