Undergraduate research program

Develop your analytical, critical thinking, and communication skills through research

The QAAFI Summer and Winter Research Programs provide UQ-enrolled students with an opportunity to gain research experience working alongside some of the university’s leading academics and researchers.

QAAFI are proud participants in the UQ Undergraduate Research Program. It is an opportunity for you to develop your analytical, critical thinking, and communication skills through research.

Research projects are open to UQ undergraduate, honours, and masters by coursework students offered in two rounds for the winter university vacation break during June and July and summer university vacation break during November and February.

All successful scholars will receive a scholarship for the duration of their research. Once you have checked eligibility and selected your preferred project, submit an application via StudentHub.

More Info from UQ Careers and Employability How to apply

Benefits for students

Include:

an opportunity to develop new academic and professional capabilities to enhance employability
experience in research as a "test-drive" before embarking on future research studies
access to research networks and connections with staff and postgraduate students
supervision by world-class UQ researchers
possibility of obtaining credit towards your degree

Benefits for staff

Include:

collaboration helps identify new areas of exploration
scholars can facilitate the process towards publication
opportunity to identify potential Honours and HDR candidates
gaining experience in supervising and mentoring students

QAAFI research projects open for applications for the Undergraduate Research Program

Animal Science

Project title:	Genomic and Transcriptomic analysis for sheep body lice (Bovicola ovis)
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is not required on-site for the project.
Description:	Sheep lice (Bovicola ovis) causes major economic losses (~$123M) to the Australian sheep industry by reducing the quality and quantity of wool produced. Although, sheep are prone to body lice, face lice and foot lice; presently only the body louse are a serious economic problem. Current control of Bovicola ovis (B.ovis) relies almost exclusively on chemical applications. The continued use of these products, with inadequate on-farm biosecurity and poor application of chemicals, has created resistant lice populations causing some flocks always remaining infested even after treatment. Eradication of lice would reduce the cost of production, promote higher quantity and quality of wool with lower insecticide residues and improve animal welfare. As sheep numbers expand nationwide, there is an urgent need to develop an innovative residue-free control measure for body lice that will support profitability by reducing the export withholding periods and slaughter intervals.
Expected outcomes and deliverables:	The student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), bioinformatics - cutting edge sequencing technologies (MinION, PacBio, Iso-Seq and Illumina) to generate a catalogue of specific lice genes expressed during the life stages of B.ovis (egg, nymph, and adult, both female and male). The student will work closely with Dr Karishma Mody and Dr Elizabeth Ross and other members of Professor Neena Mitter and Professor Ben Hayes laboratory at UQ.
Suitable for:	This project is open to applications from students with a background in molecular biology or biotechnology. Highly suitable for Masters/Honours students.
Primary Supervisor:	Dr Karishma Mody and Dr Elizabeth Ross
Further info:	Please contact k.mody@uq.edu.au or e.ross@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	RNA interference as a sustainable alternative for protecting animal health
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Insect parasites cause significant damage to livestock and are primarily responsible for significant economic losses. Conventional pesticides have issues of resistance and toxicity, and there is increasing market requirement and price premiums for low-chemical and welfare-friendly production systems. We aim to explore our RNAi delivery platform to protect animals from insect parasites that cause damage. This project will result in real-world outcomes, by translating and expanding our current biotechnologies to an industry-ready tool for livestock protection.
Expected outcomes and deliverables:	The student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), bioinformatics, material science and the application of RNAi for livestock protection. The student will work closely with Dr Karishma Mody and other members of Professor Neena Mitter’s laboratory at UQ.
Suitable for:	This project is open to applications from students with a background in molecular biology or biotechnology. Highly suitable for Masters/Honours students.
Primary Supervisor:	Dr Karishma Mody
Further info:	Please contact k.mody@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Evolutionary computing to rapidly stack desirable alleles in cereal crops: optimising haplotype building
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	A major emerging challenge in cereal breeding, such as in wheat and barley, is how to stack desirable alleles for disease resistance, drought, and end-use quality into new varieties with high yielding backgrounds in the shortest time. As the number of known desirable alleles for these traits increases, the number of possible crossing combinations that need to be considered increases exponentially. An approach using artificial intelligence (AI) platform – designed to solve highly combinatorial problems and coupled with genomic prediction could address this challenge. The computing power of AI designed according to the patterns of data that are predictive of crop performance will allow to estimate the best crossing strategy for breeding an improved wheat and barley varieties more quickly. For the student research project, the aim is to optimise building chromosome segments using different parameters considering linkage disequilibrium and penalties in the number of markers. The chromosome segment will be used to select the best parent combinations using AI-derived genetic algorithm. Using computer simulations, the AI-selected parents will be crossed to generate a ‘digital twin’ of a real-life breeding scenario.
Expected outcomes and deliverables:	Students will gain and strengthen their skills on Plant Breeding technique (i.e. crossing, population development in the speed-breeding facility, other glasshouse activities), Quantitative and Computational Genetics (i.e. basic computational analysis on simulations, genomic predictions).
Suitable for:	Suitable for students studying or interested in integrating different fields of Agriculture, Plant Breeding, Plant Pathology, Quantitative Genetics, or Computational Biology.
Primary Supervisors:	Dr Eric Dinglasan and Prof Ben Hayes
Further info:	Please contact e.dinglasan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Genotype by environment interaction in genomic prediction models for sugarcane
Project duration:	10 Weeks – Summer Program, 20-36 hours a week, can be completed either remote or on-site attendance
Description:	Sugarcane is a significant industrial crop in Australia, with Queensland accounting for nearly 95% of the country's sugar production. Sugarcane is also becoming a viable source of sustainable bioenergy. However, the increase in productivity from sugarcane has been small compared to other major crops. With the recent advances in genomics, new emerging approaches for plant breeding such as genomic selection (GS) can be used to identify elite genotypes more efficiently and quickly. The effectiveness of GS has been investigated in sugarcane. GS models were originally designed for single-environment analysis and did not take into account correlated environmental structures caused by genotype by environment (GE) interactions. One of the challenges affecting sugarcane productivity is the lack of knowledge about the degree of genotype-by-environment interaction across sugarcane growing regions. For sugarcane breeders, the varied responses of genotypes in diverse conditions is a key problem that might impact heritability and genotype ranking across environments. To our knowledge, no study has examined the effectiveness of GS models that integrate GE to predict complex traits such as, such as tonnes cane per hectare, commercial cane sugar and fibre content in sugarcane. Within the framework of the reaction norm model, the objective of this study was to assess the impact of integrating GE on prediction accuracy for complex traits using an elite sugarcane population evaluated in four growing regions in Queensland. In a commercial breeding perspective, yield performance of sugarcane in a specific growing region can be extended to predict how well sugarcane will perform at a different growing region.
