Centre for Horticultural Science - Summer Research Programs

Primary Supervisor: 
Dr Lilia Carvalhais | l.carvalhais@uq.edu.au

Please contact Dr Lilia Carvalhais before submitting an application.(l.carvalhais@uq.edu.au)

Duration: 6 weeks (20-30 h week on-site St Lucia Campus (flexible scheduling possible depending on each week's workload)

Fusarium oxysporum f. sp. lycopersici (Fol) is a major soilborne pathogen of tomatoes, capable of persisting in soil for years through resilient chlamydospores. These spores can germinate in response to chemical signals from root exudates, yet the exact compounds responsible remain unknown. Understanding which exudate molecules stimulate germination could provide a foundation for developing synthetic triggers to induce suicidal spore germination, offering a sustainable strategy to reduce soil infestation and improve crop production.

Expected outcomes: The successful candidate will gain hands-on experience in plant and fungal research, learn advanced analytical approaches such as metabolomics and bioassays, and develop skills in sterile techniques, fungal culture, and molecular biology. They will generate experimental data on tomato root exudate composition and its influence on Fol spore germination, and contribute to a written research report or presentation of findings.

Suitability: Second- or third-year undergraduate students, or Honours students with a background or strong interest in plant science, fungal biology, molecular biology, and wet-lab techniques.

Primary Supervisor: 

Dr Mobashwer Alam | m.alam@uq.edu.au
Dongxue Zhao | dongxue.zhao@uq.edu.au
Liqi Han | liqi.han@uq.edu.au
Pragya Poudel | p.dhakalpoudel@uq.edu.au

Please contact the Supervisors Dr Mobashwer Alam (m.alam@uq.edu.au), Dongxue Zhao (dongxue.zhao@uq.edu.au) Liqi Han (liqi.han@uq.edu.au) and Pragya Poudel (p.dhakalpoudel@uq.edu.au) before submitting an application.

Duration: 6 weeks (20-36 h per week): Hybrid (Nambour and Gatton)

Macadamia (Macadamia integrifolia and M. tetraphylla and their hybrids) is a perennial nut tree of high economic value, particularly in Australia. Despite its significance, macadamia breeding is constrained by a long juvenile phase, limited genetic knowledge on complex traits, and challenges in phenotyping below- and above-ground traits. Root system architecture and canopy structure are key determinants of productivity, stress resilience, and resource use efficiency, yet these traits are difficult to assess at scale using traditional methods due to destructive sampling and subjective scoring.

Advancements in artificial intelligence (AI)-assisted phenotyping offer transformative potential for accelerating macadamia breeding by enabling rapid, non-invasive, and high-throughput measurement of complex traits such as root architecture and canopy structure. These traits are pivotal for improving resource use efficiency, climate resilience, and yield in macadamia, a long-lived perennial tree crop with a slow breeding cycle. Conventional methods for assessing root and canopy phenotypes are labor-intensive and often limited to destructive sampling or subjective scoring. The integration of AI with sensor-based imaging technologies—such as LiDAR, UAV-based RGB and multispectral imaging, and ground-penetrating radar—has begun to unlock novel avenues for capturing dynamic phenotypic traits over space and time, facilitating data-driven selection of elite genotypes (Kamilaris & Prenafeta-Boldú, 2018; Mahlein et al., 2019). While studies such as Zhang et al. (2021) have demonstrated the use of UAVs in canopy trait extraction, belowground imaging remains underexplored, especially in tree crops.

In macadamia, preliminary research has demonstrated the feasibility of UAV imaging to assess canopy size, vigor, and tree health (Alam, M.M.2025, pers comm). However, comprehensive studies integrating belowground phenotyping remain sparse, primarily due to the technical challenges in imaging roots in perennial tree systems. The application of machine learning and deep learning algorithms to image-based datasets remains underutilized, particularly in linking root and canopy traits. This study aims to develop a high-resolution AI-driven phenotyping framework for simultaneous analysis of root and canopy traits in diverse macadamia genotypes, and to identify phenotypic markers predictive of climate resilience and yield efficiency. Such efforts will directly contribute to fast-tracking selection decisions in macadamia breeding and optimizing ideotypes for sustainable orchard systems.

This project will develop and implement a comprehensive AI-guided phenotyping framework for macadamia, enabling the simultaneous, high-resolution assessment of root and canopy traits. The results will support data-driven selection in breeding programs, contribute to climate-resilient orchard designs, and facilitate ideotype development.

