Table of contents school of plant biology introduction



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PROJECTS FOR 2012

The projects being offered and project ideas for development are listed below under the name of the main supervisor. The supervisors are listed alphabetically by last name.



EMERITUS PROFESSOR CRAIG ATKINS

Room 2.20 Botany Building; Ph 9380 2262; Email: catkins@cyllene.uwa.edu.au


PLANT BIOCHEMISTRY, PHYSIOLOGY AND MOLECULAR BIOLOGY
Research Interests

The regulation of gene expression in relation to nodule development, N2 fixation and N metabolism in legumes is a major area of research. Current projects include the isolation of enzymes and genes involved in ureide and purine biosynthesis, studies of enzyme and gene regulation, organelle isolation from nodules, dual targeting of single gene products to 2 organelles (plastids and mitochondria) and a detailed examination of the ultrastructure of Rhizobium infected cells. A second area involves studies of the molecular mechanisms of short and long distance transport in plants, especially of nitrogenous solutes and of factors regulating seed development. A number of projects are related specifically to the genetic improvement of the major grain legume crop of WA, the narrow-leafed lupin (Lupinus angustifolius). These will use recombinant DNA technology and genetic engineering and could involve the use of HPLC and GC/MS analysis.


Signals transported in phloem of lupin

Plants are continually responding to signals that allow them to modify their development in response to their changing environment. A good example is the way many plants analyse environmental conditions to determine when to produce flowers. The signalling molecule “florigen” involved in this most basic process (flowering) has still not been identified but it is known to be transported in phloem. We are trying to identify this and other signalling molecules in phloem by isolating peptides and small regulatory RNAs (called microRNAs, miRNA and small interfering RNAs, siRNA). We have identified a number of miRNAs in phloem and aim to determine which genes they target, how they are transported around the plant and how they affect developmental processes. Other work aims to identify peptide signals transported in phloem.


1. Use a GFP gene with a miRNA binding site within it to study sites of miRNA action in transgenic Arabidopsis.
2. Lupin seeds are currently being studied to see whether they are a good alternative to soybean as a human food. Lupin milk products have been developed and lupin protein extract can be used in a similar way to soybean meal in food processing industries. However there is evidence that lupin seed causes an extremely severe allergic reaction in some individuals. You could identify the proteins in lupin seeds which cause the allergic reactions.
Other project ideas

  • Physiological, biochemical, microbiological or structural studies of the ant:bacteria:extrafloral nectary association in cowpea and other legumes.

  • Molecular biological studies of the regulation of gene expression in N2-fixing legume nodules, particularly in relation to nitrogen assimilation and purine/ureide biosynthesis.

  • Development of techniques for genetic transformation and regeneration of transgenic lupins (Lupinus angustifolius).

  • Studies of abscission in lupins using novel non-abscising mutants.

  • Establishment of the molecular basis for source/sink relations in legumes.

  • Molecular studies of flower and pod abortion in lupins.

  • Studies on localisation of purine biosynthesis enzymes. This project will study the mechanisms by which enzymes are transported into plastids and mitochondria. This could be studied using immunolocalisation, plant transformation and in vitro import techniques.

  • The role of plant hormones in determining the partitioning of assimilates in plants.

  • Isolation and characterisation of a cytokinin-specific isomerase from developing legume embryo tissues.

  • Isolation and molecular characterization of phloem mobile ‘signals’ of biotic and abiotic stresses in lupins.

PROFESSOR MARTIN BARBETTI

Room 1.104 Agriculture Central Wing; Ph 6488 3924; Email: mbarbett@cyllene.uwa.edu.au


PLANT PATHOLOGY AND MYCOLOGY

In January 2004 I commenced with the School of Plant Biology following more than 30 years as a Plant Pathologist with the Department of Agriculture and Food Western Australia identifying, researching and resolving plant pathology issues through ‘on-farm’ research in relation to pathology problems facing the wool, oilseed, pulse, cereal, horticulture, meat and dairy industries of Western Australia. Consequently I have wide interests in relation to plant pathology and mycology applicable across the whole of the agricultural sector.