Expected outcomes and deliverables:	Students will gain and strengthen their skills on Statistical and genomic model using different software, Quantitative and Computational Genetics (computational genomic predictions).
Suitable for:	Suitable for students studying or interested in integrating different fields of Agriculture, Plant Breeding, Quantitative Genetics, or Computational Biology
Primary Supervisors:	Dr Eric Dinglasan, Dr Bailey Engle, Seema Yadev and Prof Ben Hayes.
Further info:	Please contact e.dinglasan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Genes impacting female fertility
Project duration:	10 Weeks – Summer Program, 20-36 hours a week, can be completed either remote or on-site attendance
Description:	Fertility is an important, but complex genetic trait influenced by a large number of genes and other genetic factors. Additionally, whether or not a female will become pregnant is dependent upon a large number of environmental factors such as stress and nutrition. This makes it incredibly difficult to determine the primary genetic determinants of pregnancy, and this is true not only in human medicine, but livestock as well. In beef cattle, this combination of variables affects the breeding potential of a cow. The goal of this project is to assess genetic variation leading to different pregnancy outcomes in Brahman cows. Students will use RNA-seq data for differential gene expression analyses to identify genes and genomic regions influencing pregnancy status in female cattle
Expected outcomes and deliverables:	This project will develop skills in bioinformatics and data analysis, in order to better understand female fertility in Australian beef cattle. Students will gain valuable experience working with a large RNA-seq data set.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Dr Elizabeth Ross, Dr Loan Nguyen, Dr Bailey Engle and Prof Ben Hayes
Further info:	Please contact e.ross@uq.edu.au, t.nguyen3@uq.edu.au or b.engle@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Linking cow puberty to lifetime fertility
Project duration:	10 Weeks – Summer Program, 20-36 hours a week, can be completed either remote or on-site attendance
Description:	In Brahman cattle, a heifer’s age at puberty is often a general indicator of her overall fertility and how fertile she may be during her lifetime. There is a high genetic correlation between puberty and lifetime fertility, indicating that these traits share some level of genetic control. This means, that if we can better understand heifer puberty, potentially we can select for more fertile cows. In this study, students will determine if genes associated with puberty may be used to increase our understanding of lifetime fertility and use this information to predict a cow’s potential for fertility over her lifetime. This project will combine data analysis of very large genomic and phenotypic data sets (up to 30,000 cattle), quantitative genetics, and industry relevance to help improve cow fertility in the north Australian beef industry.
Expected outcomes and deliverables:	In this project students will develop data analysis and quantitative genetics skills, and will learn techniques to handle large biological data sets. Students will have the opportunity to develop skills using a variety of programs, such as R, to learn genomic selection techniques.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Dr Bailey Engle and Prof Ben Hayes
Further info:	Please contact b.engle@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Enrichment of Genome-wide association (GWAS) variants for fertility traits in transcription start sites (TSSs) region
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will not be required on-site for the project.
Description:	Project summary: Reduced fertility could cause considerable economic loss and has become a worldwide problem in the livestock industry. Although DNA-based approaches have been used to study fertility traits, more comprehensive RNA-based techniques may be critical in furthering our understanding of gene regulation that occur in the fertility related organs. Next generation sequencing technologies including Cap-Analysis of Gene Expression (CAGE) have made it possible to accurately identify and quantify transcriptional start sites (TSSs) throughout the genome. This study will use the predicted TSSs region across tissues to investigate the enrichment of GWAS variants for fertility traits within the promoter region.
Expected outcomes and deliverables:	This project provides student with a deep understanding of bioinformatics skills, project design, scientific communication, and analysis skills in a fast-developing area of genetics research. The student will work closely with Dr Mehrnush Forutan and Professor Ben Hayes and other members of Professor Ben Hayes laboratory at UQ.
Suitable for:	Suitable for students studying or interested in genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project; however, they are not mandatory.
Primary Supervisors:	Dr Mehrnush Forutan; Professor Ben Hayes
Further info:	Please contact m.forutan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Genome-wide association study (GWAS) of birthdate to prioritize variants that are actively responding selection
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will not be required on-site for the project.
Description:	Project summary: Interest in mapping the impacts of selection on the genome is increasing. Recent studies show that polygenic selection is the major selective force both during and after domestication in agricultural species. Under directional selection, alleles will be at significantly different frequencies in more recent generations compared with distant ones. This creates a statistical association between allele frequencies at a selected locus and an individual’s generation number. Until now, most of the studies used the selection mapping methods which rely on either allele frequency differences between diverged or artificially defined populations (e.g., FST), or the disruption of normal LD patterns (e.g., ROH) to investigate the effect of selection. In cattle, these methods have successfully identified genomic regions under selection that control Mendelian and simple traits, or large-effect genes involved in domestication. Availability of the substantial number of animals genotyped from the most recent generations provide incredible power for detecting small allele frequency changes due to ongoing selection. The study will provide insight into the biology of polygenic selection and prioritize variants that are actively responding selection.
Expected outcomes and deliverables:	This project provides student with a deep understanding of bioinformatics skills, project design, scientific communication, and analysis skills in a fast-developing area of genetics research. The student will work closely with Dr Mehrnush Forutan and Professor Ben Hayes and other members of Professor Ben Hayes laboratory at UQ.
Suitable for:	Suitable for students studying or interested in genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project; however, they are not mandatory.
Primary Supervisors:	Dr Mehrnush Forutan; Professor Ben Hayes
Further info:	Please contact m.forutan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Genome-wide association study (GWAS) of microbial traits to elucidate the genetic link between cow and their associated microbiota.
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will not be required on-site for the project.
Description:	Project summary: The 3.9 billion ruminants estimated to exist today are important in sustainable agricultural practices, as they can render numerable land useful via grazing, use industrial by-products (e.g., distillers’ grains) as a food source, and synthesize energy from low-quality forages for milk and meat production. Central to ruminant production and health is the gut microbiome, the complex microbial community that resides in the ruminant gastrointestinal tract (GIT), which is now well-recognized as a crucial contributor to the maintenance of intestinal homeostasis, mucosal and lymphoid structure development, and activation of the host immune cell repertoire. The present study aims to identify associations between the host’s genetics with presence–absence and abundance patterns of microbial clades. These associations could be the result of variation in host genes leading to the availability of specific energy sources or metabolic substrates.
