Table of contents school of plant biology introduction



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PROFESSOR ROGER JONES

Room 18, Botany Top floor; Ph 9368 3269; Email: roger.jones@uwa.edu.au



PLANT VIROLOGY

The Plant Virology program at UWA under Prof. Roger Jones is a collaborative one with the Plant Virology research team at the Department of Agriculture and Food Western Australia (DAFWA) headed by Ms Brenda Coutts. All projects will have the benefit and security of joint supervision and enjoy a strong network of support from UWA and DAFWA. It is this groups’ vision to foster plant virology interest and skills development in each generation of students passing through UWA.
We currently have active research activities studying virus diseases and their vectors in grains (currently of wheat, canola, pea, lupin), vegetables (cucurbits, potatoes, tomatoes, capsicums, brassicas), pasture plants (tedera, annual medic) and wildflowers. Examples include projects developing innovative real-time PCR procedures for large-scale detection of mite and fungus vectored viruses of wheat; identifying the cause of black pod syndrome in lupin; investigating the genes controlling resistance to aphid-vectored and contact transmitted viruses in potato; unraveling the cause of viroid outbreaks in tomato; and studying the etiology and epidemiology of Solanaceous vegetable viruses in WA. Also, in conjunction with the UWA plant mycology group (Prof Martin Barbetti), a program is planned that will look at the causes, impact and epidemiology of virus diseases infecting new alternative pasture legumes.
Research is also underway to identify and understand the biological and molecular properties of viruses threatening native plants at the interface between natural and managed vegetation, at mine sites and in wildflower nurseries.

Examples of 4th Year Project, BSc Honours or MSc Ideas:

Characterisation of virus resistance genes in canola and mustard species. Australian canola and mustard germplasm contains a wide range of virus resistance phenotypes. We need to understand what these phenotypes represent and which resistance genes are present.

Characterisation of virus resistance pathotypes and genes in field pea and faba bean. Some pulse cultivars contain resistance genes specific to different virus pathotypes. We need to unravel the relationships between virus pathotypes and cultivars with resistance.

How do perennial pasture species respond to invasion by viruses? We know surprisingly little about the threats posed to perennial pasture legumes by viruses. Given the considerable research activity currently underway on perennial pasture grasses and legumes at UWA, we are ideally placed to study this here.

Understanding breakdown of virus resistance in cucurbit cultivars in tropical and subtropical environments. Single virus gene resistance in cucurbits is effective overseas but not in Western Australia. We urgently need to understand why this is so since virus disease currently threatens continuation of the states cucurbit industry.

Aphid vector biology and the roles of different aphid species as vectors of cucurbit viruses. We know surprisingly little about the biology of aphid vectors and the roles of different aphids as vectors of cucurbit viruses that currently threaten the wellbeing of continuation of the states cucurbit industry.

How do native plants respond to invasion by introduced viruses spreading from introduced crops and how do introduced crop plants respond to invasion by indigenous viruses spreading from native plants. We know very little about the threats posed to native plants from introduced viruses and to crop plants from indigenous viruses. Viruses evolve and adapt to new hosts very rapidly and, because agriculture is so recent here, we are ideally placed in Western Australia to study this process.
WINTHROP PROFESSOR GARY A KENDRICK

Room 1.24 Botany Building Link; Ph 6488 3998; Email garyk@cyllene.uwa.edu.au


ECOLOGY AND DEMOGRAPHY OF MARINE PLANTS
Gary Kendrick’s main research interest is the dynamics of populations and assemblages of marine macroalgae and seagrasses. His research has focussed on the influence of recruitment on the demography and persistence of species, and the scaling of demographic patterns to assemblage structure of marine macroalgae, and to seagrass landscapes. He is presently involved in the assessment of biodiversity for marine conservation purposes, and the relationship between recruit survival and rhizomatous growth on the distribution and abundance of seagrasses in shallow subtidal landscapes.
Project Ideas


  1. Seagrass growth patterns (Ability to SCUBA dive essential). Supervisors: Dr Gary Kendrick and Dr Marion Cambridge

  2. Recruitment ecology of Posidonia species. Supervisors: Dr Gary Kendrick and Dr Marion Cambridge

  3. Influence of clonal growth of seagrasses on the development of seagrass meadows. Supervisor: Dr Gary Kendrick

  4. Root oxygen release by seagrasses . Supervisors: Dr Marion Cambridge and Dr Tim Colmer

  5. The role of disturbance in structuring marine algal assemblages in temperate Western Australia (Applicant should be a competent and experienced SCUBA diver) Supervisor: Dr Gary Kendrick

  6. Local to regional dispersal and recruitment patterns in Ecklonia radiata and Sargassum spp. (Applicant should be a competent SCUBA diver). Supervisor: Dr Gary Kendrick

  7. Variation in the Seed Production of Posidonia. Supervisors: Dr Gary Kendrick and Dr Marion Cambridge (The applicant must be a competent snorkeller, preferably with SCUBA qualifications).

  8. The effect of epiphytes in limiting light to seagrass leaves: The role of physical structure Dr Gary Kendrick and Dr Marion Cambridge (The applicant must be a competent diver).