Expected outcomes: This project will skill up students in the use of proximal sensing technologies for precision agriculture and crop phenotyping. Students will also gain experience in generating and analysisng data, writing scientific reports for publication in high ranked journals.

Suitability: This project is open to applications from undergraduate or master’s students with a background or strong interest in Computer science, plant science, agricultural science, horticulture, and related disciplines.

Primary Supervisors: 

Dr Vivien Tsai | w.tsai@uq.edu.au
Dr Chris Brosnan | c.brosnan@uq.edu.au
Dr Narelle Manzie | n.manzie@uq.edu.au

Please contact Dr Vivien Tsai (w.tsai@uq.edu.au), Dr Chris Brosnan (c.brosnan@uq.edu.au) and Dr Narelle Manzie (n.manzie@uq.edu.au) before submitting an application.

Duration: 6 weeks (20 - 30 hours per week); On site (St Lucia)

The spray of double-stranded RNA (dsRNA), which triggers the RNA interference (RNAi) pathway, has emerged as an ecologically sustainable method for controlling insect pests and pathogens. This approach involves the application and delivery of exogenous dsRNA, which triggers the dicer-dependent RNAi pathway, forming the basis for RNA-based control strategies in insects and pathogens. Although some studies demonstrate the potential for dsRNA uptake by plant cells and translocation through the vascular tissue of certain plant species, the effectiveness of dsRNA uptake and long-distance transport following topical application remains unclear, creating uncertainty regarding control efficacy. Therefore, this project aims to investigate potential enhancements that enable exogenous dsRNA to move more efficiently to plant cells or vascular tissues, thereby controlling different types of viral pathogens more effectively. This approach will involve applying priming chemicals and priming biomolecule cargos (siRNAs) to improve RNAi efficacy against RNA viruses expressing GFP in plant cells and/or DNA viruses expressing GFP in phloem tissue. Northern blotting and/or quantitative RT-PCR will be conducted to analyse dsRNA abundance and silencing efficiency.

Expected outcomes: Through this project, the student will gain hands-on experience with RNA-based methodologies and explore RNA application in sustainable pest management. They will develop an understanding of how RNAi mechanisms can be translated into practical biocontrol strategies for agriculture. In the process, the student will strengthen skills in molecular analysis techniques, fluorescence-based tracking systems, and scientific communication, and potentially engage with impactful inventions.

Suitability: Students with a background in molecular biology or agriculture are encouraged to apply. Applications are open to all degree levels. Interested candidates should contact the supervisor before submitting an application.

Primary Supervisors:

Dr Thao Ninh | t.ninh@uq.edu.au
Chris O'Brien | c.obrien4@uq.edu.au
Andrea Putri Subroto | a.subroto@uq.edu.au

Please contact Dr Thao Ninh (p.gauthier@uq.edu.au), Chris O'Brien (p.gauthier@uq.edu.au) and Andrea Putri Subroto (a.subroto@uq.edu.au) before applying.

Duration: 6 weeks (20 hours per week); on site (Long Pocket)

Avocados are highly recalcitrant to in vitro regeneration and Agrobacterium-mediated transformation, limiting their genetic improvement. Our lab has recently developed the first successful protocol for regenerating plants from avocado leaves. Building on this advance, the project will focus on optimizing Agrobacterium-mediated transformation for avocado leaves using the visible RUBY reporter gene, which produces a distinctive red coloration for rapid, non-destructive identification of transgenic explants. The summer student will evaluate key factors influencing transformation efficiency, including bacterial strain, bacterial cell density, infection duration, co-cultivation period, and medium composition. The outcomes will contribute to developing a robust transformation system and enable future applications of genome editing for avocado improvement.

Expected outcomes: Student will gain hands-on experience in plant tissue culture, Agrobacterium-mediated transformation, and the use of reporter gene for rapid identification of transgenic explants. They will also learn how to design and optimize parameters in transformation experiments. In addition, the project provides training in DNA extraction, PCR, data collection and basis statistic analysis. Beyond that, student will have opportunity to develop transferable skills such as scientific communication, record-keeping, problem-solving and teamwork.

Suitability: The project is open to students with a background in plant sciences, agricultural sciences, or horticulture. Students should contact the supervisors before applying.

