Undergraduate research program

Project title:  

Establishing Australian Economic Management threshholds for fall armyworm in maize (rainfed and irrigated) and sorghum

Project duration: 

10 weeks - Summer Program, 20-36 hours a week.

The project can be completed under a remote working arrangement for applicant’s interested in image analysis and or crop modelling.

Description: 

Fall armyworm (FAW) Spodoptera frugiperda is a recent invasive pest causing variable degrees of seedling death, defoliation and damage to reproductive structures of maize and sorghum across Australian production systems. International reports on crop losses due to FAW feeding are similarly variable suggesting a strong eco-physiological influence on pathosystem.  This project aims to develop reliable crop loss predictions needed to inform skilled economic control threshold recommendations.

Scholars can gain research experience in a multi-disciplinary team of entomologists, crop physiologists, crop modellers and app designers.  As part of a collaborative project between the University of Queensland, Department of Agriculture and Fisheries and Grain Research and Development Corporation.

Expected outcomes and deliverables: 

Applicants will gain skills in crop and insect data collection, statistical analysis, crop modelling, image analysis and have an opportunity to generate publications from their research.  Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for: 

This project is open to applications from all students interested in developing practical outcomes for Queensland farmers.

Primary Supervisor: 

Supervisor name: Dr Joseph Eyre

Supervisor email: j.eyre@uq.edu.au

Supervisor phone: 0467 737 237

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Superior feed quality of gene edited sorghums

Project duration: 

The project will require 8-10 weeks of full-time (36hours/week) of mostly on-site work to complete. Data analysis can be achieved remotely, but will need to be discussed with supervisor

Description: 

Background: Sorghum bicolor (sorghum) is an is an important animal stock feed cereal crop growth throughout the North-eastern regions of Australia in Queensland and New South Wales. Approximately 42% of total cereals consumed are from wheat, rice and maize, however there are a variety other cereal competitor growing in popularity to combat climate instability and the growing human population. Sorghum is primarily used as a feed product for poultry and pork but its usefulness as a primary feed is less favourable than other grains due to issues with its calorific and nutritive value, as well as its high variability of protein content.

Aim: Using gene editing techniques, numerous mutant sorghum lines have been created by targeting specific genes involved in the synthesis and folding of major protein and starch genes. Assessment of the impact of these changes is needed to ascertain the role of these genes, and the potential improvement of quality that could be beneficial for feedlot industries.

Approach: Numerous gene edited lines need to be genotyped and phentoyped. This will involve fundamental molecular techniques to screen the gene of interest for the outcome edit. Phenotyping of the grain will involve performing in vitro assays to test their grain composition and digestibilities. Exogenous factours such as tannins and phytic acid could also be assessed using colorimetric assays.

Expected outcomes and deliverables: 

Researchers will gain skills in numerous aspects of molecular biology and plant physiology. Fundamental technical skills such as DNA extractions, PCRs, gel electrophoresis. Quality assessments of the grain may also be achieved using wet lab chemistry to assess their starch and protein content and digestibilities, as well as tannin content. There may be an opportunity to learn sterile tissue culture to have a chance create their own gene edited sorghum lines.

Students will be expected to write a final report summarising their findings and perform an oral presentation to the lab group.

Suitable for: 

This project is open to students with a plant/agricultural background who are interested in molecular biology research in their 3rd and 4th year. Preference will be given to who have taken or plan to take plant molecular and biotechnology courses.

Primary Supervisor: 

Dr Karen Massel  

Further info: 

Supervisor name: Dr Karen Massel

Supervisor email: k.massel@uq.edu.au

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Matching adapted chickpea genotypes with soil and climate to maximise yield and profit

Project duration: 

10 weeks 36hrs per week

The project can be completed under a remote working arrangement or if on-site attendance is required. 

Description: 

Experimentation in pulses is required to increase farmers profits, diversify income, and increase sustainability. Megatrends in global food markets favour consumption of plant-based protein. However, significant productivity gaps remain, driven by lack of understanding of pulse physiology and agronomy. As part of a collaborative effort between UQ-QAAFI Centre for Crop Sciences, CSIRO, SARDI, NSW DPI, WA DPI and VIC DPI, this project aims to improve our understanding of the impact of different water availabilities and temperature relationships on chickpea growth, development, and yield potential. This project will focus on the analysis of existing chickpea empirical data and the use of the APSIM model www.apsim.info to simulate trials. The student will join a team of field agronomists and crop physiologist that are conducting on-research station trials at UQ Gatton Campus to research the impacts of water availability and temperature regimes during critical periods of biomass partitioning and yield formation for chickpeas. The focus of the trials is to improve our understanding of the dynamics of yield formation under contrasting stresses. Frequent travelling to the field and working outdoors in the field might be required.

Expected outcomes and deliverables: 

The program aims will allow the students translate the theory learnt in their courses at UQ into practice, by joining for 10 weeks the multidisciplinary team of the largest pulse agronomy and crop physiology program in Australia. The students will interact with researchers from different disciplines and be able to make links and connections with researchers from collaborating National and Commonwealth agencies. Students will be asked to produce a report and an internal oral presentation at the end of their project.

