Centre for Horticultural Science - Winter Research Programs
General information on the program, including how to apply, is available from the UQ Student Employability Centre’s program website.
Uncover the RNAi machinery in canegrubs
Primary Supervisor:
Dr Ivy Chen | ivy.chen@uq.edu.au
Stephen Fletcher | s.fletcher@uq.edu.au
Duration: 4 weeks (20-36 hours per week); onsite
RNA interference (RNAi)-mediated gene silencing shows great potential in controlling pest insects. However, the silencing efficiency can vary due to the inherent difference in RNAi machinery in insects. This project aims to uncover the RNAi pathway in greyback canegrub (Dermolepida albohirtum) – a major sugarcane pest in Australia, and to explore the potential of using RNAi to control these pests.
The student will use our newly sequenced and annotated canegrub genome and transcriptome to identify potential genes involve in the RNAi pathways. Molecular tools such as PCR and sanger sequencing and basic bioinformatics (blast, alignment, domain analysis, phylogenetic analysis etc.) will be used in this project.
Expected outcomes: The student will work in a multidisciplinary team, gain valuable experience in experimental design, troubleshooting and data interpretation, and learn skills in molecular biology techniques and basic bioinformatic analysis.
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 or an oral presentation.
Suitability: This project is open to students with a background in molecular biology, or bioinformatics.
Understanding the genetic basis of early vigour, nut size and precocity: Genome Wide Association Study (GWAS) in macadamia
Primary Supervisor:
Dr Mobashwer Alam | m.alam@uq.edu.au
Associate Advisors: Prof Bruce Topp | b.topp@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site/hybrid
Exploring the genetic basis of a trait facilitates rapid varietal development of crops. Identification of molecular markers is important for Marker Assisted Selection (MAS), where an elite progeny is selected based on a marker associated with the trait of interest, rather than on the trait itself. Genome Wide Association study (GWAS) provides opportunities for the identification of genomic region(s) associated with the target traits by combining genome information with phenotypic data. Over the last five years, ~1000 breeding progeny, elite selections, cultivars and wild germplasm were genotyped using high throughput marker systems. Using phenotypic and genotypic data, this project aimed to identify markers associated with the trait of interest. In this project the scholar will be working on previously genotyped breeding progeny, which were phenotypically characterised for early vigour, nut size and precocity.
Expected outcomes: The scholar will develop skills in statistical genetics, genomics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences.
Suitability: This project is open to applications from students with a background in Genetics, Computational Science, Plant Breeding, Plant Biotechnology, Plant Physiology, and Quantitative Genetics.
Passionfruit breeding and disease resistance
Primary Supervisor:
Dr Mobashwer Alam | m.alam@uq.edu.au
Associate Advisors: Prof Bruce Topp | b.topp@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site/hybrid
Passionfruit is an important fruit crop in Australia, with a significant market demand for both fresh and processed fruits. However, the industry is facing significant challenges due to the lack of disease-resistant varieties, which are vital to sustain the production and profitability. Additionally, the current varieties have limited productivity and low tolerance to stresses, making them vulnerable to pests, diseases, and environmental challenges. Therefore, there is an urgent need to develop improved passionfruit varieties with enhanced disease resistance and higher productivity. This project will investigate the genetic variability in passionfruit germplasm, map the occurrence of diseases across the industry, and investigate the molecular/genetic mechanism of disease resistance. Discovering the genetic basis of the traits will be useful for future breeding decisions and planning.
Expected outcomes: The scholar will develop skills in statistical genetics, genomics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences.
Suitability: This project is open to applications from students with a background in Genetics/Botany/ Plant Breeding/ Plant Biotechnology/Plant Pathology / Quantitative Genetics.
Genetics of stomatal size and density in Macadamia
Primary Supervisor:
Dr Mobashwer Alam | m.alam@uq.edu.au
Associate Advisors: Prof Bruce Topp | b.topp@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site/hybrid
Macadamia is an Australian native crop that is economically significant due to the numerous health benefits of its extremely valuable nut. To develop climate-resistant crops, the Australian macadamia breeding programme focuses on identifying simple and heritable features associated with low water loss and high photosynthesis. Stomatal pores in a leaf's epidermis allow for water loss via transpiration and CO2 absorption for photosynthesis. Stomata size and density are important factors in plant water efficiency and carbon capture. It may be possible to maximise CO2 uptake and water loss by adjusting the size and density of stomata. Many genes and signalling pathways are involved in the complex regulation of stomatal development. The genetic basis of macadamia stomatal size and density remains unknown. This study will investigate the phenotypic variation of the macadamia stomatal apparatus in a wide range of breeding progeny, cultivars, and wild germplasm. The trait's heritability will be determined, and a genome-wide association study will be conducted to identify potential genes associated with the trait. Discovering the genetic basis of the traits in macadamia will be useful for future breeding decisions and planning.