The Plant Pathology program at UWA is a collaborative program with Professor Sivasithamparam (6488 2497; email: siva@cyllene.uwa.edu.au) and Dr Hua Li, both also in the School of Plant Biology, and all projects will have the benefit and security from joint supervision and enjoy a strong network of support within the group. Professor Siva has a wide range of expertise and has supervised many 4th year, Honours and PhD projects at UWA. It is the vision of this Plant Pathology group to foster both plant pathology and mycology interest and skills development in each generation of students passing through UWA.
DISEASES OF CROPS

We have a very active Brassica pathology program (among several other programs as well) here at the University and the plant pathology group at UWA was the first anywhere to report the occurrence of a new resistance-breaking race of the blackleg fungal pathogen, Leptosphaeria maculans, that overcame the Brassica rapa ssp. sylvestris-derived single dominant gene resistance, and which has since broken out and caused severe damage to canola crops across Australia. The Plant Pathology group at UWA currently is a world leading group in terms of diseases of oilseed Brassica crops, and has strong international linkages to leading research programmes on Brassicas both nationally (Victoria) and internationally (France, the United Kingdom and Poland). Current programs include durability of polygenic and single dominant gene-based host resistance in oilseed Brassicas and how this relates to changes in Brassica-pathogen interactions and in the pathogen populations; understanding infection processes of the blackleg pathogen; ways of disrupting the pathogen life cycle; etc.

In addition to blackleg disease, we have active in relation to Australian spring-type canola varieties for a range of other diseases such as downy mildew (Hyaloperonospora parasitica), white rust (Albugo candida), Sclerotinia (Sclerotinia sclerotiorum) and white leaf spot (Pseudocercosporella capsellae) in relation both to host resistance, host-pathogen interactions and also in relation to defining the survival mechanisms and parasitic behaviour of these pathogens under the Mediterranean conditions that prevail in much of southern Australia and particularly in WA. We also have programs investigating the race status of these pathogens in Australia.
DISEASES OF PASTURES

The Plant Pathology group at UWA currently has a strong collaborative research program on understanding and managing diseases of pasture legumes, including both those which have been (e.g. subterranean clover, annual medic) or are being developed (many new annual and perennial species) for Western Australia. Particular fungal diseases of current research include Phytophthora root rot, clover scorch disease, rust, and Cercospora on subterranean clover, Rhizoctonia root rot and Botrytis blight of new pasture legume species, and Phoma on medic and its role in stimulating phyto-oestrogens in annual medics.

All pasture disease projects will be in collaboration with Dr Ming Pei You from the Western Australian Department of Agriculture and Food. In conjunction with the UWA pathology group, a program is planned that will look at the causes, impact and epidemiology of diseases on new alternative pasture legumes.
DISEASES OF HORTICULTURE, FLORICULTURE AND FORESTRY

There are currently programs within the School investigating Lettuce Big Vein disease in Lettuce and on root and crown diseases of strawberries in Western Australia. We also have a planned program involving Sclerotinia on vegetable Brassicas


Please also contact me if you are interested in any pathogen of any other crop, including all pulse and cereal crops
ASSOCIATE PROFESSOR SUSAN BARKER

Room 1.121 Agriculture Central Wing; Ph 6488 2435; Email: sjbarker@plants.uwa.edu.au