Suitable for: 

This project is best suited for students that completed courses in agronomy, crop physiology, and data analysis / statistics.

Primary Supervisor: 

Supervisor name: Prof Daniel Rodriguez

Supervisor email: d.rodriguez@uq.edu.au

Supervisor phone: 0434075094

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

DigitalAg Building #8115 Gatton Campus of The University of Queensland

Project title:  

Growing summer crops in winter to adpat to heat stress

Project duration: 

10 weeks 36hrs per week

The project can be completed under a remote working arrangement though on-site attendance is preferred. 

Description: 

Winter sown sorghum as an adaptation to present and future climates. Water stress and extreme heat at flowering are becoming common abiotic stresses limiting sorghum production across the Northern Grains Region. These stresses can only be expected to increase in frequency and intensity as our climate changes. Winter sown sorghum has been proposed as a practice to increase sowing opportunities, avoid heat and water stress at flowering, and increase the frequency of double cropping i.e. planting a winter crop after a short summer fallow following the winter sown sorghum. As part of a collaborative effort between UQ-QAAFI Centre for Crop Sciences, NSW DPI and QDAF, this project aims to assess the likely benefits of the practice using datasets from a network of trials run over the last two years across NSW and QLD, APSIM-Sorghum (www.apsim.info), and climate projections from a wide range of global circulation models. This Honours project will focus on desktop activities that will analyse existing experimental data, parameterise and run simulation models. The student will join a team of crop physiologist, APSIM programmers and climate modellers, using QAAFI’s facilities at UQ’s Gatton Campus.

Expected outcomes and deliverables: 

The program aims will allow the students translate the theory learnt in their courses at UQ into practice, by joining for 10 weeks the multidisciplinary team of the largest sorghum agronomy and crop physiology program in Australia. The students will interact with researchers from different disciplines and be able to make links and connections with researchers from collaborating National agencies. Students will be asked to produce a report and an internal oral presentation at the end of their project.

Suitable for: 

This project is a desk top study, best suited for students that completed courses in agronomy, crop physiology, and data analysis / statistics. Having experience with APSIM or R would be an advantage.

Primary Supervisor: 

Supervisor name: Prof Daniel Rodriguez

Supervisor email: d.rodriguez@uq.edu.au

Supervisor phone: 0434075094

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Nutrition profiling of green leaves of under-utilized plant species

Project duration: 

10 weeks (30-36 hrs/week) and applicant will be required on-site for the project.

Description: 

Green leafy vegetables are known to have nutritional importance. They may have high protein, vitamin and mineral contents. Recently, there has been an interest in exploiting under-utilised plant species. Some of them are considered weeds in broadacre farming systems; however, they could be good sources of nutrients. This project will evaluate the nutrient contents of such plants at different growth stages. Plants will also be subjected to different agronomic practices (e.g., shade, water).

Expected outcomes and deliverables: 

Scholar will gain skills in data collection, be involved in analysing samples, and have an opportunity to generate publications from their research. Student will need to produce an oral presentation at the end of their project.

Suitable for: 

This project is open to students with a background in biochemistry or food science.

Primary Supervisor: 

Supervisor name:  Bhagirath Chauhan

Supervisor email: b.chauhan@uq.edu.au

Supervisor phone: 0427923272

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Agronomy of sesame

Project duration: 

10 weeks (36 hrs/week) and applicant will be required on-site for the project.

Description: 

Sesame is known for its high nutritional value. Recently, there has been an interest in growing sesame in Queensland; however, very limited information is available on its agronomy. Several small projects are available, which will evaluate its optimum planting depth, planting density and row spacing. In addition, a project will evaluate effective pre- and post-emergence herbicides for weed management in sesame.

Expected outcomes and deliverables: 

Scholars will gain skills in data collection, be involved in analysing data, and have an opportunity to generate publications from their research. Students will need to produce an oral presentation at the end of their project.  

Suitable for: 

This project is open to all students (no background knowledge needed).

Primary Supervisor: 

Supervisor name:  Bhagirath Chauhan

Supervisor email:  b.chauhan@uq.edu.au

Supervisor phone:  0427923272

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Trialling Raspi Spectral Imaging in conjunction with the "Rainfall Proof Upside Down Watering System (RPUDBWS)", to evaluate salinity tolerance in Taro (colocasia esculenta), the Pacific Islands Principal Crop

Project duration: 

10 weeks - Summer Program, 20-36 hours a week, applicant will be required on-site for the project.

Description: 

A leading threat to the Pacific region is the risk of rising sea levels and increased cyclone activity causing tidal inundations because of climate change. High coastal population densities, freshwater shortages, longer periods of drought and losses of arable land linked to the rise of the oceans and the salinization of coastal land are bound to intensify. Recent analysis on the proximity of Pacific people to the coast indicated half of the region’s population resides within 1km of the coast excluding Papua New Guinea.

Taro is one of the most important staple food crops with high cultural significance in all Pacific Island Countries and Territories (PICTs). It is also an important commercial crop in some of the countries like Fiji and Samoa which are amongst the top 10 taro exporting countries in the world in 2020 reports with export values of around 15million and 2.6million USD respectively.