Primary Supervisor: 

Chris O'Brien | c.obrien4@uq.edu.au
Dr Anne Sawyer | a.sawyer@uq.edu.au

Please conact Dr Chris O'Brien (c.obrieb4@uq.edu.au) and Dr Anne Sawyer (a.sawyer@uq.edu.au) before applying.

Duration: 6 weeks (20 - 30 hours per week); on site (Long Pocket)

Avocado is a high-value subtropical crop in Queensland. We have developed a tissue-culture propagation pipeline for avocado which allows us to grow hundreds of plants from a single cutting, accelerating the production of key rootstocks. The aim of this project is to investigate whether hydroponics can further accelerate growth of these rootstocks out of tissue culture. The project will involve learning how to grow plants in hydroponics and the use of a LI-COR to measure photosynthetic activity.

Expected outcomes: Scholars will learn tissue culture, plant physiology and hydroponic 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. Students should contact the supervisors before applying.

Primary Supervisor: Dr Inigo Auzmendi | i.auzmendi@uq.edu.au

Students are welcome to conact Dr Inigo Auzmendi (i.auzmendi@uq.edu.au) to disucss further

Duration: 6 weeks (20 - 30 hours per week); on site (St. Lucia or Gatton), 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 include the design and implementation of a programable system using microcontrollers to record photographs automatically. This system will be installed and tested to monitor and collect growth data in macadamia or mango 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.

Primary Supervisor: Dr Inigo Auzmendi | i.auzmendi@uq.edu.au

Students are welcome to conact Dr Inigo Auzmendi (i.auzmendi@uq.edu.au) to disucss further

Duration: 6 weeks (20 - 30 hours per week); on site (St. Lucia or Gatton), 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. The project will involve the use of virtual plants to simulate photosynthesis of individual leaves and whole canopy. The results of these simulations will be used to evaluate several biochemical and physiological photosynthesis models under various management conditions.

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 or master students with a background in plant science or agricultural science. Students might have previous programming knowledge or not.

Primary Supervisor: 

Dr Anne Sawyer | a.sawyer@uq.edu.au
Prof Paul Gauthier | p.gauthier@uq.edu.au

Please contact Dr Anne Sawyer (a.sawyer@uq.edu.au) & Prof Paul Gauthier (p.gauthier@uq.edu.au) before submitting an application.

Duration: 6 weeks (20 - 30 hours per week); On-site (Long Pocket)

Protected cropping environments are conducive to disease epidemics due to favourable conditions for pathogens, intense production practices and in some systems recirculation of water and air. The aim of this project is to investigate major diseases of hydroponically grown plants such as avocado and to explore sustainable control strategies such as RNA sprays. The project will involve hydroponics, fungal isolation and culturing, and disease bioassays.

Expected outcomes: Scholars will learn plant pathology, plant physiology and hydroponic 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, plant pathology or microbiology. Students should contact the supervisors before applying.

Primary Supervisors: Dr Thao Ninh | t.ninh@uq.edu.au

Please contact Dr Thao Ninh (t.ninh@uq.edu.au) before applying.

Duration: 6 weeks (20 hours per week); on site (Long Pocket)

CRISPR/Cas9 gene-editing technologies are emerging as powerful tools for crop improvement. However, a major challenge is that gene-edited plants must be transgene-free (T-DNA-free) to maintain trait stability and comply with regulatory frameworks for commercial release. In tomato, transgene-free segregants can be obtained among T1 seedlings following the self-pollination of T0 transgenic edited plants. The conventional method for identifying such seedlings relies on PCR, which is accurate but costly and time-consuming. This project will evaluate a simple method for identifying transgene-free edited tomato plants based on the antibiotic resistance marker within the T-DNA. The summer student will germinate T1 seedlings and assess the antibiotic susceptibility of their cotyledons or leaf discs, using this response to distinguish transgene-free plants from those still carrying the T-DNA. The phenotypic responses will then be benchmarked against PCR to determine the accuracy and reliability of this method.

Expected outcomes: Students will gain hands-on experience in a range of molecular techniques, including DNA extraction, PCR and Sanger sequencing, as well as tissue culture and phenotypic assays to test antibiotic susceptibility. Students will also receive training in guide RNA design, CRISPR/Cas9 construct and the analysis of edited sequence. In addition, students will strenghthen skills in scientific communication, experimental design, data recording, problem solving and teamwork. Together, these experiences will build a strong foundation for their future research.

Suitability: This project is open to students with background or strong interest in genome editing, molecular biology, plant tissue culture, plant sciences. Interested students are encouraged to contact the supervisor before applying.