Research Background
I was appointed at UWA in 1998 to help bring molecular biology and molecular genetics research tools into the Faculty. This role suits me perfectly as I have very wide ranging interests, and I have co-supervised projects as varied as: genetics of white coat colour in alpacas; development of seedless citrus; characterization of heritage olive trees in Western Australia; zinc nutrition in barley; towards cloning a self incompatibility gene from Phalaris; mapping a mycorrhizal symbiosis gene in tomato; genetic modification of lupin for improved agronomic traits including disease resistance and herbicide tolerance; characterization of the role of apoptosis in blackleg disease of canola; assessment of genetic diversity in a native pasture species; etc (for a complete list please contact me!).
Research Advice
I sometimes find myself giving advice to students about half way through their research project when they realize that they need to develop a genetic or molecular biology approach to answer their research question. If you find yourself in this situation of needing advice at any stage in your research, please feel free to contact me and I will be happy to advise you about what might be your next steps.
Research supervision
Examples of current projects are listed below. Contact me if you would also like to discuss other options, including projects that you have developed yourself, or if you would like to involve me as a second supervisor in order to accomplish a small genetic analysis as part of your project.


  • Characterisation of the genome of arbuscular mycorrhzal fungi

This challenging and novel project involves chromosomal visualization and gene amplification from arbuscular mycorrhizal fungal extracts. For students wanting to experience a classic molecular biology research endeavour and to have the opportunity of a high caliber research publication from their project work.




  • Feeding Gilbert’s Potoroo: Australia’s most endangered marsupial

This project is offered in collaboration with Dr Mark Tibbett (SEGS) and also will involve supervision by Dr Tony Friend, DEC. Identification of novel translocation sites for this endangered marsupial requires knowledge of the host plant species that support growth of the fungal fruiting bodies (truffles) on which these marsupials survive. The project will involve field collection of fungal fruiting bodies, potoroo scat and the short roots surrounding the fruiting bodies, then DNA sequence analysis to identify the plant hosts that support the fungal growth.


ASSOCIATE PROFESSOR MARK BRUNDRETT

Room 215 Botany Building; Ph 6488 2212; Email: mark.brundrettr@.uwa.edu.au


ENDANGERED WHEATBELT ORCHIDS

Quantify and understand habitat requirements and threatening processes impacting on a rare orchid in highly fragmented landscapes. Gain knowledge required for sustainable management and make direct contributions to recovery actions for an endangered species, while working in collaboration with DEC and community groups.


ECOLOGICAL IMPLICATIONS OF ORCHID FUNGAL ASSOCIATIONS

Discover the role of highly specific fungal interactions on the dispersal of on rare and common orchid species by investigating the distribution of compatible fungi in soils. Help us to gain a greater understanding of the habitat requirements of orchids by studying their fungi.


MYCORRHIZAL FUNGUS DIVERSITY IN A BIODIVERSITY HOTSPOT

Investigate the diversity of the Glomalean fungi - the oldest group of true fungi, in our ancient landscapes (collaboration with Dr Susan Barker). Investigate diversity using a range of isolation and molecular techniques. Identify fungi with help from international collaborators.


ECOLOGY OF MYCORRHIZAL ASSOCIATIONS

Study ecological and functional aspects of mycorrhizal fungus associations in natural ecosystems, by investigating the relative dominance of plants with different types of mycorrhizal fungal associations in different habitats.


POLLINATION BIOLOGY OF WINTER FLOWERING ORCHIDS

Determine if co-flowering orchids share pollinators and investigate why there are many similar looking taxa in genera such are Pterostylis (or are they really different)? Is there a link between winter orchids and fungus fruiting?




PROFESSOR TIM COLMER

Room 1.127 Agriculture Central Wing; Ph 6488 1993; Email timothy.colmer@uwa.edu.au


SALINITY AND WATERLOGGING TOLERANCE IN CROPS AND PASTURES
Crops and pastures with greater salt and waterlogging tolerance than current options are required to make saline land more productive. Several opportunities are available for research projects in this field, depending on the interests of the student. Some examples are given below:


  • Salinity and submergence tolerance in halophytes. Halophytes grow naturally in saline soils – but many of these soils are also prone to waterlogging and plants can even experience complete submergence during floods. Mechanisms of salinity tolerance in halophytes have previously been studied, but physiological responses of halophytes to complete submergence in combination with salinity need to be further elucidated. The scope for projects is large, as various physiological aspects need to be studied.