Expected outcomes: The scholar will develop skills in statistical genetics, genomics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences.
Suitability: This project is open to applications from students with a background in Genetics, Computational Science, Plant Breeding, Plant Biotechnology, Plant Physiology, and Quantitative Genetics.
Development of a diagnostic method for Phomopsis Husk Rot (PHR) disease
Primary Supervisor: Dr Vivian Rincon-Florez | v.rinconflorez@uq.edu.au
Duration: 4 weeks (30 hours per week); on-site/hybrid
In Australia, PHR disease is caused by the fungal pathogen Diaporthe australiana. Currently, molecular methods are not available for a fast and reliable diagnostic. This study will develop a qPCR for the detection of D. australiana through rigorous validation parameters.
Expected outcomes: The scholar will use bioinformatic tools, as well as plant pathology and molecular techniques. The scholar will have an opportunity to contribute to publications from the research.
Suitability: This project is open to applications from 4 year undergraduate or coursework masters students with a background in agriculture, biological sciences, or biotechnology.
Developing Aeroponic methods to grow Ginger and root vegetables in indoor and vertical farming systems
Primary Supervisor: Prof Paul Gauthier | p.gauthier@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site/hybrid
The research project will develop an aeroponic system to grow Ginger indoor and study the economics of using such a system of production. The research will involve propagating ginger and optimizing the growth environment (Air flow, humidity, temperature, light intensity and irrigation frequency) for maximizing growth vigor and sallable yield.
Expected outcomes: To be advised
Suitability: To be advised
Propagation of Coffee and Cacao in highly controlled environments and indoor farming
Primary Supervisor: Prof Paul Gauthier | p.gauthier@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site/hybrid
The research project involves developing Tissue Culture and cutting methods to accelerate the propagtion of coffee and cacao for hydroponic growth in Controlled environment chamber. The methods developed will accelerate the acclimation of coffee and cacao into vertical farming system.
Expected outcomes: To be advised
Suitability: To be advised
Investigation of the effects of environmental conditions on the growth and development of the Alternaria black core rot pathogen in vitro.
Primary Supervisor:
Miss Zali Mahony | z.mahony@uq.edu.au
Professor Andre Drenth
Duration: 4 weeks (30-36 hours per week); on-site at plant pathology laboratory, level 2CW, EcoSciences Precinct, Dutton Park, QLD
Alternaria black core rot (BCR) is a plant disease that affects the fruit of citrus in southern citrus growing regions. There is a lack of understanding of the epidemiology and as a result, the control of this disease is inconsistent. This research project involves identifying the optimal temperature and relative humidity for growth and infection of the BCR pathogen using foundational plant pathology skills. Results will inform future disease management decisions and provide a greater understanding of this plant pathogen's aetiology.
Expected outcomes: Applicants can expect to build and strengthen their skills in data collection and analysis, lab based experiments, working in a PC2 laboratory, and foundational plant pathology and microscopy methods.
Suitability: This project is open to applications from students with an interest in plant pathology and/or microbiology. It would suit an individual with foundational laboratory skills (i.e. 3-4 year) and an understanding of fungal life cycles.
What Alternaria species are causing Alternaria black core rot in Citrus?
Primary Supervisor:
Miss Zali Mahony | z.mahony@uq.edu.au
Professor Andre Drenth
Duration: 4 weeks (30-36 hours per week); on-site at plant pathology laboratory, level 2CW, EcoSciences Precinct, Dutton Park, QLD
Alternaria black core rot (BCR) is a plant disease that affects the fruit of citrus in southern citrus growing regions. A number of Alternaria species are associated with citrus in Australia, including A. alternata causing Emperor brown spot (EBS) in the northern citrus growing areas and A. alternata causing BCR. The question whether BCR and EBS are caused by the same pathogen needs to be investigated. Using foundational plant pathology techniques, this research project will investigate the pathogenicity of different species of Alternaria on citrus and the infection pathways of the pathogen (s).