Primary Supervisors: Dr Eveline Kong | e.kong@uq.edu.au

Please contact Dr Eveline Kong (e.kong@uq.edu.au) before applying.

Duration: 6 weeks (20 hours per week but flexible) on site (Long Pocket; Plant Nursery near Gold Coast)

Blueberry, a high value berry crop in Australia, has been discovered to encounter a physiological disorder(s) in the root and crown architectures in the recent years that resulted in yield loss. The impacted plants exhibited abnormal growth symptoms of root wrapping or girdling, crown restriction and stem occlusion, leading to cane(s) death from months to years after field-planting. This incidence has been identified by blueberry farms across countries with lower prevalence in Australia, but it varies between cultivars, source of planting materials, and environmentally dependent. A study on the impact of time in culture and tissue culture treatments to reduce the incidence has been performed. This requires on-going shoot and root phenotyping of the plants in the nursery and involves destructive analysis.

Expected outcomes: Students will gain hands-on experience related to shoot and root phenotyping techniques for plants grown under commercial nursery conditions. Scholars will also learn about plant physiology for blueberry and the commercial insight as well as the industry impacts of this physiological disorder in blueberry. In addition, students will develop skills in experimental design and statistical analysis.

Suitability: This project is open to students with background or strong interest in plant physiology and plant sciences. Interested students are encouraged to contact the supervisor before applying.

Primary Supervisors: Dr Lily Whelehan | l.whelehan@uq.edu.au

Please contact Dr Lily Whelehan (l.whelehan@uq.edu.au) before applying.

Duration: 6 weeks (20 hours per week but flexible) on site (Long Pocket)

This project aims to develop a method of acclimatising tissue cultured plantlets of Gossia gonoclada for planting back in its natural habitat. Our research group has hundreds of clones of this endangered Myrtaceae species ready to be planted back in its natural habitat. The project will test a variety of treatments to induce rooting, such as auxin addition, nutrient withdrawal, activated charcoal, and use of dfferent substrates. Rooted plantlets will be moved to potting mix to be hardened in preparation for replanting in the field.

Expected outcomes: Students will have the chance to develop their aseptic technique, an essential skill for plant tissue culture. The project will give a practical introduction to the effect of different plant growth media on plant health. The student will be included in discussions about experimental design to build understanding of sound experimental design and statistical principles. By the end of the project, the student will be familiar with media preparation, subculturing, phenotyping, and data analysis processes.

Suitability: This project is open to students with basic laboratory experience and passion for plant science and conservation. Do not hesitate to contact the supervisor with any questions.

Primary Supervisor: 

Dr Nga Tran | n.tran3@uq.edu.au
Prof. Andrew Geering | a.geering@uq.edu.au

Please conact Dr Nga Tran (n.tran3@uq.edu.au) and Prof. Andrew Geering (a.geering@uq.edu.au) before applying.

Duration: 6 weeks (20 - 30 hours per week); on site (Dutton Park)

Avocado is one of the most economically important horticultural industries in Australia with farmgate value over $570 million (2023). In the last decade, the industry has undergone rapid expansion to meet the increased demand in domestic consumption and favourable market prices. The growth of the Australian avocado industry has also been seen in many other nations around the world. Several major diseases and pests of avocado, such as laurel wilt (Harringtonia lauricola), Persea mite (Oligonychus perseae), and small and large seed weevil (Heilipus lauri, Conotrachelus aguacatae and Conotrachelus perseae) have emerged and expanded their geographic ranges. Australia has strict biosecurity laws and has managed to keep many of these pests and pathogens out. However, there are risks of these exotic pests and pathogens entering Australia through a mixture of both legal and illegal pathways. This research aims to improve the biosecurity diagnostic capacity and capability, through a better understanding of the population genetics, developing and validating accurate, rapid and sensitive diagnostic tools, as part of the Australian avocado industry’s preparedness if an incursion event was to occur.

Expected outcomes: The student/s will have the opportunity to improve their knowledge and skills in plant pathology, entomology, molecular biology and bioinformatics, industry connections through being involved in research to investigate the population genetics and developing molecular diagnostic assays for the high priority exotic pests of the Australian avocado industry, including H. lauri.

Suitability: Undergrad students in their 2rd – 4th year, honours or masters students with a background or interest in plant science, plant pathology, entomology, molecular biology, and agriculture. Students are encouraged to contact the supervisor before applying.