As part of an FAO funded joint UQ-SPC collaboration (CPS 19/584), we have successfully completed a pilot study at UQ to evaluate the effect of salt stress on mature taro, grown using a hydroponic pot system which can maintain a constant water table (Image Below; Hunter et al., 2018).

This simple system can effectively model the conditions faced within salt intrusion of a freshwater lens and analysis of mature specimens fills an important gap in the scientific literature. We have also begun testing the capacity to develop a high-throughput phenotyping platform for salinity tolerance in taro.  High-throughput image analysis has been developed for cereal species to detect salinity tolerance (Sirault et al., 2009) however, no cost-effective alternatives have been developed. Our initial results are promising, and with further testing will represent a cheap, rapid phenotyping technique that could easily be deployed in the Pacific region to phenotype salinity stress in diverse taro germplasm.

Expected outcomes and deliverables: 

Scholars may gain skills in experimental set-up, data collection (Stomatal conductance, Water Use Efficiency, Biomass measurements, Use of Spectral imaging, Statistical Analysis…), be involved in specific tasks, or have an opportunity to generate a publication from their research.  Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for: 

Primary Supervisor: 

Supervisor name: Dr Bradley Campbell

Supervisor email: b.campbell2@uq.edu.au

Supervisor phone: 0412648391

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Artificial Intelligence for better beans

Project duration: 

10 weeks

Hours of engagement must be between 20-36hrs per week

COVID-19 considerations: Project can be completed under a remote working arrangement if required.

Description: 

Globally, demand for protein is increasing. Future products made with pulse protein will require over 100,000 tonnes of legume protein by 2030. Mungbean is an important food and cash crop grown in tropical and subtropical regions globally. Despite increasing demand for mungbean protein, expansion of mungbean is limited in Australia due to its low yield and variability between environments. 

To meet these challenges, improved mungbean varieties are required for the future with ideal combinations of traits. However, selecting the genomic regions of interest for targeted crossing is challenging because of interactions between genotypes and their environment. Artificial intelligence is a power technology ideally suited to estimate complex network relationships and large datasets. Applying artificial intelligence to mungbean crop improvement will help to accelerate the development of improved mungbean varieties for the future.

The aim of this research project is to use artificial intelligence via deep learning algorithms to deconvolute complex relationships between genotype, the environment and phenotype. Improved algorithms will be investigated for their ability to associate key genomic regions associated with yield development in mungbean. Algorithms will be developed using in-silico breeding trial datasets and evaluated using real data from a mungbean pre-breeding population tested in the field.

Expected outcomes and deliverables: 

Skills and experience will be gained in data collection, quality control, curation, reproducible research documentation and analysis. The specific tasks will include software analyses of associations between genetic fingerprints (DNA markers) and could include taking plant measurements. Potential for inclusion of student in research publications.

Suitable for: 

Plant Science, Genetics and Computational Science Students.

Primary Supervisor: 

Supervisor name: Dr Owen Powell

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Biology and managmeent of giant rat's tail grass

Project duration: 

10 weeks (36 hrs/week) and applicant will be required on-site for the project.

Description: 

Giant rat's tail grasses (Sporobolus species) are becoming problematic weeds in pastures, grain crops and along roadsides. Limited information is available on their biology and management in Queensland. This project will study its biology and management.

Expected outcomes and deliverables: 

Scholars will gain skills in data collection, be involved in analysing data, and have an opportunity to generate publications from their research. Students will need to produce an oral presentation at the end of their project.

Suitable for: 

Primary Supervisor: 

Supervisor name:  Bhagirath Chauhan

Supervisor email: b.chauhan@uq.edu.au

Supervisor phone: 0427923272

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Exploring global genetic diversity for coleoptile length in barley using machine learning approaches

Project duration: 

10 weeks with approximately 20 - 30 hours of engagement per week. Applicant will be required to be on-site for most of the project but with some scope to work remotely at certain times.

Description: 

Climate variability coupled with increased frequency and duration of heat and drought events challenges global crop production. Drought adaptation is complex, made up of several component traits, some interacting, and all influencing crop water-use across the growth cycle. The length of the coleoptile, the protective clear sheath surrounding the emergent leaf, determines sowing depth and is a potential drought avoidance trait of interest to farmers. A long coleoptile enables deeper sowing to capture soil moisture at depth. As a result, reducing the reliance on rainfall events and enabling earlier sowing to avoid energy intensive development during periods of increased heat and limited water availability. Despite the importance, there is limited knowledge of the genetic control of coleoptile length in barley.
This project aims to explore the genetic architecture of coleoptile length as well as identify new sources of diversity through the examination of a large globally diverse barley panel. Recently developed machine learning approaches for genome-wide association analysis (support-vector regression and random forest) will be applied to previously collected phenotypic and genotypic data sets. To compare the effectiveness of these new approaches, single-maker, and haplotype-based genome-wide association studies (GWAS) will also be run. In addition, phenotypic and genetic relationships between coleoptile length and other early development traits, like early vigour, biomass, and seminal root angle, will be explored.

Outcomes of this project will deliver novel insight into the genetic architecture of coleoptile length in barley as well as highlight opportunities for increased genetic diversity within Australian germplasm that can be harnessed by breeders. Further the project will explore the advantages of machine learning approaches for GWAS compared to haplotype-based and more traditional single marker approaches.