Expected outcomes and deliverables:	This project provides student with a deep understanding of bioinformatics skills, project design, scientific communication, and analysis skills in a fast-developing area of genetics research. The student will work closely with Dr Mehrnush Forutan and Dr Elizabeth Ross and other members of Professor Ben Hayes laboratory at UQ.
Suitable for:	Suitable for students studying or interested in genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project; however, they are not mandatory.
Primary Supervisors:	Dr Mehrnush Forutan; Dr Elizabeth Ross and Prof Ben Hayes
Further info:	Please contact m.forutan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Integration of methylation profile with transcription start sites (TSSs) data
Project duration:	10 Weeks – Summer Program, 26-36 hours a week.
Description:	Although genetic changes are involved in the inactivation of genes with important anticancer functions (e.g., tumor suppressor and DNA repair genes), DNA methylation in a promoter region is an important epigenetic mechanism for the downregulation (silencing) of expression of these genes. DNA methylation plays an important role in individual growth, development, gene expression patterns and the stability of the genome. It refers to the chemical modification process which transfers the active methyl to the specific base on the DNA chain under the catalysis of DNA methyltransferase. Next generation sequencing technologies including Cap-Analysis of Gene Expression (CAGE) have made it possible to accurately identify and quantify transcriptional start sites (TSSs) throughout the genome. This study will use the predicted TSSs region across tissues as well as methylation epigenetic data to better understand important genes related to northern beef cattle production by bringing together data from various cutting-edge technologies.
Expected outcomes and deliverables:	This project provides student with a deep understanding of bioinformatics skills, project design, scientific communication, and analysis skills in a fast-developing area of genetics research. The student will work closely with Dr Mehrnush Forutan and Professor Ben Hayes and other members of Professor Ben Hayes laboratory at UQ.
Suitable for:	Suitable for students studying or interested in genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project; however, they are not mandatory.
Primary Supervisors:	Dr Mehrnush Forutan and Prof Ben Hayes
Further info:	Please contact m.forutan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	DNA pooling for genomic profiling of cattle herds
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	Genetic improvement is a key pathway to sustainability, productivity and improved welfare of Australian beef herds. This project will develop a new tool for benchmarking individual beef herds, for key traits such as fertility, temperament and parasite resistance. The successful student will have the opportunity to analyse very large genomic and phenotypic data sets using advanced computer algorithms, as well as interacting with key players in the Northern Australian beef industry.
Expected outcomes and deliverables:	Students will gain and strengthen their skills in analysis of extremely large genomic and phenotypic data sets, as well as acquiring new skills in the latest sequencing technologies.
Suitable for:	Suitable for students studying or interested in integrating different fields of Agriculture, Molecular genetics, bioinformatics and computational Biology
Primary Supervisors:	Prof Ben Hayes, Dr Liz Ross and Dr Loan Nguyen
Further info:	Please contact b.hayes@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Rangeland Flora Profiling using Nanopore sequencing of cow pats
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	The next generation of Agriculture will seek to balance environmental concerns and productivity. In this project, you will contribute to this vision, by using the latest sequencing technology to profile what cattle are consuming in Australia’s very extensive rangelands, with DNA extracted from cow pats.
Expected outcomes and deliverables:	Students will gain and strengthen their skills in analysis of extremely large genomic data sets, as well as acquiring new skills in the latest sequencing technologies.
Suitable for:	Suitable for students studying or interested in integrating different fields of Agriculture, Molecular genetics, bioinformatics and computational Biology
Primary Supervisors:	Prof Ben Hayes, Dr Liz Ross and Dr Loan Nguyen
Further info:	Please contact b.hayes@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Rangeland Flora Profiling using Nanopore sequencing of cow pats
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	The next generation of Agriculture will seek to balance environmental concerns and productivity. In this project, you will contribute to this vision, by using the latest sequencing technology to profile what cattle are consuming in Australia’s very extensive rangelands, with DNA extracted from cow pats.
Expected outcomes and deliverables:	Students will gain and strengthen their skills in analysis of extremely large genomic data sets, as well as acquiring new skills in the latest sequencing technologies.
Suitable for:	Suitable for students studying or interested in integrating different fields of Agriculture, Molecular genetics, bioinformatics and computational Biology
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact b.hayes@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	DNA extraction method for faecal metagenomics to assess cattle diet
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant must work on-site for the project
Description:	Cattle diet history information can be obtained by studying non-invasive samples, like dried faecal samples. Additionally, the analysis of faecal samples can also provide the information about the digestive efficiency of an animal. The advent of improved sequencing methodologies has simplified the characterization of complex faecal DNA and allows for the characterization of diet profiles by matching the faecal sequence data with available sequence databases of potential food sources. In this study, student will employ different extraction protocols to isolate DNA from faecal samples using a variety of molecular techniques in the lab.
Expected outcomes and deliverables:	This project will develop skills in molecular biology and genetic lab technologies. Students will learn to do different laboratory methods, sample handling and organization, and laboratory safety.
Suitable for:	Suitable for students studying or interested in molecular genetics, molecular biology or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact t.nguyen3@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Exploring tissue specific methylation sites in cattle
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant can work remotely for the project
Description:	DNA methylation is an epigenetic mechanism driving the gene expression in specific tissues at a particular stage. However, the mechanism of how DNA-methylation regulates gene expression in cattle is still unknown. Here, the student will use two types of datasets, whole genome sequencing from Oxford Nanopore sequencing versus RNA sequencing, to explore the relationship between methylation and gene expression. This will be conducted in two tissues, lung and liver.
Expected outcomes and deliverables:	This project will develop skills in bioinformatics as well as molecular biology. Students will also learn how to manage very large sequence data sets.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact t.nguyen3@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Identification of differentially methylated regions between young and old cattle
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant can work remotely for the project
Description:	DNA methylation is known to influence gene expression. Methylation patterns are also known to change with age, and therefore may be used as a marker for predicting age. This has been documented in many species including humans, mice, dogs, bat, cat and elephant. Additionally, DNA methylation has been used as marker for reproductive aging in cattle. In this project, students will use cutting edge data sources, including reduced representation bisulphite sequencing data and whole genome bisulphite sequencing data, to identify differentially methylated regions between old and young animals and validate those regions with modern molecular technologies.