Expected outcomes: Applicants can expect to build and strengthen their skills in data collection and analysis, lab based experiments, working in a PC2 laboratory, and foundational plant pathology and microscopy methods.
Suitability: This project is open to applications from students with an interest in plant pathology and/or microbiology. It would suit an individual with foundational laboratory skills (i.e. 3-4 year) and an understanding of fungal life cycles.
Automated acquisition of fruit tree growth data
Primary Supervisor: Dr Inigo Auzmendi | i.auzmendi@uq.edu.au
Duration: 4 weeks (30 hours per week); on-site or remotely
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 using microcontrollers to record the required growth data automatically. This system will be installed and tested to monitor avocado or macadamia plants.
Expected outcomes: 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.
Suitability: 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.
Modelling fruit tree architecture and physiology
Primary Supervisor: Dr Inigo Auzmendi | i.auzmendi@uq.edu.au
Duration: 4 weeks (30 hours per week); on-site or remotely
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 offers the chance to simulate plant architecture using L-systems or graph theory, employing data already collected in avocado, macadamia or mango.
Expected outcomes: 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.
Suitability: 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.
Using virtual plants to simulate photosynthesis in horticultural plants
Primary Supervisor: Dr Inigo Auzmendi | i.auzmendi@uq.edu.au
Duration: 4 weeks (30 hours per week); on-site or remotely
Plants assimilate carbon for maintenance and growth through photosynthesis. Estimating photosynthesis is not straightforward in horticultural plants with a complex canopy structure like avocado, macadamia and mango, because individual leaves within the canopy present different photosynthetic characteristics. This project will involve the use of virtual plants to simulate photosynthesis of individual leaves and whole canopy with specific management practices like mechanical hedging or topping, different planting density and tree shape. The results of these simulations will be used to evaluate several biochemical and physiological photosynthesis models under various management conditions. The final goal is to determine on each case the most adequate photosynthesis model, and propose new approaches if necessary.
Expected outcomes: Scholars may gain skills in online tools for remote collaboration, simulation software, understanding photosynthesis, data analysis, fruit tree management, and computer simulations using virtual plants. Scholars with previous knowledge in programming can learn to develop their own photosynthesis models. Students may be asked to produce a report or oral presentation at the end of their project.
Suitability: This project is open to applications from 3rd and 4th year students with a background in plant science. Students might have previous programming knowledge or not.
Investigating stem anatomy of in vitro macadamia cultures under the effects of auxin
Primary Supervisor: Dr Albert Chern Sun Wong | albertchernsun.wong@uq.edu.au
Duration: 4 weeks (20-36 hours per week); on-site
Adventitious root (AR) formation is critical for the efficient propagation of elite horticultural and forestry crops. ARs can initiate from internodes, callus formed at the base of cuttings, or the hypocotyl of herbaceous plants. Despite many rooting successes from cuttings and in vitro cultures of many horticultural crops, the cellular processes and molecular mechanisms underlying AR induction in woody plants remain obscure. This project aims to investigate stem anatomy of in vitro macadamia cultures under the effects of auxin to corelate stem anatomical changes with root induction ability.
Expected outcomes: The student will gain the following knowledge and skill:
- Aseptic and technical skills in plant tissue culture.
- Basics and concepts of plant tissue culture media preparation.
- Exploring plant growth regulators for macadamia root induction.
- Dissection and microscopy on in vitro plant cultures.
- The ability to work independently and as a team in a plant tissue culture laboratory.
Student will produce a short report on findings and present findings in a research meeting. Gathered data are components for future publications. Student will be appropriately acknowledged when article(s) is submitted for publication.
Suitability: This project is open to applications from students with a background in plant science, horticultural science, molecular biology, biotechnology, or related fields.
Analysis of the auxin transport and response pathways in Macadamia.
Primary Supervisor: Dr Albert Chern Sun Wong | albertchernsun.wong@uq.edu.au
Duration: 4 weeks (20-36 hours per week); on-site
Adventitious root (AR) formation is critical for the efficient propagation of elite horticultural and forestry crops. ARs can initiate from internodes, callus formed at the base of cuttings, or the hypocotyl of herbaceous plants and usually requires application of the plant hormone auxin. This project aims to search the macadamia genome for gene families known to be involved in the auxin transport and response process in plants using bioinformatic tools. Targets include PIN, AUX/IAA and ARF gene families, in addition to microRNAs. The student will also be able to design future experiments to evaluate gene expression profiles (and, if time permits, learn to design CRISPR/Cas9 gene editing constructs).
