CILR research

Legumes have several distinct advantages as experimental material: this is why we chose to investigate them.

  1. are significant to human food, animal feed and biofuel;
  2. have a major ecosystem contribution;
  3. are genetically, ecologically and developmentally diverse;
  4. perform key plant processes, such as nutrient uptake, photosynthesis, nitrogen fixation, specialised metabolite biosynthesis, seed, root, flower and leaf development, disease (biotic) and abiotic (i.e., drought, acidity) stress responses;
  5. They enter a complex symbiotic interaction with soil bacteria to develop de novo a new organ, namely the nitrogen root nodule;
  6. They are often larger plants, allowing effective biochemical analysis of gene products;
  7. They have a large data base in genomics (four genomes sequenced by 2011), transcriptome profiling, proteomics, metabolomics and biochemistry, plant physiology, and agronomy due to the significance of major legume crops.

Reseach program information

Soybean Nodulation Control

Soybean

Bradyrhizobium japonicum Nod Factor responses

  1. Analysis of soybean Nod Factor (NF) receptors GmNFR1 and GnNFR5
  2. Analysis of soil stress responses specifically acid soil
  3. Analysis of the role of GmNORK genes
  4. Determination of the 3D protein structure of the GmNRF1/5 complex and ligand interaction
  5. Analysis of gene function in early nodulation

Autoregulation of Nodulation (AON) control

  1. Analysis of GmNARK 3-D structure and ligand interaction
  2. Analysis of CLE-peptide signals in infection as well as nitrate response (site-directed mutagenesis, peptide detection, receptor binding)
  3. Chemical structure determination of the shoot-derived inhibitor (SDI)
  4. Analysis gene expression in soybean leaf after xylem sap feeding
  5. Development of peptide-feeding method
  6. Analysis of supernodulation in Phaseolis vulgaris (common bean): genomics, CLE overexpression
  7. Hormonal cross-talk (cytokinins, ethylene) during AON in Lotus japonicus

Pongamia pinnata

Pongamia pinnata: Genomics and Biotechnology of sustainable biofuel production.

Pongamia genetics and genomics

  1. Trait definition and arboretum collection
  2. Illumina deep-sequencing database
  3. Pongamia transcriptome database
  4. Pongamia gene discovery
  5. Pongamia gene expression analysis
  6. Pongamia molecular markers (ISSR/SSR)
  7. Pongamia seed storage protein genes
  8. Pongamia sexual hybridisation
  9. Pongamia VIGS (Virus induced gene silencing)
  10. Pongamia nodulation and nitrogen fixation
2. Pongamia cell culture and transformation
  1. In vitro organogenesis/embryogenesis
  2. Hairy root transformation with Agrobacterium_rhizogenes
  3. Stable transformation
  4. Pongamia clonal propagation (rooted cuttings/grafting/tissue and organ culture)
3. Pongamia eco-climatic growth analysis

Immature seeds at Gatton (15 months old Pongamia).

Legume Stress-Hormone Responses

1. Ethylene insensitive mutants and transgenics

  1. AtEtr1-1 ethylene insensitive L. japonicus transgenics
  2. EIN-2 mutant (Enigma) of Lotus japonicus

2. ABA insensitive mutants

  1. Characterisation of the BEYMA ABA insensitive mutant
  2. Gene description
  3. Pongamia pinnata stress related genes

Brassica Genomics and Genetics

Next generation sequencing and genotyping in the Brassicaceae

B juncea inflorescence

  1. Development of a 6K and 50K Illumina Infinium SNP genotyping chip for Brassica napus
  2. Characterising genetic variation in Brassica napus and links to agricultural traits - QTL and SNP analyses
  3. Characterising genetic diversity across the Brassicaceae - Goldengate and Infinium analysis
  4. Mapping recombination blocks in Brassica
  5. Identifying genomic regions associated with domestication

Genomics and evolution of Leptosphaeria maculans (blackleg fungus)

  1. Illumina Goldengate analysis of L. maculans isolates
  2. Population and diversity analyses
  3. Linkage disequilibrium
  4. Identification of candidate avirulence genes

The Brassica-L. maculans interaction

  1. Physical mapping, discovery and conservation analysis of blackleg disease resistance genes across the Brassicaceae
  2. Expression of candidate resistance genes in B. napus
  3. Stable transformation of B. napus for gene function analyses - knockouts and complementation.
  4. High density genotyping and sequencing of L. maculans isolates and B. napus cultivars for co-evolution analyses.

Evolution and functional Analysis of Symbiosis genes across the Brassicaceae

  1. Sequencing of nodulation gene homologues across the Brassicaceae
  2. Quantitative gene expression analyses
  3. TILLING and phenotyping of B. rapa mutants
  4. Phenotyping of Arabidopsis gene mutants
  5. Microbe response assays
  6. Hairy root complementation of legume mutants with Brassica genes

5. Epigenetic regulation of important agricultural traits in Brassica napus

  1. Whole genome methylation sequencing
  2. Correlation of methylation profiles, gene expression and phenotype at Methyl-QTL regions
  3. Illumina Methylation Goldengate/Infinium
  4. Comparative genome methylation analysis

Windmills in Canola6. Chromosome behaviour, polyploidy and speciation in Brassica

  1. Creating a new Brassica allohexaploid crop species
  2. Tracing chromosome inheritance and fertility through generations of interspecific hybrids
  3. Using fluorescent in-situ hybridisation to observe chromosome behaviour during meiosis in different Brassica hybrids
  4. Unreduced gametes and polyploid formation mechanisms