Expected outcomes and deliverables:	This project will develop skills in bioinformatics as well as molecular biology. Students will also learn how to manage very large sequence data sets.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact t.nguyen3@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Predicting age using methylated sites
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	In humans, the methylation state of CpG sites changes with age and can therefore be utilized as an accurate biomarker for aging. In cattle, biological age prediction based on methylation status could provide key information for genetic improvement programs. Additionally, comparing chronological age with biological age (based on methylation status) can provide important information about the stress an animal has been under during its lifetime. However, relatively little is known about DNA methylation patterns in cattle. Students will use cutting edge data sources including reduce representation bisulphite sequencing data, whole genome bisulphite sequencing, long read sequencing and human methylation data to identify differentially methylated regions between old and young animals and validate those regions with modern molecular technologies.
Expected outcomes and deliverables:	In this project students will develop a broad range of data analysis and bioinformatics skills as well as gain experience with project design, scientific communication and analysing very large sequence data sets.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact t.nguyen3@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Understanding host response to cattle tick infestation by measuring variation in serum proteomes
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	The cattle tick, Rhiphicephalus microplus, and the diseases it transmits lead to massive economic losses to cattle industries in tropical and subtropical countries. The emergence of widespread resistance to acaricide drugs and the absence of an effective vaccine for tick control had led to genetic selection of host resistance as a method of choice for non-chemical control of cattle tick. Research to identify host genetic markers associated with tick susceptibility or resistance has been limited to the comparison of local breeds in specific geographic regions. Several studies have attempted to identify genetic markers for the resistance of cattle to tick burden, for example, protein-based analyses, immunological methods, genome-wide analysis studies, and quantitative trait analysis in tropically adapted genotypes. Given the fact that gene expression results and actual dynamics occurring at the protein level often do not correlate due to post-transcriptional, posttranslational and degradation regulation. Host proteomics may provide reliable biomarkers to assist in selection to support traditional breeding programs. Recently, we used sequential window acquisition of all theoretical ions mass spectrometry (SWATH-MS) with serum samples from Santa Gertrudis cattle and reported that the tick-resistant cattle showed higher abundance of proteins involved in immune response and lipid metabolism pre- and post-infestation. These findings require further validation in different breeds of cattle and to select a panel of proteins to be used a biomarker in the future. Based on the previous findings, we hypothesised that tick-resistant and susceptible individuals from other cattle breeds also develop different responses to tick infestation detectable at protein level. Therefore, in this study, SWATH-MS with serum samples from Brangus cattle (3/8 Brahman and 5/8 Angus) will be used to reveal the changes in proteomes of tick-resistant and -susceptible cattle, subsequently exploring the systemic host response to tick infestation.
Expected outcomes and deliverables:	The student will gain skills in experimental planning, sample preparation for Mass Spectrometry, Data analysis with variety of software including Protein Pilot, PeakView, R, and various online database resources for functional annotation of the proteins. The student may have an opportunity to generate a publication from this research. At the end of the project, the student may also be required to present their research work as an oral presentation.
Suitable for:	This project is open for students who are interested in Immunology, Ectoparasites, learning Mass Spectrometry and data analysis for discovery of biomarker(s) for disease resistance. Highly suitable for Masters/Honours students
Primary Supervisors:	Ali Raza
Further info:	Please contact a.raza@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Reducing methane emissions through improved understanding of the rumen microbiome
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	Ruminants such as cattle are host to a vast array of microbial species which reside in a specialised chamber of their stomach called the rumen. Microbes in the rumen digest the feed which the animals eat. Cutting edge sequencing technologies now allow for accurate profiling of microbiome communities. This study will analyse the microbes that live inside the rumen of cattle fed a methane mitigating diet. Methane is a potent greenhouse gas that is produced as a by-product of ruminant digestion. The goal of this study is to identify the species of microbe that have a changed abundance in response to the diet and therefore increase our understanding of how the rumen microbiome can be manipulated to reduce methane emissions from ruminants.
Expected outcomes and deliverables:	In this project students will develop molecular genetics, bioinformatics, quantitative genetics, and analysis skills in a fast developing area of research.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Dr Elizabeth Ross
Further info:	Please contact e.ross@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Combining omics: Examining genome structure and function for health and welfare
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance
Description:	Students will use literature review skills to select genes that are relevant to traits important to the beef industry, including those related to health and welfare, adaptation, fertility and production. Using a broad range of data the student will then examine the selected genes for structural variations, expression level changes, epigenetic signals, and population wide variation. Data types included short and long DNA sequence, short and long expression data, as well as methylation epigenetic data. The goal of the project is to better understand important genes related to northern beef cattle production by bringing together data from various cutting edge technologies.
Expected outcomes and deliverables:	In this project students will develop a broad range of data analysis and bioinformatics skills as well as gain experience with project design, scientific communication and industry relevance.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, molecular genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Prof Ben Hayes, Dr Elizabeth Ross and Dr Loan Nguyen
Further info:	Please contact t.nguyen3@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	The long and the short of it: investigating the effect of incorporating long read sequencing data into variant discovery pipelines
Project duration:	10 Weeks – Summer Program, 36 hours a week, applicant can work remotely for the project
Description:	Genomic methodologies are evolving. Methods considered cutting edge 10 years ago are now becoming redundant. This means that traditional analysis pipelines need to adapt to the new technology. This project will investigate one of the most fundamental uses of genome sequencing: genome variation discovery. Genomic variants such as SNP (single nucleotide polymorphisms) underpin all genetic analysis, from predicting disease risk to identifying family relationships. This project will evaluate the usefulness of now long read sequencing data against older short read data, and evaluate the changes required to reliably discover new genetic variants from long read sequencing data. Students are encouraged to contact the supervisor before applying.
Expected outcomes and deliverables:	Scholars may gain skills in data analysis and bioinformatics. Scholars are also required to produce a short summary report and oral presentation at the end of their project to the research team.
Suitable for:	Suitable for students studying or interested in bioinformatics, statistics, molecular genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.
Primary Supervisors:	Dr Elizabeth Ross
Further info:	Please contact e.ross@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Crop Science