Expected outcomes and deliverables: 

Suitable for: 

The project is open to applications from 3rd and 4th year students with a background in basic genetics or statistics.

Primary Supervisor: 

Supervisor name: Dr Hannah Robinson

Supervisor email: h.robinson1@uq.edu.au

Supervisor phone: 0488 279 694

Further info: 

This project is not suitable for remote, online delivery.

Project title:  

Monitoring crop water use and root activity in 3D

Project duration: 

10 weeks 36hrs per week 

The project can be completed under a remote working arrangement though on-site attendance is preferred.   

Description: 

The ongoing climate change has increased the intensity and frequency of drought and heat events in Australia, increasing the vulnerability of farming and urgency to optimise crop design for increased adaptation. Phenotyping plays a key role in improving the climate adaption as it provides essential information on how genetics, environmental pressures, and crop management (farming) can guide selection toward productive crops suitable for their environments. However, so far, most of the crop phenotyping works have focused on characterizing the above ground parts of crops, mostly ignoring the “hidden half”, the root system and its activity due to the opaque nature of soils and a lack of efficient sensing tool. As part of a GRDC Postdoctoral fellowship project (Understanding sorghum root growth and function in cold soils), this project aims to assess the ability of proximal sensing techniques for 3D characterization of crop water use and root activity in the field using datasets from last two-years trails. This Honours project will focus on desktop activities that will analyse existing experimental data and develop models. The student will join a team of crop physiologist, soil science and modelling, using QAAFI’s facilities at UQ’s Gatton Campus.  

Expected outcomes and deliverables: 

The program aims will allow the students translate the theory learnt in their courses at UQ into practice, by joining the multidisciplinary team of the largest sorghum agronomy, crop physiology and soil science in Australia for 10 weeks. The student will get opportunity to develop skills in using proximal sensors for monitoring spatial variations of crop water use. The students will also interact with researchers from different disciplines and be able to make links and connections with researchers from collaborating National agencies. Students will be asked to produce a report and an internal oral presentation at the end of their project. 

Suitable for: 

This project is a desk top study, best suited for students that completed courses in agronomy, crop physiology, soil science, and geospatial analysis / statistics. Having experience with R would be an advantage.

Primary Supervisor: 

Supervisor name: Dr Dongxue Zhao

Supervisor email: dongxue.zhao@uq.edu.au

Supervisor phone: 0451731233

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Application of visible near-infrared spectroscopy for predicting soil and physical and chemical properties

Project duration: 

10 weeks 36hrs per week 

The project can be completed under a remote working arrangement though on-site attendance is preferred.   

Description: 

Soil is a fundamental natural resource on which the production of food, fiber and energy relies. Soil is also the largest sink of carbon. To improve the profitability of agricultural production and to mitigate the climate change, reliable information on soil physical (e.g., particle size fraction) and chemical properties (e.g., organic carbon) is needed. However, traditional laboratory methods for generating soil information are expensive and time-consuming and demand chemical reagents. Visible near-infrared (vis-NIR) diffuse reflectance spectroscopy has shown the potential to be an effective alternative to the traditional laboratory methods given its advantages e.g., they are rapid, cost-effective and accurate. The vis-NIR measures the soil reflectance in the visible (vis, 350 – 700 nm) and near-infrared (NIR, 700 – 2500 nm) regions. A single vis-NIR spectrum encode extensive information on the soil composition, which includes minerals, organic compounds and water. It has therefore been used to simultaneously characterize various soil properties. To extract soil information from the vis-NIR spectra, statistical or machine learning techniques are required. As part of a collaborative effort between UQ-QAAFI Centre for Crop Sciences, UQ-SMI Centre for Water in the Minerals Industry and UQ-SEES, this project aims to develop a vis-NIR spectral library using various modelling techniques (e.g., machine learning algorithms) to monitor various soil properties for assessing the potential use of mine de-watering resources for food and fibre production and carbon sequestration. This Honours project will have an opportunity to develop abilities on using vis-NIR spectrometer, processing the soil spectral data and developing models for rapid generating various soil information. The student will mainly focus on desktop activities that will process and analysis existing soil spectral data. The student will join a multidiscipline team of crop science, soil science and modelling, using QAAFI’s facilities at UQ’s Gatton Campus.   

Expected outcomes and deliverables: 

The program aims will allow the students develop ability and experience on using the proximal visible near-infrared spectrometer for rapidly predicting various soil attributes which are critical for agricultural and environmental management. The students will join one of the largest multidisciplinary team of agronomy, crop physiology and soil science in Australia for 10 weeks. The students will interact with researchers from different disciplines and be able to make links and connections with researchers from collaborating National agencies. Students will be asked to produce a report and an internal oral presentation at the end of their project. 

Suitable for: 

This project is a desk top study, best suited for students that completed courses in soil science, and data analysis / statistics. Having experience with R would be an advantage.

