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Toward the Ecological Genomics Underlying Plant Adaptation. Toward the Ecological Genomics Underlying Plant Adaptation. Deer mouse burrow. Birds/insects in a cotton wood. Fresh water and marine invasives. Aquilegia, Arabidopsis, Mimulus?.

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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


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




Seasonal Variation

Matt Horton

Megan Dunning


Local Population Structure

common haplotypes

149 Non singleton SNPs >6000 accessions

Global, Midwest, and UK

Megan Dunning, Yan Li


Diversity within and between populations
Diversity within and between populations

80 Major Haplotypes

Google Earth

Fly By


Diversity within and between populations1
Diversity within and between populations

17 Major Haplotypes

80 Major Haplotypes


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

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


Migration of clonal lines
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


Begin with regions spanning the native geographic range
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


Sweden spain

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


Solar Calc II

  • Kurt Spokas

  • Version 2.0a June 2006

    • USDA-ARS Website Midwest Area (Morris,MN)

    • http://www.ars.usda.gov/mwa/ncscrl


    *

    *

    *

    *

    *

    *

    *

    *

    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


    Kas col flowering time qtl
    Kas/Col floweringtime QTL

    FLM

    FRI


    Next species

    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.


    Aquilegia columbines
    Aquilegia (Columbines)

    Recent adaptive radiation, 350Mb genome


    Genetics of speciation along a hybrid zone
    Genetics of Speciationalong a Hybrid Zone


    Aquilegia columbine nsf genome complexity
    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)


    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)


    Which arrays should be used
    Which arrays should be used?

    BAC array

    cDNA array

    Long oligo array


    Which arrays should be used1
    Which arrays should be used?

    Gene array

    Exon array

    Tiling array

    35bp tile, 25mers 10bp gaps


    Which arrays should be used2
    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


    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



    Sfp s and cc gg methylome

    *

    *

    * *

    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


    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%


    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


    Natural copy variation on tiling arrays
    Natural Copy Variation on Tiling Arrays

    Segregating self seed from wild ME isolate (Early – Late)


    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)




    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



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