Permanent Visiting Senior Research Fellow SIEGY KRAUSS

Senior Research Scientist (Conservation Genetics), Kings Park and Botanic Garden;

Ph 94803673; Email: siegy.krauss@bgpa.wa.gov.au

Web: http://www.bgpa.wa.gov.au/science/staff/siegy-krauss


CONSERVATION GENETICS
I head up the conservation genetics laboratory team at Kings Park, where we are applying molecular tools such as AFLP, microsatellites, population genomics and DNA sequencing for largely practical genetic contributions to native plant conservation, ecological restoration, systematics and native plant breeding. We also use these tools for a better understanding of key evolutionary processes within natural plant populations such as mating and dispersal. In collaboration with Dr Matt Barrett, Dr Janet Anthony, Dr Ann Smithson, Dr Kristina Hufford, Dr Dean Carter, Dr Liz Sinclair and Dr TianHua He, we offer honours and 4th year research projects within the following broad topics:
Seed sourcing for ecological restoration. A major issue affecting restoration success. How do we determine the extent of the local genetic provenance? Applying molecular tools such as AFLP or microsatellites for the rapid genetic assessment of population genetic structure is one powerful contribution. Various species from the Swan coastal plain and Darling Scarp (as well as marine seagrass meadows) are available for population genetic assessment in a genetic provenance context. In addition, there are opportunities to develop and assess patterns of variation in non-neutral markers being developed for iconic species such as tuart, to more directly assess adaptive variation. What are the consequences of sourcing seed from non-local populations? Opportunities exist for cross-pollination experiments to assess the negative genetic consequences of wide outcrossing (outbreeding depression). Additionally, glasshouse growth trials and/or reciprocal transplant experiments provide powerful tests for the extent of local adaptation and “home-site advantage”.
Direct assessment of dispersal within and among native plant populations. Quantifying dispersal of pollen and seed within and among plant populations is critical for understanding these important evolutionary dynamics that affect, and are affected by, genetic structure, especially in a conservation and management context with widespread habitat fragmentation and climate change. Are fragmented populations doomed, or able to move, in response to climate change? Is inbreeding increased in fragmented populations due to genetic isolation, and does this affect the long-term viability of populations? What is the impact of introduced honeybees on pollen dispersal and mating in plants historically pollinated by vertebrates? Powerful molecular tools such as microsatellites and AFLP, coupled with statistical approaches for paternity and/or population assignment, offer the potential to generate exciting new data on direct estimates of dispersal in banksias, peas, seagrass, darwinias, orchids, and sedges.
Resolving evolutionary relationships and taxonomies using DNA sequences. DNA sequences provide powerful data to generate accurate taxonomies, and to identify the systematic evolutionary relationships among taxa. The accuracy of this knowledge underpins the effectiveness of all other biodiversity conservation and management activities. In addition, recent interest and progress internationally in DNA barcoding offers exciting opportunities for the rapid identification and cataloguing of species, but still requires development and local application. We offer a wide range of opportunities in molecular systematics, that extend to horticulturally and/or conservation significant groups such as grevilleas, kangaroo paws, sedges, wax plants and seagrasses, as well as research in the development of DNA barcoding tools in key local plant taxa.
More information, see the BGPA page in this booklet, or www.bgpa.wa.gov.au/science

Assistant Professor Etienne Laliberté

Email: etienne.laliberte@uwa.edu.au

Homepage: http://www.elaliberte.info


Main research interests
Why do certain plant communities have more species than others? How/why do plant communities change in composition along environmental gradients? These are some of the questions that I try to answer in my research. These questions are particularly interesting to explore in south-western Australia since it is one of the world’s plant biodiversity hotspots.
Several theories of plant species coexistence deal with competition for limiting resources (e.g., soil nutrients) and/or productivity (how fast vegetation grows). Both nutrient availability and productivity vary predictably with soil age. Therefore, gradients of soil age (also called soil “chronosequences”) are great model systems to study how changes in nutrient availability and productivity influence plant species diversity.

Field work
My research is rooted in theory but is strongly field-based. Much of my current research focuses on a sequence of coastal dunes of increasing age (present day to well over 1,000,000 years old) around Jurien Bay (2.5 hours north of Perth). Good accommodation, close to a beautiful beach… and, importantly one of the most floristically diverse regions in Australia! A number of small research projects in community/ecosystem ecology could be done there. I would provide support for field work (transport, accommodation, etc). Following are a few ideas:

Some ideas for projects
Changes in plant trait distributions with soil age. How do leaf and/or root trait distributions vary with soil age? What particular plant strategies are favored under increasing soil age and decreasing nutrient availability? (Several collaborators possible within the School: W/Prof Hans Lambers, Asst/Prof Charles Price, Assoc/Prof Erik Veneklaas, etc)
Multiple nutrient limitation and species coexistence. Theory predicts that if growth is co-limited by many resources, then many species can coexist. What nutrient(s) are limiting/co-limiting along the dune sequence, and can this explain variation in species richness?
Productivity and species turnover. Higher productivity is thought to lead to greater species turnover (i.e. spatial variation in plant species composition). The Jurien Bay dune sequence provides a perfect system to test this hypothesis because it forms a natural productivity gradient. This hypothesis could also be explored via a simulation model (collaborator: Asst/Prof Michael Renton).
Species coexistence and nutrient-acquisition strategies. Are individuals exhibiting particular nutrient-acquisition strategies more likely to be surrounded by neighbors showing different strategies? Does this depend on soil nutrient availability?