Primary Supervisor: 

Supervisor name: Dr Dongxue Zhao

Supervisor email: dongxue.zhao@uq.edu.au

Supervisor phone: 0451731233

Further info: 

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Understanding the effect of carbon stress at different growth stages on grain abortion in sorghum

Project duration: 

This project will occur for 10 weeks 36hrs per week.

The student will be required to be on site. Accommodation will be provided, if needed.

A face-face engagement mode would be preferable.

Description: 

Grain sorghum is an important dryland crop which is used for food, feed and fuel. Sorghum yield are impacted by stress events occurring primarily during the reproductive phase. Hence, there is a need to clearly define the most sensitive growth stage in sorghum. This project will investigate the effects of carbon stress, induced through removal of leaves, applied at different growth stages on grain development and abortion in sorghum. The carbon stress will be applied at vegetative, flag leaf, at flowering and post flowering to understand the dynamics of carbon balance and its effects on grain development and abortion at different growth stages in sorghum.  

The hypothesis is that the carbon stress applied at flowering will have the largest impact on grain filling and increase grain abortion in sorghum.

Objectives:

1. Assess the impact of carbon stress at different growth stages in sorghum
2. Quantify extent of grain abortion in response to carbon stress at different stages of growth in sorghum

Expected outcomes and deliverables: 

The project will help students gain insights into conducting scientific research, specifically, running experiments, conducting data collection, learn some basic statistical procedures as part of this project. In addition, the student will get the opportunity to interact with world renown experts in sorghum physiology and breeding.

Deliverables

1. Student will be required to implement carbon stress treatments at different growth stages, conduct data collection via flowering and harvesting records
2. Student will be required to conduct simple data analysis
3. Student will need to present experiment results (if interested)

Suitable for: 

This project is open for applications from students with a background in Agricultural science (preferably 3rd – 4th year students), who have completed courses in Agronomy, Crop physiology or crop science.

Primary Supervisor: 

Supervisor name: Dr. Geetika Geetika

Supervisor email: g.geetika@uq.edu.au

Supervisor phone: 0481266089

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Project title:  

Isolation of Sorghum Biofuel Variants form a Large Mutant Library

Project duration: 

The applicant will be required to be onsite for most if not all activities. The duration of the project will be 10 weeks (36 hrs weekly).

Description: 

Background: Sorghum (Sorghum bicolor) is a C4 crop which is utilised for food, animal feed, alcohol and biofuels. Mutagenesis is generally a spontaneous event generated via normal cellular processes or via erroneous DNA repair or replication and is a key factor in the evolution of species. As instances of mutagenesis create new diversity within genomes, this process has been harnessed by plant breeders to create novel traits, utilising chemical, biological and physical mutagens. We have generated 150,000 variant lines of an inbred Sorghum bicolor variety BTx623, using low doses of the chemical mutagen ethyl methanesulphonate. Seeds were collected and bagged in bulks containing the seed from 100 variant lines. DNA will then be extracted from bulk subsamples, followed by digital PCR screening (FIND-IT) of pre-determined variants. The newly developed FIND-IT protocol has previously been utilised to isolate variants of interest in a large variant library of barley (x500,000). The use of this protocol will dramatically reduce the need for backcrossing compared to TILLING collections. This large sorghum variant library will provide a new source of genetic diversity, contributing to sorghum breeding efforts focused on enhancing disease resistance, drought tolerance, plant microbial interactions, and biofuel production traits. 

Aim: In this project, the applicant will be screening seed for mutations of interest, using the PCR based FIND-IT protocol. Seeds containing the desired variant will then be propagated.  Gene isoforms from the UDP-Glucose dehydrogenase gene family and UDP-Xylose Synthase gene family are the target genes. These genes were selected due to their key role in the formulation of the cell wall. Mutations in these genes may cause alterations in Sorghum cell walls that are favourable to biofuel production.

Expected outcomes and deliverables: 

The applicants will gain practical knowledge in new PCR based screening techniques for mutant plant populations. From a practical molecular biology perspective the applicant will be undertaking non-destructive seed sampling for DNA, DNA extraction, and PCR screening of mutant seed via the FIND-IT protocol. Additionally, the applicant will be assisting in the seed germination and subsequent care of Sorghum plants found to have a mutation of interest.  Where possible the applicant will also be included in monthly meetings with our research partners (Carlsberg Research Laboratories and the University of Copenhagen).

Key Deliverables:

-Assist supervisor and visiting PhD student in Sorghum mutant seed screening process.

-Attendance at 2 x monthly meetings between Carslberg/Uni of Copenhagen Research Team. Applicant will be expected to assist in the preparation of presentation material displaying outcomes of the screening work.

Assisting in the reporting of outcomes in the two aforementioned meetings will count as the report component in this research program.

Suitable for: 

The project will be based in molecular biology, with a heavy focus on the following techniques:

1. Non-destructive seed sampling for DNA
2. DNA extraction
3. PCR screening (FIND-IT) protocol
4. Data collation
5. Seed germination/plant care

Preferably the candidate will have a background in Plant Science based Genetics/Molecular Biology, who is in their 3rd or 4th year.