Project title:	Unlocking the secrets of mungbean physiology and genetics to increase yield production and reliability
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	Mungbean is an important cash and food crop grown in tropical and subtropical regions globally. Over the last three decades, the demand for mungbean has increased by over 60% and is now cultivated over 6 million hectares of land. Despite this increase in demand, the expansion of mungbean production is limited due to its low yield production and variability. A major reason for this is due to mungbean’s indeterminate reproductive behaviour which results in staggered maturity and the crop accumulating vegetation, flowers and pod components simultaneously. This behaviour has different implications for hand and mechanical harvesting systems. This project aims to dissect the behaviour and genetics of a diverse mungbean population and to identify potential combinations of key agronomic traits that could be deployed to generate high yielding and reliable mungbean cultivars. The student will be assisting with the field trial being undertaken at Gatton. This trial aims to collect a range of phenology and physiological measurements that will contribute to identifying key genes of traits that are associated with high yields. This project is also a part of ACIAR’s International Mungbean Improvement Network Project and the student will be able to attend the regular IMIN meeting and engage with mungbean researchers located across Asia.
Expected outcomes and deliverables:	The student will gain an understanding of plant physiology, as well as the process of organising and managing a research field trial. They will gain skills in a wide range of data collection methods and will be able to undertake basic data analysis using the statistical program, R. The student will gain confidence with conducting field experiment activities and operating in a research environment. The scholar’s work will be incorporated into a manuscript for peer-reviewed journal publication and will be a co-author on the paper. A short presentation will be required at the end of the project detailing their experience and their findings.
Suitable for:	This project is open to students with a science background. Students with some knowledge/interest in plant physiology and genetics is recommended for this project. Note, the project will also involve considerable time out in the field collecting data, so an ability to work full days outside is also essential.
Primary Supervisor:	Professor Lee Hickey
Further info:	Please contact l.hickey@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Optimising winter cereals root system architecture using CRISPR/Cas9
Project duration:	10 Weeks – Summer Program, 20-36 hours a week, applicant is required on-site for the project.
Description:	Producing more food with less, land and fertilisers is one of our greatest challenges facing humanity today. Winter cereals, such as barley and wheat, are some of the most widely consumed grain crops worldwide and are critical to the global food market. One mechanism to boost water and nutrient acquisition is through modifications of the plants root system architecture. This project focuses on using gene editing approaches to develop and help optimise transformation systems, as well as implement them to alter key genes involved in root architecture. Further, phenotypic glasshouse experiments will be performed on gene-edited germplasm with various root-related genetic alterations, such as root angle assessments.
Expected outcomes and deliverables:	Expected outcomes from this project will be the development and preliminary assessment of gene edited barley and wheat lines with altered root traits. They will learn the core molecular skills, such as DNA and RNA extractions, primer design, PCR, gel electrophoresis and sequencing. They will develop biotechnological skills through performing tissue culture tests and performing particle bombardment creating transgenic crops. Preliminary assessment of root traits will be performed in the glasshouse if time permits. Students will be expected to work within a larger project with a diverse group of people, attend lab meetings and eventually give an oral presentation of their progress.
Suitable for:	Successful applicants should be enthusiastic about plant science and keen to learn molecular/biotechnological techniques. Although they will mostly be working in a team with other researchers, some independence will be required and therefore it’s essential the student is detail-oriented
Primary Supervisor:	Dr Karen Massel
Further info:	Please contact k.massel@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Understanding the genetic basis of shoot branching - Phenotypic & genomic analysis of the 1001 Genomes Project
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, can be completed either remote or on-site attendance.
Description:	This project offers to opportunity for a student to gain real-world experience and skills in gene discovery. The skills learned are applicable to plant, animal and human research. As part of a collaboration between staff in QAAFI and the School of Biological Sciences, data will be collected on shoot branching behaviour in Arabidopsis plants from the 1001 Genomes project. This project will aid in this data collection and perform computational analyses called Genome Wide Association Studies (GWAS) to detect associations between regions of the genome and traits of interest.
Expected outcomes and deliverables:	Students will gain skills and experience in data collection, quality control, curation, and analysis. The specific tasks could include measurements taking in growth chambers and glasshouses, software analyses of associations between genetic fingerprints (DNA markers) and plant measurements. The time split between data collection and computer work can be adjusted to suit the student. Potential for inclusion of student in research publications. The student may be asked to produce a report or an oral presentation at the end of their project.
