2. Testing the DNA decay hypothesis of ecological specialization


DP0985013

 

ARC Discovery Project.

 

Prof. Ary A. Hoffmann, Charles Robin, W.Jason Kennington

 

2009-2012

 

Australia’s biodiversity has been increasingly threatened by climate change and fragmentation from habitat loss.  To conserve biodiversity we need to identify species most at risk of extinction.  One way species avoid extinction is to evolve and adapt to changing conditions, however, it now appears that many species have a limited adaptive potential.  Here we develop and test a new idea that helps to predict species most threatened by climate change and other types of stresses.  We also identify the sets of genes that are involved in adapting to dry/cold conditions and toxins.  This information provides a rapid way of identifying species most at risk and least likely to adapt, and a new perspective on Australia’s biodiversity.

 

RESULTING PUBLICATIONS FROM MY LAB's CONTRIBUTION:

  1. Schmidt, J. M., Good, R.T., Appleton, B., Lydall, J., Bogwitz, M. R., Martin, Daborn, P.J., Batterham, P and Robin, C. (2010) Copy Number Variation and Transposable Elements feature in an adaptive walk at the Cyp6g1 locus Plos Genetics 6(6): Art. No. e1000998

  2. Griffin, P.C., Robin, C. and Hoffmann, A.A. (2011). A next generation sequencing method for overcoming the multiple gene copy problem in polyploidy phylogenetics, applied to Poa grasses. BMC Biology Vol 9 article 19.

  3. Joshua M. Schmidt and Charles Robin (2011)  An Adaptive Allelic Series Featuring Complex Gene Rearrangements. PloS Genetics Volume 7 | Issue 10 | e1002347

  4. M. J. Blacket, C. Robin, R. T. Good, S. F. Lee and A. D. Miller (2012) Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Molecular Ecology Resources 12 (3), 456-463.

  5. AA Hoffmann, MJ Blacket, SW McKechnie, L Rako, M Schiffer, RV Rane, RT Good, C Robin, SF Lee (2012). A proline repeat polymorphism of the Frost gene of Drosophila melanogaster showing clinal variation but not associated with cold resistance .Insect Molecular Biology 21(4) 437-445.

 

 

 

3. Using Comparative Genomics to Identify Genes Responsible for Adaptation to Environmental Toxins
 
DP0557497
 
ARC- Discovery Project.
 
Prof. Phil Batterham, Charles Robin
 
2005-2007

 

The US National Human Genome Research Institute has committed to sequencing the genomes of ten different Drosophila (fly) species.   We will search these genomes, and two others that are already available, for genes that allow flies to cope with environmental toxins found in the plants upon which they feed and breed.  These same genes have the potential to degrade many of the insecticides used to control insect pests.  Hence, this research will contribute to ongoing efforts to minimize the threat to agriculture posed by the insecticide resistance that frequently evolves in pest species. 

 

RESULTING PUBLICATIONS BY MY LAB:

  1. Willoughby, L., Chung, H., Lumb, C., Robin, C. Batterham, P., Daborn, P.J. (2006) A comparison of Drosophila melanogaster detoxification gene induction responses for six insecticides, caffeine and Phenobarbital. Insect Biochemistry and Molecular Biology 36 (12) 934-942.

  2. Low, W.Y., Ng, H.L., Morton, C.J., Parker, M.W., Batterham, P., Robin, C., (2007) Positive selection of Glutathione S-Transferases in the genus, Drosophila. Genetics 177(3) 1363-1375.

  3. Drosophila Comparative Genome Sequencing and Analysis Consortium. (2007) Genomics on a Phylogeny: Evolution of Genes and Genomes in the Genus Drosophila. Nature 450 :203-218.

  4. Sztal, T., Chung, H., Gramzow, L., Daborn, P.J., Batterham, P., Robin, C. (2007) Two independent gene duplications forming the 307a genes of Drosophila. Insect Biochemistry and Molecular Biology 37(10):1044-1053. 

  5. Robin, C, Daborn, P.J., Hoffmann, A.A. (2007) Fighting Fly Genes. Trends in Genetics 23(2) 51-54.

  6. C. Robin, L. M. J. Bardsley, C. Coppin and J. G. Oakeshott (2009)  Birth and Death of gene function in the beta-esterase cluster of Drosophila. Journal of Molecular Evolution 69, 10-21.

  7. Low, W.Y, Feil, S., Ng, H.L., Gorman, M.A., Morton, C.J., Pyke, J., McConville, M.J., Michael Bieri, Yee-Foong Mok, Robin, C+, Gooley, P.R., Parker, M.W., and Batterham, P. (2010) Structural insights of the binding of glutathione and DDT to Drosophila melanogaster GSTD1. Journal of Molecular Biology. 399(3): 358-366. 