Primary Supervisor: 

Supervisor name: Dr. Patrick Mason (Postdoctoral Researcher in Robert Henry’s Lab)

Supervisor email: p.mason1@uq.edu.au

Supervisor phone: 0438886534

Further info: 

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Lab C220 Hartley Teakle Building (83) at the UQ St Lucia campus, most work will be taking place in the aforementioned lab. Office space will be provided in RmC202 in the Hartley Teakle Building.

Project title: 

Genetic variability of macadamia cultivars to husk rot

Project duration, hours of engagement & delivery mode:

Duration of the project 8 – 10 weeks and hours of engagement must be between 20-36 hours per week.

The applicant will be required on-site for the project from November, which coincides with the macadamia fruit development stage.

Description:

The scholar will undertake research in the biology of husk rot, an emerging fungal disease affecting macadamia fruit. Husk rot is an insidious disease resulting in severe yield loss to macadamia growers. Breeding for disease-resistant macadamia variety has been proffered as a suitable control option. The scholar will contribute to an existing research program, to evaluate husk rot incidence and severity among macadamia breeding progenies under field conditions. The scholar will undertake the research using various plant pathology techniques and analytical tools to estimate the genetic variability of macadamia to husk rot.

Scholar will have an opportunity to contribute to publications from the research.

Expected outcomes and deliverables:

Scholars may gain skills in data collection, be involved in specific tasks, or have an opportunity to generate publications from their research.  Students may also be asked to produce a report at the end of their project.

Suitable for:

This project is open to applications from 3rd or 4th year undergraduate or coursework or research postgraduate students with a background in agriculture, biological sciences, biotechnology or molecular biology.

Primary Supervisor Details:

Supervisor name: Assoc Prof Femi Akinsanmi

Supervisor email: o.akinsanmi@uq.edu.au  (Preferred mode of contact)

Supervisor phone: 0734432453

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

Placement location for laboratory work is Ecosciences Precinct, Boggo Road Dutton Park, which is located ~ 10 min. walk or 1 min bus ride from UQ Lakes bus terminal in St Lucia Campus

Project Title

Automated acquisition of fruit tree growth data

Project duration, hours of engagement & delivery mode:

10 Weeks – Summer Program, 26-36 hours a week, applicant can complete the project under a remote working arrangement.

Description:

The analysis of fruit tree growth data can be useful to better understand the underlying physiology, as well as to parameterize mathematical models of fruit tree growth and phenology. However, the acquisition of plant growth data at short intervals, i.e., daily, can be a laborious task. The implementation of an automatic system could greatly benefit data acquisition in the field during the whole growing season. This project will review similar approaches in order to design and implement a programable system than can record the required growth data automatically. This system will be installed and tested to monitor avocado or macadamia plants.

Expected outcomes and deliverables:

Scholars may gain skills in tools for remote collaboration, electronics, programming, as well as plant physiology and data collection. Students may be asked to produce a report or oral presentation at the end of their project.

Suitable for:

This project is open to applications from 3rd and 4th year students with a background in engineering, computational science, and/or quantitative biology or previous experience with electronics and programming. It is suitable for students interested in understanding how sensors and automatisms can be applied to study biological systems.

Primary Supervisor Details:

Supervisor name: Dr Inigo Auzmendi

Supervisor email: i.auzmendi@uq.edu.au

Supervisor phone: 07 344 32702

Further info:

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

Queensland Alliance for Agriculture and Food Innovation

Centre for Horticultural Science

Room s632, Level 6, Hartley Teakle Building 83

The University of Queensland

St Lucia QLD 4072

Project title: 

Modelling fruit tree architecture and physiology

Project duration, hours of engagement & delivery mode:

10 Weeks – Summer Program, 26-36 hours a week, applicant can complete the project under a remote working arrangement.

Description:

Mathematical modelling of plant architecture can offer insights into the underlying biology, with the eventual outcome of increased yields in Queensland agriculture. In complex plant canopies like fruit and nut trees, simulation of plant architecture at the scale of internodes, leaves and fruit can help to understand aspects of organ growth and development. These models can subsequently be used to study interactions between management practices, environmental factors, plant carbon balance and growth. This project will use data already collected in avocado, macadamia or mango for modelling an aspect of orchard management of interest to the student, such as different training systems, planting densities and cultivars.

Expected outcomes and deliverables:

Scholars may gain skills in tools for remote collaboration, L-systems, computational modelling and simulations, as well as plant physiology. Students may be asked to produce a report or oral presentation at the end of their project.

Suitable for:

This project is open to applications from 3rd and 4th year students with a background in mathematics, computational science, and/or quantitative biology or previous experience with computational modelling. It is suitable for students interested in understanding how mathematics and modelling can be applied to study biological systems or in improving their computer programming knowledge in areas like simulation or complex systems modelling.

