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Oat Innovation: synthetic hexaploid oat Emir Islamovic USDA-ARS Aberdeen ID [email protected] CORE Meeting March 7-8, 2013, Ottawa, Canada

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  • Oat Innovation: synthetic hexaploid oat

    Emir IslamovicUSDA-ARS Aberdeen ID

    [email protected]

    CORE MeetingMarch 7-8, 2013, Ottawa, Canada

    PresenterPresentation NotesPAG 2013, San Diego, CAStrimagdo: diploid and tetraploid oat transcriptome interactions in a synthetic hexaploid oatEmir Islamovic1, Rob Reid2, Raad Gharaibeh2, Cory Brouwer2, Jessica A. Schlueter2, Shannon D. Schlueter2, Gongshe Hu1, Robert Campbell1, Irene Shackelford1, Gideon Ladizinsky3, Eric N. Jellen4, Jeff Maughan4, Rachel Redman5, Melissa Coon4, Joseph Lutz6, Lane Johnson6, Rebekah E. Oliver6, Ryan H. Brown6 and Eric W. Jackson6, (1)USDA-ARS, Aberdeen, ID, (2)University of North Carolina at Charlotte, Charlotte, NC, (3)The Hebrew University of Jerusalem, Israel, (4)Brigham Young University, Provo, UT, (5)University of Utah, UT, (6)General Mills, Kannapolis, NC ABSTRACTThe genomic origins of the natural hexaploid oat Avena sativa are still uncertain. However, it is certain that the evolution of hexaploid oats, whether through allopolyploidy (merging of different oat genomes) or autopolyploidy (duplication of existing oat genomes) or a combination of both, required the existence of two genomes (tetraploid) prior to addition of another genome (diploid) in a common nucleus. The advantage of an additional genome had to be immediate for this new species to survive and this advantage had to be a product of altered “tetraploid” gene expression. In this study, we compared transcriptomes of diploid oat, tetraploid oat and a merged diploid/tetraploid in a synthetic hexaploid oat to elucidate genome interactions and alterations to gene expression. Briefly, a synthetic hexaploid oat, ASASCCDDM (2n=42), was previously generated by hybridization of Avena strigosa diploid oat, ASAS (2n=14), and Avena magna tetraploid oat, CCDDM (2n=28), in Gideon Ladizinsky's oat genetics program. RNA was extracted from immature seed embryos and each transcriptome was assembled de novo using RNA-Seq. We will discuss gene expression, gene silencing and derepression, and present possible underlying mechanisms of this phenomenon.

    mailto:[email protected]

  • World oat production?

    Innovation

  • Boguslaw Lapinski and Maciej Kala (Poland)

    Innovation:Interspecies cross

  • Innovation:Synthetic Hexaploid

    AADiploid X

    CCDDTetraploid

    AACCDDSynthetic Hexaploid

    Gideon Ladizinsky (2000) Euphytica 116:2313-235

  • Understanding oat transcriptome

    AACCDDAvena sativa

    AACCDDSynthetic Hexaploid

    AADiploid X

    CCDDTetraploid

  • Rick Jellen (unpublished)

    C-banding changes

  • Avena sativa (cultivated oat)

    Sanz et al (2010) TAG

    •Translocation 7CS‐17AL•Translocation 3CS‐14DL• Rearranged 19A/20D and 17A• NOR heterochromatin• 2C arm‐ratio• 9D centromeric heterochromatin• 5CL telomeric heterochromatin• HiFi bands: Amagalon chromatin?• Pg16 tetrasomy

    C-banding changes

  • Oat Quest

  • Oat Quest

  • Oat Quest

  • RNA-seq

    AACCDDAvena sativa

    AACCDDSynthetic Hexaploid

    AADiploid

    X CCDDTetraploid

    80% common

    80% common

    Poster P0299 – Robert Reid

    PresenterPresentation Notes“Talking Genomes” - Transcriptome comparison of diploid, tetraploid and newly synthesized hexaploid oatRobert W. Reid1, Emir Islamovic2, Raad Gharaibeh1, Cory Brouwer1, Jessica Schlueter1, Shannon Schlueter1, Gongshe Hu2, Robert Campbell2, Irene Shackelford2, Gideon Ladizinsky3, Rick Jellen4, Jeff Maughan4, Rachel Redman Hulse5, Melissa Coon Fogarty4, Lane Johnson6, Rebekah Oliver6, Ryan Brown6, Joe Lutz6, Eric Jackson6

    Poster P0299

    Our study showed that newly synthesized hexaploid, with 39497 gene candidates, maintained a similar transcriptome, about 80%, as combined Avena magna and Avena strigosa transcriptomes, with 49983 gene candidates. This suggests that diploid and tetraploid genomes mostly conserved their gene expression after merging into a new hexaploid state. Interestingly, the similarity of transcriptomes between evolved oat genome (Leggett) and newly merged hexaploid is also about 80%.This leaves 20% of transcriptome differences to be explained by either directed genetic or epigenetic changes. Current thought is that the genetic and epigenetic repatterning of transcriptome is programmed rather than a chaotic response to the new merger, suggesting allopolyploidy being sensed by cell machinery and triggering a complex but methodical cellular response, which is observed in transcriptome changes.

    25 million reads per sample

  • β-glucan in oats or 2+5=3

    β-glucan levels:Diploid 5.0 %Tetraploid 2.2 %Synthetic Hexaploid 3.1%Cultivated Hexaploid 5.4%

    AACCDDAvena sativa

    AACCDDSynthetic Hexaploid

    AADiploid

    X CCDDTetraploid

    80% common

    80% common

  • β-glucan pathway in barley

    Islamovic et al (2013) Mol Breeding

  • β-glucan pathway gene expression

    0

    0.5

    1

    1.5

    2

    2.5

    UGP2 CslF6 CesA2 GPI AGP2 Eng1 GBSSI Sbe1 Amy

    Diploid

    Tetraploid

    Synthetic Hexaploid

    Cultivated Hexaploid

    Fold

    cha

    nges

  • CslF6 expression

    Diploid15%

    Tetraploid37%

    Synthetic Hexaploid

    48%

    CslF6β-glucan levels:Diploid 5.0 %Tetraploid 2.2 %Synthetic Hexaploid 3.1%Cultivated Hexaploid 5.4%

  • CslF6 alleles

    990 2409/24932178

    124 126 489 1455

    213 612 978

    A Genome

    C Genome

    D Genome

    A genome expression haplotype (TAAA)

    C genome expression haplotype (TGTC)

    D genome expression haplotype (ACA) Melissa Coon Fogarty (unpublished)

  • CslF6 alleles expressionRe

    lativ

    e Ex

    pres

    sion

    0

    0.1

    0.2

    0.3

    0.4

    0.5

    0.6

    Diploid Tetraploid Synthetic Hexaploid Cultivated Hexaploid

    C

    D

    A

    β-glucan levels:Diploid 5.0 %Tetraploid 2.2 %Synthetic Hexaploid 3.1%Cultivated Hexaploid 5.4%

    Melissa Coon Fogarty (unpublished)

  • ClsF6 structure

    CslF6 C-allele CslF6 A and D allele

    Melissa Coon Fogarty (unpublished)

  • Future Steps

    Methylation – Epigenetic repatteringAllelic expression Non-random elimination of DNA sequences Activation of retroelements –gene silencing

  • ACKNOWLEDGEMENTS

    http://www.usda.gov/wps/portal/usda/usdahomehttp://www.csrees.usda.gov/http://www.generalmills.com/

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