Drought_PhD Booklet 2012 v2

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  • 7/31/2019 Drought_PhD Booklet 2012 v2



    GroupPhD research areas


  • 7/31/2019 Drought_PhD Booklet 2012 v2


  • 7/31/2019 Drought_PhD Booklet 2012 v2


    The teams

    Forward genetics: from phenotype to geneWe observe and analyse the characteristics of drought tolerance in wheat and barley

    and seek to identify the genes responsible of the tolerance. The following projects have

    been initiated:

    Detailed physiological analysis ofdrought tolerant and intolerant wheat

    lines under controlled environment

    and field conditions

    Genetic analysis of drought toleranceunder field and growth room

    conditions in three large populations

    of wheat Genetic dissection of root

    development and architecture under

    normal and drought conditions

    Development of metabolite andtranscript profiles of parental lines

    under water limited conditions

    Reverse genetics: from gene to phenotypeWe seek to isolate gene sequences

    important for conferring drought

    tolerance from both model and crop

    species. Cloned gene sequences are

    introduced into our target crop

    species by either biolistics (wheat) or


    transformation (barley). Transgenic

    plants are then assayed under

    controlled and field conditions fordrought tolerance. Project areas


    Bioinformatics and the identificationof drought related gene sequences

    Transcription factors and theregulation of drought-stress responses

    Development of commercially viabledrought tolerant GM wheat and barley

  • 7/31/2019 Drought_PhD Booklet 2012 v2


    Our collaboratorsBBG University of Adelaide (South Australia)

    DPI La Trobe University (Victoria)

    INRA Clermont-Ferrand (France)

    SCRI Dundee (Scotland)

    IPK Gatersleben (Germany)

    CIMMYT (Mexico)

    Pioneer Hi-Bred International/DuPont (USA)

    INRA Montpellier (France)

    University of Bologna (Italy)

    The techniques

    Molecular biology

    DNA and RNA extractions

    PCRs and restriction digests

    Transcript profiling by microarrays and


    Metabolite and protein profiling

    Confocal microscopy

    BAC library screening


    Biolistics andAgrobacterium-mediated plant


    Fluorescent reporters (GFP, mCherry)


    Plant Physiology

    High throughput phenotyping by imaging

    Chlorophyll content

    Stomatal conductance


    Plant and soil water potentials

    Canopy temperature

    Root and shoot anatomy

    Root morphology


    QTL mapping

    Molecular markers

    Positional cloning

    Marker assisted selection

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    Potential PhD supervisors:

    Dr Ute Baumann

    Dr Omid Eini

    Dr Delphine Fleury

    Dr Chunyuan Huang

    Dr Nataliya Kovalchuk

    Prof. Peter Langridge

    Dr Sergiy Lopato

    Prof Diane Mather

    Dr Boris Parent

    Dr Bujun Shi

    Dr Ryan Whitford

    Adelaide node of the ACPFG at the Plant Genomics Centre

    (Waite Campus, University of Adelaide)

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    PhD projects:

    Project title: Genetic and physiological characterization of tolerance to heat-

    induced floret sterility in wheat

    SUPERVISOR: Dr Nick Collins



    Brief periods of heat stress severely impact on wheat production, and this situation will worsen with

    climate change. However, it is difficult for breeders to select for heat tolerance in the field, because

    heat affects wheat in different ways depending on the growth stage, and because natural heat

    events are unpredictable in severity and timing. Therefore, there is an urgent need for reproducible

    growth chamber assays for heat tolerance that are relevant to the field, molecular markers linked to

    genes controlling heat tolerance, or cloned heat tolerance genes for transformation breeding.

    One type of heat damage is the floret sterility (decrease grain set) following heat events at around or

    just before pollination. Anecdotal reports indicate that Australian durum wheat varieties are more

    prone to this form of heat damage than bread wheats, however this difference needs to be formally

    tested. Besides this, there is virtually nothing known about how much wheat genotypes naturally

    vary for tolerance to heat-induced sterility effects.


    Use a growth chamber to characterize the precise developmental stages where durum andbread wheat are most sensitive to heat-induced sterility. Use this information to design

    tolerance assays targeting sterility effects of heat.