Primary Supervisor Details:

Supervisor name: Dr Inigo Auzmendi

Supervisor email: i.auzmendi@uq.edu.au

Supervisor phone: 07 344 32702

Further info:

This project is suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

Queensland Alliance for Agriculture and Food Innovation

Centre for Horticultural Science

Room s632, Level 6, Hartley Teakle Building 83

The University of Queensland

St Lucia QLD 4072

Project title: 

RNA biopesticides for sustainable control of myrtle rust

Project duration, hours of engagement & delivery mode:

10 weeks, 20-36 h per week

Applicant will be required on-site for the project 

Description:

Myrtle rust is a highly invasive fungal disease of Myrtaceae species and is threatening Australian ecosystems and native plant industries. Management of myrtle rust in nurseries and plantations predominantly relies on the use of fungicides, however, fungicides can lack specificity, run-off into the environment, may be toxic to humans and non-target organisms, and can lead to the development of pathogen resistance. Fungicide treatments are also not feasible for natural environments. The aim of this project is to explore RNA based biopesticides as a novel control for myrtle rust in native Australian Myrtaceae species. The project will involve screening previously identified dsRNA molecules for their protective effects on different native Myrtaceae hosts. Molecular techniques such as PCR, in vitro dsRNA synthesis, RNA extraction and northern blotting will be used.

Expected outcomes and deliverables:

Scholars will be trained in a PC2 laboratory and learn molecular biology and plant pathology techniques. Students may be asked to give an oral presentation at the end of their project.

Suitable for:

The project is open to applications from students with a background in plant sciences, mycology and/or molecular biology. 

Primary Supervisor Details:

Supervisor name: Dr Anne Sawyer

Supervisor email: a.sawyer@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

St Lucia and Ecosciences Precinct, Dutton Park

Project title: 

RNA delivery to trees

Project duration, hours of engagement & delivery mode:

10 weeks, 20-36 h per week

Applicant will be required on-site for the project 

Description:

Exogenous RNA interference (RNAi) is a promising tool for the control of plant pests and pathogens. However, RNA delivery needs to be optimised, especially for trees. We have found that RNA can move systemically in plants, however, movement varies between species. The aim of this project is to compare different RNA delivery methods in different tree crops (avocado and Myrtaceae). This will involve assessing the ability of different plant tissues (leaves, stems and roots) to take up RNA and examining whether RNA moves to distal/newly forming tissues (i.e. new leaves, new roots). The presence of RNA in distal tissues/new growth will be assessed by extracting RNA and performing northern blots. Glasshouse infection assays will also be performed to confirm that the plants are protected from disease (Phytophthora root rot and/or myrtle rust). Protection will be monitored through symptom development and pathogen gene knockdown, which will be assessed by quantitative reverse transcriptase PCR.

Expected outcomes and deliverables:

Scholars will be trained in a PC2 laboratory and learn molecular biology and plant pathology techniques. Students may be asked to give an oral presentation at the end of their project.

Suitable for:

The project is open to applications from students with a background in plant sciences, mycology and/or molecular biology. 

Primary Supervisor Details:

Supervisor name: Dr Anne Sawyer

Supervisor email: a.sawyer@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

St Lucia and Ecosciences Precinct, Dutton Park

Project title: 

Tissue culture to feed the world

Project duration, hours of engagement & delivery mode:

10 weeks, 26-36 hours a week, applicant will be required on-site for the project.

Description:

The Mitter Lab has received global media coverage for developing the world’s first tissue-culture production system for avocado plants. This is important as a sustainable, cost-effective and climate-secure way to produce plants. Since this landmark success the group has developed programs to propagate horticulturally valuable plant species such as vanilla, fingerlime and macadamia in addition to pharmaceutically valuable species such as Duboisia. The Mitter group’s research is strongly industry orientated with research outcomes translated into real world solutions for Australia’s horticulture needs.   

Dedicated students will be part of our expanding research in a new $20M tissue-culture facility at Long Pocket UQ, developing systems for other crop species as well as endangered or high value native species where prior research is lacking or proved too challenging. Students may get a chance to work with industry and research partners to value-add student experience.

Projects available:

1. Tissue culture propagation for the horticultural/native species such as macadamia, custard apple, Duboisia and Gossia
2. Cryopreservation of horticultural/native plant species to future-proof germplasm

Expected outcomes and deliverables:

Students will gain skills in plant tissue culture, plant physiology, experimental design, data collection, be involved in specific tasks, or have an opportunity to generate publications from their research.  Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for:

Dedicated students who are interested in plant biology and the technologies that can make a difference to industry and sustainability.

Primary Supervisor Details:

Supervisor name: Dr Alice Hayward

Supervisor email: a.hayward@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

Elkhorn State-of-the-Art Tissue Culture Facility

Queensland Alliance for Agriculture and Food Innovation

UQ LongPocket Campus

80 Meiers Rd, INDOOROOPILLY

There is a free shuttle bus for all UQ students/staff between St Lucia and Long Pocket campuses.

Project title: 

Novel biopesticide to control sugarcane pests

Project duration, hours of engagement & delivery mode:

10 weeks, 20-36 hrs per week, and applicant will be required on-site for the project.

Description:

Greyback canegrub is a major pest throughout Australian sugarcane growing regions with its control relying on imidacloprid application. Located along 2,000 km of the country’s east coast in tropical and subtropical regions, the sugarcane industry needs to proactively respond to the pesticide contamination detected in the Great Barrier Reef and possible regulatory constraints on imidacloprid use against canegrubs.