Suitable for:	A background in plant biology/genetics and an interest in data science. OR A background in mathematics/computer science/data science and an interest in plant biology/genetics.
Primary Supervisor:	Owen Powell
Further info:	Please contact o.powell2@uq.ed.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	*Dormancy and herbicide resistance in feathertop Rhodes grass (Chloris virgata) populations*
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, The student needs to be at Gatton at least 3 days per week.
Description:	Feathertop Rhodes grass (FTR) has emerged as the most difficult-to-control weed in summer crops in the eastern region of Australia. Populations of this weed behave very differently in terms of dormancy and response to herbicides, especially glyphosate. This project will study the dormancy level in FTR populations and establish a relation, if any, between dormancy and herbicide resistance.
Expected outcomes and deliverables:	Students will gain skills in data collection. Students will also have the opportunity to visit growers’ fields.
Suitable for:	The project is open for BS or MS students. No prior knowledge is needed.
Primary Supervisor:	Bhagirath Chauhan
Further info:	Please contact b.chauhan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Evaluation of weed-competitive pigeonpea varieties
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, The student needs to be at Gatton at least 3 days per week.
Description:	Pigeonpea has great potential as a summer legume rotational crop in cereal farming systems of subtropical Australia. The crop requires season-long weed control, but options for controlling weeds in pigeonpea are limited. Weed-competitive varieties could be an important tool in integrated weed management practices. Weed-competitive ability is often evaluated based on weed-suppressive ability and weed-tolerance ability parameters; however, there is little information on these aspects for barley genotypes in Australia. In this study, the effects of weed interference on pigeonpea varieties will be assessed.
Expected outcomes and deliverables:	Students will gain skills in data collection. Students will also have the opportunity to visit growers’ fields.
Suitable for:	The project is open for BS or MS students. No prior knowledge is needed.
Primary Supervisor:	Bhagirath Chauhan
Further info:	Please contact b.chauhan@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Gaining new insight into mungbean physiology to increase yield potential and reliability
Project duration:	10 Weeks – Summer Program, 20-36 hours a week, applicant is required on-site at St Lucia Campus for the project.
Description:	Mungbean is an important cash and food crop grown in tropical and subtropical regions globally. Over the last three decades, the demand for mungbean has increased by over 60% and is now cultivated over 6 million hectares of land. Despite this increase in demand, the expansion of mungbean production is limited due to its low yield production and variability. A major reason for this is due to mungbean’s indeterminate reproductive behaviour which results in staggered maturity and the crop accumulating vegetation, flowers and pod components simultaneously. This behaviour has different implications for hand and mechanical harvesting systems. Other physiological components and behaviours have yet to be completely explored in mungbean (i.e. photosynthetic capacity), offering the opportunity to be exploited for increased crop productivity. This project aims to dissect the behaviour and genetics of a diverse mungbean population and to identify potential combinations of key agronomic traits that could be deployed to generate high yielding and reliable mungbean cultivars. The student will be assisting with two glasshouse experiments being undertaken simultaneously at St Lucia. The first experiment aims to collect detailed flower and pod development measurements to gain insight into how flowering behaviour influences yield potential and reliability. The second experiment aims to take detailed fluorometer measurements to determine whether the initial slope of the light response curve can be used to predict the maximum photosynthesis capacity of mungbean, which has yet to be done in any crop. Understanding these behaviours will contribute to identifying key genes of traits that are associated with high yields. This project is also a part of ACIAR’s International Mungbean Improvement Network Project and the student will be able to attend the regular IMIN meeting and engage with mungbean researchers located across Asia
Expected outcomes and deliverables:	The student will gain an understanding of plant phenology and physiology, as well as the process of organising and managing glasshouse research experiments. They will gain skills in a range of data collection methods and will be able to undertake basic data analysis using the statistical program, R. The student will gain confidence with conducting glasshouse research activities and operating in a research environment. The scholar’s work has the potential to be incorporated into two manuscripts for peer-reviewed journal publications and will be a co-author on the paper/s. A short presentation will be required at the end of the project detailing their experience and their findings.
Suitable for:	This project is open to applicants from students with a science background. Students with some knowledge/interest in plant physiology and genetics is recommended for this project.
Primary Supervisor:	Dr Millicent Smith
Further info:	Please contact millicent.smith@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Horticultural Science