  • Variation for salt tolerance within Medicago polymorpha. Recent experiments have found variation in salt tolerance within a commercial cultivar of burr medic (Medicago polymorpha). Further experiments are needed to determine the source of this variation and utilise it for developing a more salt tolerant burr medic cultivar.

  • Waterlogging/salinity tolerance in clones of puccinellia. Puccinellia is a halophytic grass used for pasture on saltland. It is a cross-pollinating plant and seed lines are therefore genetically diverse. This species can be exceptionally tolerant to waterlogging under saline conditions, with increased growth under waterlogged/saline compared with drained/saline conditions (most rare amongst higher plants). However, we suspect that different accessions/seed sources vary in tolerance. This project will screen a range of vegetatively propagated clones of puccinellia for tolerance to waterlogging/salinity. The best selections will be further tested for K+/Na+ regulation and traits associated with better root aeration.

  • Screening barley cultivars for tolerance to salinity at germination. Barley is well known as a relatively salt-tolerant cereal. However, this reputation is based mainly on its tolerance to salt after establishment. Saltland in Western Australia is generally most salty at the start of the growing season as seeds germinate. However, little is known about how this salt impacts on the germination of different barley cultivars. This project will assess the salt tolerance at germination for a range of barley cultivars. There are two critical research questions: (a) Do cultivars differ in their ability to withstand salt before germination occurs? (b) Do cultivars differ in their ability to tolerate salt during germination?

  • Interactive effects of waterlogging and salinity on rhizobia for Melilotus siculus. Melilotus siculus (messina) is a new annual pasture legume that can grow in highly saline and waterlogged soils. Messina roots form a special layer called ‘phellem’, which is filled with air spaces that act as a ‘snorkel’ to allow oxygen transport to roots. However, the role of phellem in supplying oxygen to waterlogged nodules is not known. This project will determine if phellem on roots and nodules is important to waterlogging and salinity tolerance of messina inoculated with rhizobia.

  • Salt tolerance of Australian wild rice. Cultivated rice (Oryza sativa) is one of the most important grain crops worldwide, but is notoriously sensitive to salinity. Wild relatives of rice could provide a source of genes to improve salt tolerance in cultivated rice. This project will investigate salt tolerance in Australian wild rice species, Oryza australiensis and Oryza meridionalis.

Contacts: Tim Colmer timothy.colmer@uwa.edu.au AND/OR Ed Barrett-Lennard (Centre for Ecohydrology (DAFWA)/Plant Biology) egbarrettlennard@agric.wa.gov.au AND/OR Natasha Teakle (Centre for Ecohydrology/Plant Biology) natasha.teakle@uwa.edu.au

ASSISTANT PROFESSOR MICHAEL CONSIDINE

Room 2.131 Agriculture Central Wing; Ph 6488 1783; Email: michael.considine@uwa.edu.au


Research Interests

The sensitivity of metabolism, development and phenology to environmental stress, particularly heat, is my primary interest. This spans physiology and agronomy through to redox and carbohydrate metabolism; i.e. primary metabolism and the energy transactions and signalling. Major crops of interest are grape and apple. Many of my projects involve industry interaction, particularly with the Department of Agriculture and Food (DAFWA) and grape growers.


Current projects include

  • The effects of high temperature (low latitude) on the phenology, particularly bud initiation, dormancy, flowering and flower retention, in grape. This is an ARC Linkage grant with the Centre of Excellence in Plant Energy Biology and two industry partners; DAFWA and the Gascoyne Table Grape Growers’ Association. This research spans physiological field-research through to detailed molecular and metabolic profiling technologies. There are many opportunities to travel and participate in a range of disciplines. Equally, there is much to be done in glasshouse trials, from physiological and developmental observation to microscopy and metabolic analysis.
    Examples: Is the temperature or duration of dormancy critically important to fertility and if so, what metabolic events underlie this? What is the effect of warm climate on the relationships between leaf and inflorescence development? Does climate affect relative sink strength of the leaf and inflorescence? We’d like you to be part of this team.