I am open to discuss any other ideas for research projects in plant community ecology: field projects, glasshouse experiments, or simulation models. Just send me an email and we can arrange a meeting to discuss your ideas!



WINTHROP PROFESSOR HANS LAMBERS

Room 1.120B Agriculture Central Wing; Ph 6488 7381; Email: hans.lambers@uwa.edu.au

Web: http://ps-hlambers.agric.uwa.edu.au/
ECOPHYSIOLOGY OF MANAGED AND NATURAL SYSTEMS
In collaboration with Greg Cawthray, Professor Kingsley Dixon, Dr Patrick Finnegan, Dr Etienne Laliberté, Dr Martha Ludwig, Dr Stuart Pearse, Dr Pieter Poot, Dr Michael Renton, Dr Megan Ryan, Dr Mike Shane, Dr François Teste, Dr Erik Veneklaas and others

For more information, please refer to Prof Lambers’ website:


http://ps-hlambers.agric.uwa.edu.au/


  • Carbon metabolism, exudate production and phosphorus acquisition in cluster roots of Proteaceae and Fabaceae: physiological and molecular processes involved in nutrient acquisition from severely nutrient-impoverished soils.




  • Understanding how phosphite protects native plants from the pathogen Phytophthora cinnamomi (dieback)- this is part of a larger project titled “Phosphate toxicity and susceptibility to Phytophthora cinnamomi (‘dieback’) in Proteaceae: why are they linked?”.




  • Trialing chemical alternatives to phosphite for dieback management in low-phosphorus ecosystems.




  • Improving P efficiency in agriculture by understanding phosphorus acquisition and utilisation strategies in crop or potential crop species.




  • Rarity of species in the Banksia genus: highly specialised nutrient-acquisition mechanisms appear superior on severely nutrient-impoverished sites, but maladaptive in other habitats.




  • Phosphate-acquisition strategies in native legumes with potential as pasture species.



  • Understanding root interactions and their implications on plant coexistence, interplant nutrient transfer, community-level nutrient retention in poor soils



  • In situ development (minirhizotron) of Proteaceae cluster roots in the field and interaction with other roots from surrounding vegetation

DR ROWENA LONG

Room 3.57 Bayliss Building; Ph 6488 4430; Email: rowena.long@.uwa.edu.au


SEED & WEED ECOPHYSIOLOGY

Research interests

My research focuses on understanding the ecological and physiological processes that determine when and why seeds lose dormancy, germinate and age in natural and agricultural systems.


Murder versus manslaughter in the soil

Do weed seeds age and die before soil microbes degrade them, or are soil microbes silent killers? Understanding seed persistence is critical for effective management of weeds; seeds can persist in the soil long after weeds are removed, and act as a reservoir for re-invasion. It is thought that soil microbes may accelerate seed death, but does it really happen, and if so, under what conditions? This project will study how seeds and soil microbes interact by studying the anti-microbial properties of seeds and their susceptibility to microbial attack during ageing. The relative threat of different soils will be compared by measuring microbial biomass and respiration, collectively contributing to an improved understanding of how weed seeds age and die in soils.


Co-supervised by Dr Natasha Banning (UWA Soil Biology Group); Ph: 6488 3969; Email: natasha.banning@uwa.edu.au
Live and let die: triggering weed seeds to germinate and die at depth

The smoke-derived compound, karrikinolide, shows promise as a tool for triggering weed seeds to germinate in unison, enabling more efficient weed control. Aside from being a germination-stimulant, karrikinolide can also affect the development of seedlings, such that stems do not elongate under certain light conditions. Together, these attributes may enable us to trigger weed seeds to germinate below the soil such that they then die before emerging. In this project, we will investigate how karrikinolide and other smoke-derived chemicals affect the development of weed seedlings following germination, including studying the development of roots, hypocotyls, cotyledons and true leaves. There is also scope to explore the interaction between karrikinolide and another chemical that is believed to inhibit the karrikinolide activity in seeds and plants using molecular (genetics) approaches.


Co-supervised by Prof Steven Smith (UWA Centre of Excellence for Plant Energy Biology); Ph: 6488 4403; Email: steven.smith@uwa.edu.au; and Dr Jitka Kochanek (UQ Gatton); Ph: (07) 5460 1286; Email: j.kochanek@uq.edu.au

Passing on the smoke signal from generation to generation

The smoke-derived chemical karrikinolide can stimulate seeds to germinate, but what happens when an adult plant is exposed to karrikinolide? Does karrikinolide fed to adult plants affect its growth, reproductive capacity and senescence? And are the seeds produced by a plant that has developed in the presence of karrikinolide more or less dormant? And longer- or shorter-lived? These questions are all important when assessing the possible impacts of using karrikinolide to manage weeds, as the chemical may persist in the environment beyond when it triggers the seeds to germinate. This project will explore the intergenerational effects of karrikinolide and other smoke/ash products on plant and seed development and physiology using glasshouse and laboratory studies.