Project title:	RNA interference against world’s most invasive pest Fire-Ant
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	Red Imported Fire Ant (RIFA) are a serious exotic pest that can inflict painful bites on people, pets and livestock. They cause extensive damage to the environment, agriculture and significantly impact our way of life. RIFA were first detected in Brisbane in 2001, and in September that year the National Fire Ant Eradication Program was formed in partnership with state governments. At the time, the Australian Bureau of Agricultural and Resource Economics predicted to cost Australia $8.9B over 30 years if the ant was not controlled. According to the most recent analysis, the total impact to South-east Queensland alone will top $45B over 30 years. In this project, we aim to explore our RNAi delivery platform to control RIFA. This project will result in real-world outcomes, by translating and expanding our current biotechnologies to an industry-ready tool.
Expected outcomes and deliverables:	The student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), bioinformatics, material science and the application of RNAi. The student will work closely with Dr Karishma Mody and other members of the Mitter laboratory at UQ.
Suitable for:	This project is open to applications from students with a background in molecular biology or biotechnology. Highly suitable for Masters/Honours students.
Primary Supervisor:	Dr Karishma Mody
Further info:	Please contact k.mody@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Modelling fruit tree architecture and physiology
Project duration:	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 3^rd and 4^th 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:	Dr Inigo Auzmendi
Further info:	Please contact i.auzmendi@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Using virtual plants to simulate photosynthesis in horticultural plants
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant can complete the project under a remote working arrangement.
Description:	Plants assimilate the carbon required 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. Therefore, different approaches to simulate photosynthesis could result into different estimates of carbon assimilation. 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 and deliverables:	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 programing 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.
Suitable for:	This project is open to applications from 3^rd and 4^th year students with a background in plant science. Students might have previous programing knowledge or not.
Primary Supervisor:	Dr Inigo Auzmendi
Further info:	Please contact i.auzmendi@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	DNA markers for Australian avocado
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Our Lab in QAAFI has been part of a large effort sequencing the genomes of major sub-tropical fruit crops including avocado. We have developed a DNA marker set that can distinguish avocado cultivars available in Australia – this is important for industry to be able to rapidly identify and track plants. This project will test these markers across a large number of seedling plants to provide confidence for industry in the system. The student will day-travel around QLD and N-NSW for sample collection, extract DNA, run our marker assay and critically analyse results, with valuable connections to industry and academia.
Expected outcomes and deliverables:	Students will gain skills in field travel, molecular biology (e.g. DNA extraction, PCR), 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 that can make a difference to industry and sustainability.
Primary Supervisor:	Dr Alice Hayward, Stephen Fletcher and Prof Neena Mitter
Further info:	Please contact a.hayward@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Saving Our Plant Species!
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Plants possess the incredible ability of cell totipotency, with each cell having potential to regenerate into a new plant. Taking advantage of this property, The Mitter lab is dedicated to developing cryopreservation (cryostorage at -196C) protocols to save plant species from climate-change, disease pandemics (e.g. myrtle rust), deforestation and ultimately extinction. This is essential for plants that do not survive seed-banking – including our food species such as avocado. This technology allows us to safely freeze plant cells and tissues at -196C and then revive them to grow into whole new plants. This provides an insurance bank to conserve incredible genetic diversity of precious species including crops and endangered species that cannot be seed-banked. This project will focus on cryopreservation of endangered Queensland plants – Gossia gonoclada and Macadamia. Students will learn techniques of plant tissue culture and cryopreservation.
Expected outcomes and deliverables:	Students will gain skills in plant tissue culture, cryopreservation, plant physiology, 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 that can make a difference to industry and sustainability.
Primary Supervisor:	Chris O’Brien
Further info:	Please contact c.obrien4@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Tissue culture to feed the world
Project duration:	10 Weeks – Summer Program, 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 - the world's most instagrammed fruit. This is important as a sustainable, cost-effective and climate-secure way to produce plants. Dedicated students will be part of our expanding research in a new $20M tissue-culture facility at 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: Tissue culture propagation for the native species, Lomandra and macadamia. Tissue culture propagation of high-value crops vanilla and cocoa.
Expected outcomes and deliverables:	Students will gain skills in plant tissue culture, plant physiology, 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 that can make a difference to industry and sustainability.
Primary Supervisor:	Chris O’Brien
Further info:	Please contact c.obrien4@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Optimising nut maturity in macadamia: investigating husk traits
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Identification of optimum maturity stage is the key deciding factor of planning orchard harvest. Harvesting macadamia nut at correct maturity stage is important for storage life, quality and also for maximum economic return. Currently, the colour of inner husk is being used as an indicator of the maturity. However, there is no experimental evidence on this relationship. In this summer scholarship program, the scholar will measure the oil contents, inner husk colour and husk hardness. Statistical analysis will be conducted to identify the optimum maturity stage of the cultivars. Results from this study will support breeders to identify variability in maturity in varieties, and growers in their harvest decision.
Expected outcomes and deliverables:	The scholar will develop skills in Plant phenotyping, 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.
Suitable for:	This project is open to applications from students with a background in Biology/Botany/Genetics/ Plant Breeding/Ecology/ Plant Physiology/ Quantitative Genetics.
Primary Supervisor:	Dr Mobashwer Alam
Further info:	Please contact m.alam@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Rootstock effect on scion architecture and branching in macadamia