  8. Good, R.T., L.Gramzow, P.Battlay, T.Sztal, P.Batterham, C.Robin (2014). The Molecular Evolution of Cytochrome P450 genes within and between Drosophila species. Genome Biology and Evolution  6(5)1118-1134.

Summary of the whole project:
 
Caterpillar control using genes from the soil bacterium Bacillus thuringiensis (Bt) inserted into major crops has demonstrated massive financial benefits globally. Sap-sucking aphids and allied insects (Homoptera) remain as the major remaining insect constraint.  Drought, exacerbated by global warming, enhances their impact and that of the numerous viruses they vector.  Resistance to conventional insecticides is increasing rapidly. The project will use brassicas as a model to add RNA interference (RNAi) control of major aphid pests of a wide range of crops, to Bt control of caterpillars.  In doing so this work opens up a new era in the delivery of precisely targeted self control of key pests ‘in the seed’. Genes controlling vital metabolic processes in aphids will be identified for knocking out. Transgenic constructs encoding double stranded RNA molecules (RNAi genes) will be generated and inserted into plants, initially Arabidopsis then into related commercial crops in India (mustard, cabbage and cauliflower) and Australia (canola).  The RNAi in the plants binds to the target aphid RNA, preventing it from producing proteins vital to the aphids’ survival. Effective RNAi constructs will be transferred into crops with Bt genes that have appropriate ‘landing sites’ engineering into them. Close linkage of the Bt and RNAi genes on the plant chromosomes will prevent accidental deletion of genes by breeders producing commercial hybrids. Demonstration of insect control and the first stages of selection of the final plant material for commercialisation will be undertaken.
 
The Indian Council for Agricultural Research will provide the stacked-gene Bt constructs used in the successful proof of concept in brassicas in India undertaken by the CIMBAA programme (Collaboration on Insect Management for Brassicas in Asia and Africa) led by Project Manager Dr Russell (Univ. of Melbourne) and partially funded by AISRF. The process will be supported by Bioplatforms Australia with the Grains Research and Development Corporation’s  National Brassica Genetics Improvement Programme as the uptake pathway to multiple seed companies in Australia, and in India by the Indian Council of Agricultural Research’s technology transfer platform. The Indian Agricultural Research Institute will develop plant material actively sought now by commercial seed companies. 

 

 

 

Research Funding

1. Caterpillar and Aphid Resistance in Brassica (CARiB)

 

GCF010009: Originally entitled 'Crop plants which remove their own major biotic constraints'

 

Australia- India Strategic Research Fund: Grand Challenge

 

2012->

 

This project is a collaboration between Australian and Indian partners and is championed by Dr. Derek Russell.

 

The Australian partners are:

  • the University of Melbourne,

  • the University of QLD,

  • CSIRO

The Indian partners are:

  • The International Centre for Genetic Engineering and Biotechnology,

  • The Indian Agricultural Research Institute

  • The National Bureau of Plant Genetic Resources

Our labs role:

Originally we were to charged with (i) making sure the anti-aphid RNAi constructs would specifically target pest species and not others species - particularly beneficial insects and (ii) explore the potential for resistance to RNAi to evolve. However our role has expanded to help demonstrate that RNAi can be effective when fed to aphids and to explore the genomic and transcriptomics of the three pest aphid species (The Green Peach Aphid Myzus persicae, the cabbage aphid Brevicoryne brassica and the turnip aphid Liphaphis erysimi).

 

The grant has supported the reseach of Amol Ghodke who is featured in the inaugural GEAR magazine about Indian students doing Global Engaged and Active Research at the University of Melbourne

4. Bayers Grants4Targets scheme has funded research into novel insecticide targets

We have been awarded a small grant under Bayer's Grant4Target- targets for crop protection scheme.

"We are thrilled that Bayer’s ‘Grants4Target’ initiative is supporting our science which ultimately aims to develop insecticides that are safer for farmers and the environment. The first step has been to identify novel ‘targets’ that have the potential to be targeted by chemistries that will be developed down the track. It is early days and the odds are not short, to pick up a horse racing analogy, but it is wonderful that Bayer is investing at such an early stage of research. Admittedly the investment to our project is small but Bayer appears to be spreading their bet and we are keenly jockeying to get to the next stage. The ‘horse’ we have chosen is called ‘X-kinase’ and we reckon it’s very druggable, which is a good thing for potential targets!  These potential targets are only found in insects, will interfere with the insect hormone system, and will be specific to pest insects rather than beneficial insects. It’s too early to say which pests will be our main focus but broad-acre crop pests such as armyworms, diamond back moth,  bollworms, aphids, or  leaf miners are all possible . Bec and Jack, two keen PhD students, have got  ‘X-kinase’ in good nick and are raring to go!