Co-supervised by Dr Jason Stevens (Kings Park and Botanic Garden); Ph: 9480 3639; Email: jason.stevens@bgpa.wa.gov.au
Showing your age: detecting signs of ageing in weed seeds

Predicting the how long weed seeds can persist in soils is a holy grail for land managers, policy makers and weed researchers alike. Traditional methods for predicting seed persistence are costly and time-consuming, as they involve burying seeds in soils indefinitely to see how long the seeds remain alive. In a bid to find a quicker way of predicting seed persistence, this project will explore a range of physiological and molecular tests to identify correlates of seed ageing. DNA integrity, enzyme and hormone activities will be targeted, with tests carried out on seeds that are aged naturally in soils and artificially in the laboratory.



ASSISTANT PROFESSOR MATTHEW NELSON

Room 1.129 Agriculture Central Wing; Ph 6488 3671; Email: matthew.nelson@uwa.edu.au


CROP GENOMICS AND BREEDING

We are entering a pivotal period in crop breeding. The bad news is that crop productivity is struggling to keep up with increasing demand for food and fodder, with projections that the World will demand 70% more than current production levels by 2050. The good news is that there are more tools than ever in the hands of plant breeders to create more productive and adaptable varieties. One of the most powerful tools is genomics, which can transform the efficiency of selection in breeding programmes. New genome sequencing technologies are making the discovery of genes underlying important crop traits much easier than could have imagined even 5 years ago.

I am part of the UWA / CSIRO team sequencing the genome of Australia’s most important grain legume species: narrow-leafed lupin (Lupinus angustifolius). There is plenty of scope for students wanting to make their mark on crop breeding by identifying genes controlling key domestication traits in lupin: the genes that make the difference between crop varieties and their wild relatives. I particularly focus on genetic and environmental influences on flowering time in lupin and canola. There are also ongoing projects in Brassica species (such as canola) and in the drought tolerant legume pasture species Tedera, where your input could result in new discoveries and new genomic tools for crop breeding.

If your research interests lean more to basic genetics and evolution, you can join me in asking questions about genome evolution such as how polyploidy has shaped chromosome evolution in crop species and their wild relatives, and in exploring the mechanisms for polyploid formation.


Here are some specific project ideas:


  • Finding genes underlying domestication traits such as early flowering, pod shattering and alkaloid content in narrow-leafed lupin. This project will draw resources from the lupin genome sequencing project (a collaborative project between UWA and CSIRO) and a new UWA-based project aimed at discovering genes underlying domestication and productivity traits.

  • Investigating allelic diversity of different gene pools of narrow-leafed lupin such as Australian and European cultivars, landraces and collections from the wild (in collaboration with Dr. Bevan Buirchell (DAFWA) and Dr. Jens Berger (CSIRO)).

  • Mining genomic resources for marker-assisted breeding of Tedera (Bituminaria bituminosa), a drought tolerant pasture legume. Traits that could be targeted are drought tolerance, flowering time or furanocoumarin biosynthesis (in collaboration with Dr. Daniel Real (DAFWA) and Dr. Natasha Teakle (UWA)).

  • Despite the massive impact that the time to flowering makes on canola yields, we know surprisingly little about how genes and environment interact to control flowering time in canola. With climate change already upon us, we must get a clearer understanding of how the environment (temperature and day-length) interacts with genes to result in flowering time variation in canola varieties. Join with us to redress this knowledge gap to help develop canola adapted to climate change (in collaboration with Prof. Wallace Cowling).

  • Every chromosome of every eukaryote species has one functioning centromere that is crucial for cell division. Despite the vital role of centromeres, we don’t know even know where they are located in the genetic maps of most species, including Brassica species (e.g. canola). We have developed a model system using the interspecific hybrid F1 of Brassica napusB. carinata for mapping Brassica centromeres.


PROFESSOR JULIE PLUMMER

Room 2.125 Agriculture Central Wing; Ph 6488 1786; Email: jplummer@cyllene.uwa.edu.au


FORESTRY - Tree breeding and genetic deployment of hardwood species, fine timbers and extractives.

Forestry has the opportunity to solve a number of the major environmental challenges facing Australia, for example, stabilisation of salinity, carbon sequestration, production of biofuel and other industrial products. Forestry also has the challenge to meet Australia's insatiable demand for wood products through the selection and deployment of highly site-efficient wood producing trees ranging from the low rainfall areas of the south-west to the high rainfall tropical regions of northern Australia. 

Several projects are available on the trees that produce high value wood, which contains essential oils. These include tropical (Santalum album), native sandalwood (S. spicatum) and agarwood (Aquilaria agallocha).  Research projects include cell biology of sandalwood, essential oil biosynthesis, biochemistry and molecular biology, fungal-induced oil biosynthesis.  Projects are co-supervised by Professor Emilio Ghisalberti (Chemistry), Dr Chris Jones and Dr Kessarin Tungngoen (Plant Biology).
SEED BIOLOGY

A range of projects is available on Australian, agronomic or weedy species. Projects relate to seed collection and handling, seed storage, dormancy and germination and seedling establishment in rehabilitation areas.


LANDSCAPE MANAGEMENT

Plant Management

A range of projects is available related to management of streetscapes, parks, gardens and remnant bushland.
AGRICULTURE

Development of Australian native perennials as new pasture species. In particular the assessment of secondary metabolites in pasture species that have antimicrobial action and influence rumen digestion (Linked with Dr Megan Ryan and Dr Phil Vercoe).