    Screen local and exotic durum and bread wheat varieties for variation in tolerance to heat-induced sterility.

    Characterize the biological basis for the tolerance in various sources. Use new or established populations to map chromosome regions (QTLs) controlling variation

    in tolerance.

    Initiate positional cloning of heat tolerance genes via candidate genes.


    Growth chamber assays for heat tolerance. Characterize tiller stages by examining developing spikes by microscopy (stage of meiosis or

    development of female reproductive structures).

    In vitro pollen viability/tube-growth assays. Chlorophyll fluorescence measurements (Fv/Fm). SSR, DArT and SNP markers. Comparative mapping and sequence analysis for targeted marker generation and candidate

    gene identification.

    Gene transcript quantification and tissue-localization by qRT-PCR.

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    Barnabas B, Jager K, Feher A (2008). The effect of drought and heat stress on reproductive processes

    in cereals. Plant, Cell and Environment 31:11-38.

    Saini HS, Sedgley M, Aspinall D (1984). Developmental anatomy in wheat of male sterility induced byheat stress, water deficit or abscisic acid. Australian Journal of Plant Physiology 11:243-253.

    Singh SK, Kakani VG, Brand D, Baldwin B, Reddy KR (2008). Assessment of cold and heat tolerance of

    winter-grown canola (Brassica napus L.) cultivars by pollen-based parameters. Journal of Agronomy

    & Crop Science 194:225-236.

    Heat treatment of

    wheat plants using a

    growth chamber. Plants

    are grown in thegreenhouse before and

    after a brief heat

    treatment applied at a

    specific developmental


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    Project title: Positional cloning of QTL for drought tolerance in wheat

    SUPERVISORS:Dr Delphine Fleury, Prof. Peter Langridge

    CONTACT DETAILS:delphine.fleury@acpfg.com.au,peter.langridge@acpfg.com.au


    The key objective of the drought program of ACPFG is to generate detailed knowledge of the

    mechanisms of drought adaptation under the Mediterranean type growing conditions, with a view

    to developing plants tolerant to multiple components: osmotic & oxidative stress, heat, dehydration.

    This type of drought is characterised by water deficit at the late stages of crop development, usually

    during flowering and grain filling.

    We have identified several QTLs of wheat controlling yield in dry environment. Four QTL are

    targeted for map-based cloning, for which we already have large populations of recombinant inbred

    lines. The availability of new genomics resources, particularly the next-generation sequencing data,

    enables now to make tremendous progress in gene cloning in wheat. We are now increasing the

    number of markers for fine-mapping of each region to the resolution of each local map to

  • 7/31/2019 Drought_PhD Booklet 2012 v2


    Project title: Genetic study of floral architecture for hybrid wheat systemSUPERVISORS:Dr Delphine Fleury, Dr Ryan Whitford

    CONTACT DETAILS:delphine.fleury@acpfg.com.au,ryan.whitford@acpfg.com.au

    BACKGROUNDOne of the Green revolution technologies was the hybrid seeds. Hybrid plants obtained by inter-

    crossing inbred lines show an increase in biomass and production. This heterotic effect is particularly

    strong in out-breeding species such as maize. Past studies showed that yield increase is possible to

    achieve in hybrid wheat compared to the conventional inbred lines. However due to its self-

    pollinated nature, inter-crossing plants is difficult. One of the factors that impair out-crossing in

    wheat is its flower architecture and biology: the spike is compact, male and female are enclosed in

    spikelet, anthers and styles are short, flowering time isnt synchronised between male and female

    parental lines.

    Chasmogamic species are characterized by open flowers and exposed stamens and styles that

    facilitate inter-pollination. These traits are usually controlled by few major genes. Heritability of

    flower architecture is medium to high suggesting that progress could be made in improving thecross-pollinating ability of parental lines. The aim of this project is to identify wheat loci and genes

    that will increase chasmogamy and facilitate inter-crossing using hybridization systems.

    AIMS AND SIGNIFICANCE:Identify QTL and genes controlling flower architecture of wheat for increasing

    hybridization rate in hybrid seed production.