Compared to conventional chemical pesticides, RNAi-based biopesticide have significant advantages in terms of sustainability, target specificity, safety to human health and the environment. The ground-breaking transformational platform BioClayTM, using clay particles as carriers to deliver RNAi molecules, developed by the Mitter Lab, has made significant advancement in non-toxic, environmental friendly, RNAi-based crop protection applications. 

In this project, you will further define the utility of BioClayTM to control greyback canegrubs by identifying effective target genes. This work will be based on our newly generated canegrub genome and transcriptome analysis data. Dedicated students will design and clone dsRNA constructs targeting selected genes which are critical to the growth or survival of the canegrubs. A subset of optimal dsRNA constructs will then be selected for screening in insect bioassays.

Expected outcomes and deliverables:

Scholars will work in a multidisciplinary team, gain valuable experience in experimental design, troubleshooting and data interpretation, and learn skills in bioinformatics and molecular biology techniques (include DNA/RNA extraction, molecular cloning, qPCR, etc.).

In addition, students will have the opportunity to contribute to publications from their research and engage with industry partners, work in a dynamic laboratory with molecular biologists, bioinformaticians, plant pathologists, and entomologist. At the end of their project, students will be expected to produce a report and an oral presentation.

Suitable for:

This project is open to applications from students with a background in biotechnology, molecular biology, entomology, crop protection, or related fields.

Primary Supervisor Details:

Supervisor name: Dr Ivy Chen; Prof Neena Mitter

Supervisor email: ivy.chen@uq.edu.au; n.mitter@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

St Lucia

Project title: 

RNAi-based biopesticide for sugarcane

Project duration, hours of engagement & delivery mode:

10 weeks, 20-36 hrs per week, and applicant will be required on-site for the project.

Description:

RNA interference (RNAi) is a powerful approach for combating biotic and abiotic stresses in plants. However, its potential is currently limited in its adoption to genetically modified crops. The non-transgenic approach of

spray-induced gene silencing, which relies on spray application of double-stranded RNA (dsRNA) to induce RNAi, has shown great advantages with its versatility and environmental benefits. The ground-breaking transformational platform of using clay particles as carriers of exogenous dsRNA named BioClayTM, developed by the Mitter Lab, has made significant improvement on the stability and persistence of sprayed dsRNA for controlling pests or pathogens.

In this project, we aim to use BioClayTM to combat sugarcane root feeding pests. To achieve robust RNAi response through sprayed dsRNA, plant uptake and systemic translocation of dsRNA is required for delivery to the target organisms. Dedicated students will investigate the uptake and movement of foliar applied dsRNA in sugarcane plants, using both molecular biochemical tools and fluorescence imaging microscopy.

Expected outcomes and deliverables:

Scholars will work in a multidisciplinary team, gain valuable experience in experimental design, troubleshooting and data interpretation, and learn skills in molecular biology techniques (include confocal microscopy, RNA extraction, molecular cloning, northern blot, etc.).

In addition, students will have the opportunity to contribute to publications from their research and engage with industry partners, work in a dynamic laboratory with molecular biologists, bioinformaticians, plant pathologists, and entomologist. At the end of their project, students will be expected to produce a report and an oral presentation.

Suitable for:

This project is open to applications from students with a background in plant science, horticultural science, molecular biology, biotechnology, or related fields.

Primary Supervisor Details:

Supervisor name: Dr Ivy Chen; Prof Neena Mitter

Supervisor email: ivy.chen@uq.edu.au; n.mitter@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

St Lucia

Project title: 

Caring for a healthier chicken starts “in ovo”

Project duration, hours of engagement & delivery mode:

10 weeks and applicant will be required on-site full time.

Description:

Chicken’s gastrointestinal tract undergoes significant physiological changes during the first days after hatch, including the establishment of a microflora when transitioning from a clean close-to-sterile hatchery environment to the adopting “dirty” farm ecosystem. In that context, establishing a beneficial and protective microflora before to the arrival to the farm would reduce the possibility of enteric pathogens colonizing the gut. This, in turn, would decrease disease burdens later in the life of the chicken, thus, reducing the need of preventive or curative (antibiotic) treatments. The early development of a healthy gut including early microbiome development, could be facilitated during the embryonic stages. In ovo techniques have been developed in recent years to supplement nutrients to the chick just before hatch. However, little is known about the potential of programming the future microbiome (ex ovo) during the embryonic stage. This project will study use of essential oils with antioxidant and antimicrobial activities during embryonic stages, to improve gut health early in the life of chicks. The project will systematically evaluate all the parameters related with an effective inoculation of essential oils in the egg to produce healthy hatchlings. The ultimate goal of this project is to make on farm antibiotic use redundant.

Expected outcomes and deliverables:

Applicant will have the opportunities to involve and learn different skills such as in-ovo injection technology, incubation and hatchery at experimental scale, handling chicken embryos, lab analyses such as PCR and qPCR.

Suitable for:

Animal or Veterinary Sciences/ Nutrition / Biomedical Science / Computational Science / Microbiology

Primary Supervisor Details:

Supervisor name: Dr Shahram Niknafs

Supervisor email: s.niknafs@uq.edu.au

Further info:

This project is not suitable for remote, online delivery.

Applicants for this project must contact the listed supervisor to discuss the project ahead of commencing the application process.

Site:

St Lucia