ASSISTANT PROFESSOR PIETER POOT

Room 2.127 Agriculture Central Wing; Ph 6488 2491; Email: pieterp@plants.uwa.edu.au

Co-affiliation with the Department of Environment and Conservation (DEC).
PLANT CONSERVATION BIOLOGY/PLANT ECOPHYSIOLOGY

SW Australia is one of the world’s 34 biodiversity hotspots as a result of its extraordinary plant diversity AND the great threats that many species face. Over 50% of the flora is endemic with many of these species restricted to a small geographic range. However, other species are much more widespread. What factors cause these large differences in success amongst species? Why are some species extremely rare and others very common? What roles do chance, local specialization, competitive ability, or phenotypic plasticity (i.e. the ability to adapt to a variety of environments) play in explaining species distribution patterns? I have mainly been researching these types of questions by focusing on species from shallow-soil habitats (granite outcrops, ironstone communities) as these habitats contain many restricted-range species and contain up to 25% of our flora. Below you will find some examples of possible project topics. Note that for some of the suggested projects timing is crucial (most species only flower during a few months a year!) and a project may need to start earlier then is indicated in this booklet. Also, I’m more then happy to discuss and consider any of your own project ideas!


Specialisation of rare species to shallow-soil habitats: comparisons with common congeners

Recently we showed that rare species from shallow-soil ironstone communities have a specialized root system morphology that may explain their success in their own habitat as well as their failure in others. However, we do not know how general these observations are and how plastic the root systems of these rare species are compared to those of common ones. Possible projects involve: (a) testing whether species restricted to other shallow-soil environments (e.g. granite outcrop communities) have similar root system morphologies, (b) determining how plastic their root systems are compared to that of common congeners, in response to water and nutrient availability, and (c) determining their drought tolerance


Rare plant species biology/ecology and translocation success (with DEC)

DEC is responsible for the conservation of our rare and threatened flora. For many of the critically endangered species either Interim or Full Recovery Plans have been written or are currently being prepared. However, despite these efforts, for many species we do not have enough understanding of their biology/ecology (i.e. habitat requirements, pollination biology, associations with other species) or the specific threats facing them. Due to the large number of declared flora species and the many DEC officers involved in managing them, there are numerous possibilities for projects. One of these projects involves the assessment of the reproductive success, breeding system and pollination ecology of one of our rarest plants, Banksia (formerly Dryandra) montana, of which only 45 plants survive in the wild. Other possible projects involve the translocation of glasshouse grown seedlings of DRF flora back into their native habitat to either augment existing populations or create new ones. These projects would involve various treatments (e.g. fencing, watering, removing existing vegetation etc) to ascertain how translocation success can be improved. Note that for all these DEC related projects timing is crucial and you need to contact me or Dave Coates (see DEC section) soon!


Weed biology/ecology (with Rachel Standish and Kings Park)

For many of our declared rare flora weeds are listed as one of the major threats. However, a lack of knowledge of the biology of many weed species hampers our efforts to eradicate them. Often an increase in nutrient and/or water availability (e.g. on roadsides) is thought to give weeds an advantage. Possible projects could involve glasshouse studies that compare growth and development of some major weed species, with that of native species they compete with, under different levels of watering and nutrition.


Role of facilitation in Wheatbelt restoration (with Rachel Standish and Michael Renton)

The aim of this project is to determine if there is evidence of facilitation between nearest neighbours in restoration plantings. Do some plant species improve the success of others by ameliorating the local environment? This project would include fieldwork and computer-based modelling.


Is climate change responsible for woodland decline (with Erik Veneklaas, Michael Renton)?

There are several opportunities for projects within the newly funded Centre of Excellence for Climate Change, Woodland & Forest Health (also see Erik’s and Michael’s sections). Some scholar ships for 4th year projects will be made available within the next year.



WINTHROP PROFESSOR STEPHEN POWLES & Dr’s Roberto Busi, Danica Goggin, Todd Gaines, Michael Walsh and Qin Yu

AUSTRALIAN HERBICIDE RESISTANCE INITIATIVE (AHRI)

Room G.008 Agriculture North Wing; Ph 6488 7833; Email: stephen.powles@uwa.edu.au


HERBICIDE RESISTANCE IN CROPS & WEEDS: RESEARCH PROJECTS FROM MOLECULAR GENETICS OF RESISTANCE THROUGH TO ON-FARM MANAGEMENT ISSUES
AHRI is a GRDC and ARC funded multi-disciplinary research team investigating herbicide resistance in weed and crop species. Full details of AHRI people and research projects can be seen on the website http://ahri.uwa.edu.au 
Potential AHRI supervisors for 2011 student research projects are Prof. Powles, Dr’s Busi, Goggin, Gaines, Walsh, Yu.
Each year, students undertake their final year research project within AHRI. Some students who see their future in broadacre cropping undertake applied projects whereas others acquire more fundamental training by undertaking a biochemical/genetics based research project. Because of the diverse projects underway in AHRI (see website http://ahri.uwa.edu.au), fourth year students can conduct research ranging from biochemistry and molecular genetics of resistance, simulation modeling of crop weed management, herbicide evaluations in the lab, glasshouse and field, agro-ecology of resistance, seedbank dynamics, through to on-farm management. We aim for students to undertake a research project of sufficient quality to result in them being an author on a scientific paper published in an international research journal.
AHRI has close contacts with grain growers, farmer groups, public and private sector crop agronomists and with the Department of Agriculture and there is the opportunity to work with individuals from these groups.
AHRI research projects in 2011 include work on resistance in annual ryegrass, wild radish and wild oats.
ASSISTANT PROFESSOR CHARLES A. PRICE