Expected outcomes: The student will gain the following knowledge and skill:
- Analyse genes of interest using publicly available genomic databases and bioinformatic tools.
- Create phylogenetic tree of selected gene of interest and analyse evolutionary relationships among a group of plant species.
- Design primers for genotyping and gene expression studies.
- Design CRISPR/Cas9 gene editing constructs
Student will produce a short report on findings and present findings in a research meeting. Gathered data are components for future publications. Student will be appropriately acknowledged when article(s) is submitted for publication.
Suitability: This project is open to applications from students with a background in plant science, horticultural science, molecular biology, biotechnology, or related fields.
Development of RNAi biopesticide for controlling canegrubs
Primary Supervisor:
Dr Ivy Chen | ivy.chen@uq.edu.au
Prof Neena Mitter | n.mitter@uq.edu.au
Duration: 4 weeks (20-36 hours per week); on-site
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.
The main aim of this project is to investigate the fate of sprayed dsRNA in sugarcane and to evaluate the potential of using sprayed dsRNA as a novel biopesticide to control canegrubs. Molecular biology techniques such as RNA extraction, northern blot, qPCR and confocal microscopy etc. will be used to investigate the uptake and translocation of dsRNA in sugarcane plants.
Expected outcomes: Student 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, 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 or an oral presentation.
Suitability: This project is open to students with a background in molecular biology, biotechnology or plant science.
Study of Self-Fertility in Macadamia Breeding: Deciphering the Variation and Mechanism of Self-Fertility
Primary Supervisor:
Prof Bruce Topp | b.top@uq.edu.au
Dr Mobashwer Alam | m.alam@uq.edu.au|
Duration: 4 weeks (36 hours per week); on-site
Macadamia exhibits self-incompatibility due to which only few cultivars can set seed following self-pollination and some cultivars are self-sterile. The research project identifies the morphological, biological and genetic differences among the self-fertile and self-infertile groups of cultivars. Explores the variability in self-fertility across the wide gene pool of Macadamia. Finally, the mechanism regulating the self-fertility in Macadamia.
Expected outcomes: The scholar will develop skills in Plant phenotyping, microscopy, genetics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences. Students may also be asked to produce a report or oral presentation at the end of their project.
Suitability: This project is open to applications from students with a background in Genetics, Plant Breeding, Plant Physiology.
Molecular identification of threatened Australian Gossia species for Conservation
Primary Supervisor: Dr Alice Hayward | a.hayward@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site
The research project includes identifying threatened Australian Gossia species by extracting DNA from foliar samples, amplifying by PCR, and sequencing and analysing diversity of sourced Gossia plants with published microsatellite markers. It also involves participation in a plant tissue culture lab.
Expected outcomes: Students will learn techniques of plant molecular biology (PCR, gel electrophoresis, marker analysis) and also plant tissue culture, focused on an endangered Australian plant.
Suitability: This project would be best suited to a 3rd year student, with a focus on biotechnology, molecular biology or plant biology.
RNA vaccines for Australian native plants
Primary Supervisor: Dr Anne Sawyer | a.sawyer@uq.edu.au
Duration: 4 weeks (20-36 hours per week); on-site
The research project involves exploring RNA vaccines as a novel control for myrtle rust in native Australian Myrtaceae species including lemon myrtle and tea tree. The fungicidal activity of the RNA will be tested in preventative and curative plant assays. Molecular techniques such as northern blotting and qPCR will be used to assess the longevity of the vaccine and to confirm pathogen gene knockdown.
Expected outcomes: 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.
Suitability: The project is open to applications from students with a background in plant sciences, mycology and/or molecular biology.
Effects of oomycetes on macadamia root systems
Primary Supervisor: A/Prof Femi Akinsanmi | o.akinsanmi@uq.edu.au
Duration: 4 weeks (36 hours per week); on-site
Oomycetes include some notorious plant pathogens that cause devastating diseases like root rot. Accurate pathogen identification will contribute to better control and management. This study will identify the species of Pythium and Phytopythium associated to root rot and characterize pathogenicity levels.
Expected outcomes: The scholar will use plant pathology techniques and molecular tools to examine the topic. Scholar will have an opportunity to contribute to publications from the research.
Suitability: This project is open to applications from 4 year undergraduate or coursework masters’ students with a background in agriculture, biological sciences, or biotechnology.