  • Identifying the metabolic effects of sulphur dioxide in grape. Conventionally it is thought that SO2 merely acts as an antimicrobial but our research shows significant activation of antioxidants and large scale effects on the molecular network in grape. The extent and pathways of sulfur assimilation are not known, nor are the resulting pathways to stress. These have been explored in other plants but only in leaves. This of great interest, both intellectually and for industry to find an alternative to and antimicrobial which is increasingly “on the nose”. Your contribution to this project could include investigating the effects on sulfur assimilation into “higher” sulphur compounds or the effects on redox-sensitive metabolites such as ascorbate and glutathione.

  • Identifying apple and plum varieties with elite levels of flavonoids and validating pharmacological effects, including antioxidant activity. This project works in collaboration with the Pharmacology group at RPH and the Department of Agriculture and Food (DAFWA) via and ARC Linkage grant.

Technologies employed in my research include metabolic profiling, photosynthetic and respiratory activity, enzyme kinetics, and molecular technologies.


This is just a snap-shot of potential projects. Please contact me if any of the ideas or keywords grab your attention. I have broad connections in molecular biology, pharmacology and agriculture so just knock on my door or send me an email.
Thanks, Mick

WINTHROP PROFESSOR WALLACE COWLING

The UWA Institute of Agriculture, Room 2.102 Agriculture Central Wing; Ph 6488 7979; Email: wallace.cowling@uwa.edu.au


PLANT MOLECULAR GENETICS and PLANT BREEDING

Our group works towards sustainable plant breeding for changing environments – including the application of population genetics, genomics and evolutionary theory to improve crop disease resistance, stress tolerance and adaptation. A wide range of research is undertaken within the group, for example:



  • Interspecific crossing in Brassica species to improve canola (Brassica napus)

  • Heat and drought stress tolerance in Brassica rapa

  • Mapping and identifying genes for blackleg disease resistance in canola

  • Understanding the molecular basis of disease resistance and susceptibility in blackleg of canola

  • Finding gene-specific markers for oil quality traits in canola, such as high oleic and low linolenic oils

  • Testing concepts of strategic evolution for crop breeding, based on whole genome marker selection

  • Building the first gene-based map of narrow-leafed lupin (Lupinus angustifolius)

  • Developing new pre-breeding populations of peas and lupins

  • Introgression of genetic diversity between canola and related species.

  • The genetic basis of heterosis (hybrid vigour) in canola.

Honours or MSc Project Ideas:

How do genes & environment influence flowering time in canola? (with Assist Prof Matthew Nelson). We know surprisingly little about how genes and environment interact to control flowering time in canola. In order to adapt canola to changing climates, we need to understand how the environment (temperature and day-length) interacts with genes to alter flowering time in canola.

Development and characterisation of an allohexaploid Brassica DH population (with Dr Sheng Chen)

A golden opportunity exists to hasten the agricultural evolution of a new allohexaploid Brassica species. This new allohexaploid Brassica research was initiated in 2008. In this project, we will develop a double haploid population and characterize it at morphological, cytogenetic and molecular levels.



Studies on centres of origin and diversity in Brassica juncea (with Dr Sheng Chen)

B. juncea is genetically diverse, with two main centres of diversity in India and China. Whole-genome molecular marker diversity analysis showed two major genetic subgroups of B. juncea. In this project, we will explore association mapping of genes of interest for key traits in a global collection of B. juncea.

Tolerance of Brassica rapa to heat and drought stress (with Dr Sheng Chen & W/Prof Neil Turner)

Oilseed Brassica napus lacks heat and drought tolerance, and has narrow genetic diversity. Oilseed B. rapa (annual turnip rape or field mustard), one of the progenitors of B. napus, is genetically extremely diverse. This project will evaluate the effects of heat and drought stress on B. rapa. The aim is to develop effective and reproducible protocols for large-scale screening for heat and drought tolerance in B. rapa, and to find genes for heat and drought tolerance for incorporation into B. napus.




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