Email: charles.price@biology.gatech.edu (no UWA address yet)

Will join UWA from the end of 2010



Biological Scaling

Life involves the maintenance of an internal homeostatic environment that differs from external surroundings. In order to remain alive, organisms must use energy to move resources along energetic gradients and across semi-permeable membranes. The rate at which this occurs, is to a first approximation, a function of the surface area available for exchange and the mass of the organism. Natural selection has operated on these two fundamental dimensions (and many others of course) to produce a dizzying array of organic form. By itself, this variety of form is overwhelming. However, evolutionary convergence and functional trait analysis have demonstrated that organisms living in similar environments often share physiological, morphological and functional traits. This suggests that simple rules and physical laws may determine many aspects of organic form. In my lab, we work on furthering our understanding of how physical laws help to govern the ecology and evolution of organic form and flux, with special emphasis on plant geometry and in particular, plant distribution networks due to their potential to integrate across so many other aspects of plant form and function.

The general approach I use to investigate this variability is called biological scaling. Put simply this is the investigation of how changes in size, usually mass, influence traits that contribute to survival and reproduction both within and across species. For example, if surface area for exchange scaled as the 2/3 power of organism volume, this would suggest that organisms can be approximated by simple geometric objects (i.e. a sphere, or cylinder). However, scaling analyses often reveal that such exponents differ from simple geometric expectations. How and why does this occur?

I use tools ranging from modeling, image analysis, allometry, trait measurement, gradient analysis and a variety of statistical tools to investigate these questions both within and across species. To date I have used terrestrial plants and a model system, however I am eager to apply these questions to marine systems as well.



Designing student projects

I find student projects are most successful when we identify projects that are of interest to us both. Biological scaling is a broad field, and many types of projects fit within its domain. Below are just a few examples of the types of questions students might investigate: there are many others. These questions are general and could be applied to natural or managed systems.

How does photosynthetic surface area and mass scale with total plant mass within and across species, and how does this scaling lead to species segregation within and across communities? What determines how plants partition leaf, stem and root mass and surface area and how is this partitioning influenced by factors like competition or resource availability? Are the dimensions of key photosynthetic apparatus, such as the number of chloroplasts per unit leaf tissue, or the density of stomates, invariant or allometric with interspecific plant size? Why are leaf networks redundant (loopy), how does redundancy scale, and do different species have different levels of redundancy due to factors like water stress, disease or herbivore pressure?

ASSISTANT PROFESSOR MICHAEL RENTON

Agriculture Central Wing; see Plant Biology Office; Ph 6488 1959 Email: michael.renton@uwa.edu.au


As a plant modeller, I am interested in using computer, mathematical and statistical models to help understand all aspects of how plants grow and interact with their environments. This can be at the scale of genes, physiology, structural development, environmental interactions, ecological interactions, or the long-term processes of evolution. I am fascinated by the way models can give us insight into the relationships between plant processes occurring at different scales eg. how the ways that different species compete for resources in different ways lead to varying degrees of productivity in a field of crops or a forest; or how the interaction between genetics, management, seed ecology, inter-species competition and environment can increase or decrease the risk of developing herbicide resistance; or how the interaction between environmental effects and physiological processes lead to the intricate structure of a tree. I also think models can play a very important role in experimental design, in identifying which areas of enquiry need to be focused on.
Honours scholarships of up to $6000 may be available for these projects, from organisations including CSIRO, GRDC, DAFWA, the Centre of Excellence for Climate Change, Woodland and Forest and Health and several CRCs. I have listed some possible projects below, and encourage you to talk to me about any other projects you might be interested in, especially if you have some background or interest in modelling, maths or computer science. I also encourage you to talk with me about including some modelling work in any other plant biology Honours project you are developing with another supervisor, especially if you are interested in adding invaluable and sought-after modelling skills to your repertoire!
Tactical and Strategic Decisions in Agro-ecological Systems – Dealing with Risk, Variability, Uncertainty and Tradeoffs in a Changing Climate (in conjunction with CSIRO)

This project will investigate the tradeoffs, risk, variability and uncertainty in agro-ecological systems with the aim of identifying strategies for dealing with them most effectively. The project will use existing models and possibly develop these models further. These issues are of particular relevance in a time of conflicting demands (between agricultural production, carbon sequestration and conservation for example) changing climate and increasing climate variability.


Modelling Plant Interactions and Ecosystem Resilience (with DAFWA or Centre for Forest Health)

Plant competition and interaction occurs in crop fields, pastures, forests, deserts, and any other place that plants grow. What makes some plants more successful than others, and how can we predict what the result will be when different species are competing in different conditions and adapting to changing climates?


Modelling the Evolution of Resistance (in conjunction with DAFWA, CRC Plant Biosecurity and/or AHRI)

Understanding what factors lead to the evolution of resistance in weeds and insect pests, and how this resistance can be avoided is one of the most important challenges facing agriculture, and computer models are an essential tool in gaining this understanding. This project will involve using existing simulation models of population dynamics and the development of resistance. The models will be used to simulate previously conducted field trials and experiments in order to validate the models and/or prioritise areas for future improvement and/or to investigate and evaluate possible management strategies for avoiding and/or delaying the development of resistance.


Modelling Weed Seedbank Dynamics and/or Crop-Weed Competition (in conjunction with DAFWA, GRDC)

This project will involve using existing simulation models of weed seedbank dynamics, such as the Weed Seed Wizard and RIM. The models will be used to simulate field trials that have been conducted around Australia, in order to validate the models and prioritise areas for future improvement. The focus of the project will depend on the background and interest of the applicant – no prior expertise in modelling is required.


Modelling the Interactions between Physiology, Structure and Environment

The beautiful and intricate structures of plants (from seagrass, to wheat, to frangipanis) are a result of complex and dynamic interactions between inbuilt rules of morphogenesis, physiological processes and environmental influences. Can models give us insight into how these structures emerge, how they are optimised to take advantage of their environments, and how we can make use of them in agriculture and restoration?



ASSOCIATE PROFESSOR MEGAN RYAN

Ground Floor Agriculture CLIMA/CRC Wing; Ph 6488 2208; Email: megan.ryan@uwa.edu.au


Areas of interest

  • Phosphorus (P) dynamics in pastures and revegetated areas in the Peel Harvey region

  • Ability of native legumes to remediate hydrocarbon contamination of soil

  • Herbaceous native plants with novel P nutrition

  • Arbuscular mycorrhizal fungi and plant P nutrition

  • New annual and perennial pasture legumes


Note

  • As I will be on long-service leave in second semester 2012, all projects will be co-supervised.


Projects being offered
1) P dynamics in the Peel Harvey region

  • A large new project funded by Alcoa and Greening Australia will investigate flows of P through pastures and native revegetation areas in the Peel Harvey.

  • Available student research projects include novel plant P nutrition, role of arbuscular mycorrhizal fungi in pasture P uptake, interactions between waterlogging plant adaptation and plant P nutrition, physiology and ecology of native grasses and sedges, and P movement through shallow groundwater and waterlogged areas.

  • Students will be part of a large supportive team, have access to technical help and receive a generous operating budget. Students will also interact with industry partners, community groups and farmers.

  • Choice of co-supervisor will depend on topic but could include Ed Barrett-Lennard, Rachel Standish, Mark Tibbett (SEE) and Carlos Ocampo (Centre for Ecohydrology).


2) Ability of native legumes to remediate petroleum contamination of soil

  • A new ARC-linkage project will investigate novel ways to use native plants and soil microbes to remediate petroleum contamination of soil.

  • Student research projects are available that examine the tolerance of native herbaceous legumes to petroleum contaminated soil and their ability to stimulate (through rhizosphere processes) degradation of petroleum contamination.

  • Students will be part of a large supportive team, have access to technical help and receive a generous operating budget. Students may have opportunity to interact with industry partners, which include Chevron Australia and Horizon Power.

  • Co-supervision will be provided by project collaborators in SEE (Suman George, Mark Tibbett).

PROFESSOR ERIK VENEKLAAS

Room 2.104 Agriculture Central Wing; Ph 6488 3584; Email: Erik.Veneklaas@uwa.edu.au


Plant Physiological Ecology
My main interest is in how plants are affected by their environment (e.g. climatic and soil conditions), but also how plants affect their environment (e.g. invading weeds affecting native plant communities, revegetation effects on rehabilitated land, positive effects of companion crops and rotational crops, legumes mobilising soil P). The main factors of interest in SW Australia are water and mineral nutrients (especially P). Below is a list of possible topics, but I also welcome your own ideas! Do contact me if you want to know more!
Ecophysiology of native species under stress

  • Decline of SW Australian eucalypts (Eucalyptus wandoo). Our State Centre of Excellence for Climate Change, Woodland and Forest Health offers various opportunities to do research projects into tree declines that are occurring in woodlands and forests of the region, and appear to be related to reduced rainfall. Projects may include tree water relations, nutrition, pathology, competition, modelling, etc. For scholarship info see website (http://www.treehealth.murdoch.edu.au/index.html). Collaborations with Pieter Poot and Michael Renton. Martin Bader, Jerome Chopard and several others outside UWA.

  • Samphire ecophysiology at the Fortescue Marshes in the Pilbara: drought, flooding, salinity. Tissue tolerance, water use and C balance, root dynamics, population dynamics, ecohydrology Collaboration with Tim Colmer.

  • Fitness differences between different provenances of native species, and their crossbred offspring, exposed to abiotic stress. Collaboration with Siegy Krauss and Hans Lambers.


Plant water relations and ecohydrology

  • Ecological engineering and ecohydrology: achieving defined hydrological outcomes through optimal combinations of plant species and soil conditions. Collaboration with Christoph Hinz and Hans Lambers.

  • Dryland crops: water use efficiency and drought tolerance.


Photosynthesis and transpiration of native plants

  • Sclerophyllous leaves: are they physiologically and biochemically different or just a different way of ‘packaging’ photosynthetic tissue?


Plant nutrition

  • Phosphorus economy of native plants: relationships between P acquisition efficiency, P use efficiency, growth and dominance status in native ecosystems. Collaboration with Hans Lambers, Kingsley Dixon and Francois Teste.

  • Phosphorus use efficiency of crops.

  • Timing and placement of cluster roots – costs and benefits in terms of C and P.

ASSISTANT PROFESSOR THOMAS WERNBERG

School of Plant Biology & Australian Institute of Marine Biology, UWA Oceans Institute, Fairway, Ph. 6369 4047, thomas.wernberg@uwa.edu.au


ECOLOGY OF MARINE PLANTS ON REEFS AND IN ESTUARIES; CLIMATE CHANGE AND INVASIVE SPECIES
Thomas Wernberg’s main research interests are ecological interactions involving marine plants on and around subtidal reefs and in estuaries (e.g., the Swan River). His research has a strong empirical focus and relies on field and laboratory observations and experiments to tease apart the causes of species distribution in nature. He is particularly interested in the nexus between physiology, ecology and biogeography, and the need to understand current and future patterns of global change (climate change, invasive species, eutrophication).
Most, but not all, of his projects will require an ability to scuba dive, and many projects will require willingness to participate in field trips to remote coastal areas (e.g., temperate south coast, tropical northwest coast). Projects will be co-supervised by one or more of his current collaborators – Prof Gary Kendrick (UWA), Dr. Dan Smale (UWA), Andrew Heyward (AIMS), Martial Depcynski (AIMS), Dr. Mat Vanderklift (CSIRO), and Dr. Mads Thomsen (Danish National Research Institute).
Project Ideas


  1. Ecology of macroalgae in coral reef lagoons;

  2. Distribution and diversity of coastal macroalgae in the Kimberley region;

  3. Influence of climate on reproduction, recruitment, growth, productivity and mortality of canopy algae;

  4. Temperature adaptation in marine macroalgae (ecophysiology);

  5. Combined effects of multiple stressors on macroalgae (e.g., temperature, pH and eutrophication);

  6. Consequences of ocean climate on seaweed-herbivore interactions;

  7. Biogeography of marine macroalgae;

  8. Comparative ecology and ecophysiology of invasive and non-invasive Caulerpa species;

  9. Interactions between an invasive snail (Battilaria australis), algae and seagrasses in the Swan River.

ASSOCIATE PROFESSOR GUIJUN YAN

Room 1.127 Agriculture Central Wing; Ph 9380 1240; Email: gyan@plants.uwa.edu.au


PLANT CYTOGENETICS, MOLECULAR GENETICS, PLANT BREEDING AND CONSERVATION OF PLANT BIODIVERSITY
Research interests

My main research focuses on the understanding of interspecific and intergeneric genome relationships and genome interactions of wide hybrids using cytogenetic and molecular approaches. In collaboration with my colleagues, I worked on the breeding, genetics, identification of barriers to wide hybridization, cytoevolution, chromosome inheritance, molecular evolution, molecular phylogenetics and molecular marker-assisted breeding of Ziziphus, Actinidia, Chamelaucium, Verticordia, Boronia and Leucadendron. Currently, I am interested in understanding the reproductive biology, molecular genetics and cytogenetics of Proteaceous plants, Brassica and field pea wide hybridisation and barley and wheat genomics and proteomics. I strongly believe that the best way to conserve biodiversity is to bring the plants to cultivation through collection, selection and breeding.


Project Ideas

1. Reconstruction of phylogenetic relationships in plants

Selected publications in this area:

George N, Byrne M, Maslin B, and Yan G (2006) Genetic differentiation among morphological variants of Acacia saligna (Mimosaceae). Tree Genetics and Genomes 2:109-119.

Yan G, F Shan, JA Plummer (2002) Genomic Relationships within Boronia (Rutaceae) as Revealed by Karyotype Analysis and RAPD Molecular Markers. Plant Systematics and Evolution 233: 147-161

2. Any projects related to cytogenetics and molecular cytogenetics of plants

Selected publications in this area:

Shan F, G Yan, and JA Plummer (2003) Cyto-evolution of Boronia genomes revealed by fluorescent in situ hybridisation with rDNA probes. Genome 46: 507-513.

Shepherd KA, G Yan (2003) Chromosome number and size variations in the Australian Salicornioideae (Chenopodiaceae) – evidence of polyploidisation. Australian Journal of Botany 51: 441-452



3. Any project on wide hybridisation and overcoming wide hybridization barriers

Selected publications in this area:

Liu H, Yan G and Sedgley R (2006) Interspecific hybridization in the genus Leucadendron through embryo rescue. South African Journal of Botany 72:416-420.

Astarini IA, Yan G and Plummer JA (1999) Interspecific hybridisation in Boronias. Australian Journal of Botany 47: 851-864.



4. Molecular fingerprinting of plants

Selected publications in this area:

Yuan H, Yan G, Siddique KHM and Yang H (2005) RAMP based fingerprinting and assessment of relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars. Australian Journal of Agricultural Research 56:1339-1346.

Pharmawati M, Yan G and Finnegan PM (2005) Molecular variation and fingerprinting of Leucadendron cultivars (Proteaceae) by ISSR markers. Annals of Botany 95: 1163-1170.



5. New endeavors – Cereal genomics and proteomics and the production of “super Brassica” for oilseed and/or vegetable production.

OTHER ORGANISATIONS AFFILIATED WITH THE SCHOOL OF PLANT BIOLOGY





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