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Most macadamia orchards are planted with grafted trees and use seedling rootstocks. More recently there has been some interest in developing clonally propagated rootstocks that have specific traits to reduce tree vigour. The management of excessive vigour through pruning and hedging is a major expense in commercial orchards. Recently, Queensland Department of Agriculture and Fisheries (QDAF) and the University of Queensland (UQ) took initiatives to control scion vigour by using rootstocks through two consecutive Horticulture Innovation (HI) Australia funded projects: “Transforming subtropical/tropical tree crop productivity” (AI 13004) and National Tree Crop Intensification in Horticulture Program (AS18000). A diverse range of germplasm of macadamia rootstocks were planted at Nambour with a single scion cultivar. Investigating the effect of rootstocks on the variability in the architectural traits and branching pattern of the scion will be useful to select rootstocks for vigour management. In this project, the scholar will collaborate with a research higher degree student and measure the traits, including height, width, limb length, internode length, and branching pattern of a common scion. A branching index equation will be developed to characterise trees for the variability in branching. Statistical analysis will be conducted to find out the effect of rootstock genotypes on scion vigour.
Expected outcomes and deliverables:	The scholar will develop skills in Plant phenotyping, 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.
Suitable for:	This project is open to applications from students with a background in Biology/Genetics/ Plant Breeding/ Ecology/ Plant Physiology/ Quantitative Genetics.
Primary Supervisor:	Dr Mobashwer Alam
Further info:	Please contact m.alam@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Stomatal characterisation for early selection for husk spot resistance
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Husk spot, caused by Pseudocercospora macadamiae, is one of the key diseases of Australian macadamia industry. Stomata is the entry point of this fungal pathogen. Recent investigation on a few cultivars revealed a significant linear relationship between the incidence of husk spot disease and husk stomatal density. Therefore, stomatal characterisation can be used as a tool for selecting husk spot resistant cultivars. In a current PhD program, a large number of breeding progeny are being screened for husk spot susceptibility. This project will collaborate with the PhD research scholar and investigate the relationships between husk stomata size and density with disease susceptibility in the breeding populations. In addition, the scholar will estimate the heritability of the traits and identify the relationship between husk and leaf stomata to develop an early selection method for husk spot resistance in macadamia.
Expected outcomes and deliverables:	The scholar will develop skills in plant phenotyping, genetics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research and presenting in conferences. 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 students with a background in Biology/Genetics/ Plant Breeding/ Ecology/ Environmental Science/ Botany / Plant Physiology
Primary Supervisor:	Dr Mobashwer Alam
Further info:	Please contact m.alam@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Investigating rootstock effect on plant vigour in low chill peach
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Rootstocks play a vital role on the performance of horticultural crops. As a part of a dual plant system, rootstocks translocate water and nutrients to the above ground scion and thereby, regulate resource supply for growth and development of vegetative and reproductive parts. In several tree crops, rootstocks have been widely used to manage the size and vigour of the scion. Although extensive studies have been conducted previously in peach, but the investigation on low-chill rootstock effect on low chill peach cultivars is limited. In this project, the scholar will collect data on growth traits of 3 low-chill scion cultivars grafted onto 7 different low chill rootstocks. Statistical analysis will be conducted to identify best vigour managing rootstocks.
Expected outcomes and deliverables:	The scholar will develop skills in Plant phenotyping, 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.
Suitable for:	This project is open to applications from students with a background in Genetics/ Plant Breeding/ Ecology/ Plant Physiology/ Quantitative Genetics/ Biology.
Primary Supervisor:	Prof Bruce Topp
Further info:	Please contact b.topp@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Molecular and biological characterization of a virus from the native plant Commelina cyanea7035941
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Studies on viruses of Australian native plants have been limited. Commelina cyanea (scurvy weed) is a plant native to eastern Australia and in 2011 a potyvirus was partially described from a specimen from Bateman’s Bay NSW. We have found symptomatic plants in northern NSW and on surveys in Norfolk Is. This project aims to investigate whether the originally described Commelina mild mosaic virus (CMMV) and/or other viruses are present in these recently collected samples. The complete genome of CMMV or other virus(-es) present will be sequenced and some of the biological properties determined, in order to more fully characterise the virus(-es) and extend the known distribution.
Expected outcomes and deliverables:	The student will gain skills in experimental design and data recording, molecular techniques (RNA/DNA extraction, PCR, high throughput sequencing, bioinformatics) and biological characterisation (virus transmission, host range). There is the opportunity to generate a publication from this research. The student may also be asked to produce a report or oral presentation at the end of their project.
Suitable for:	The student will ideally be in the later years of undergraduate study, having studied some plant pathology, and be enthusiastic to learn both molecular skills and hands-on work with plants.
Primary Supervisor:	A/Prof. Andrew Geering
Further info:	Please contact a.geering@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	RNA biopesticides for sustainable protection of crops and native plants from fungal pathogens
Project duration:	8 Weeks – Summer Program, 26-36 hours a week, applicant will be required on-site for the project.
Description:	Food production relies on chemical pesticides to control destructive plant diseases, however, resistance, lack of pathogen specificity, residues on food, run-off into waterways, potential harm to human health and the environment, and the cost of developing new fungicides are major issues with current crop protection practices. The Mitter lab have developed innovative biodegradable RNA interference (RNAi)-based biopesticides to protect high-value crops from aggressive pests and pathogens. The aim of this project is to design and test RNA constructs targeting plant fungal pathogens. The project will involve PCR, in vitro dsRNA synthesis, fungal culturing and bioassays on various host plants.
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:	Dr Anne Sawyer
Further info:	Please contact a.sawyer@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Nutrition and Food Sciences

Project title:	Exploring non-invasive and smart technologies to monitor and predict composition and microbial load in black soldier fly larvae
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	In 2011, the FOOD and Agricultural Organisation of the United Nations, estimated that around 1/3 of food was lost or wasted annually. As part of its Sustainable Development Goals, the FAO calls for halving per capita global food waste at retail and consumer levels by 2030 as well as reducing food losses along the production and supply chains. In recent years, black soldier fly larvae (BSFL) have been regarded as effective transformers of post-consumer organic waste streams into valuable animal feedstuff and alternative protein sources for human consumption, in the form of their last larval stage (prepupal stage). In this project, BSFL will be grown on different bio-waste streams to determine the influence of these waste streams on their microbiota to determine their safety. Recently, non-destructive methods and techniques based in vibrational spectroscopy such as near (NIR) and mid infrared (MIR) spectroscopy own intrinsic benefits such as being non-invasive, rapid, and almost no sample preparation required. These methods have being able to determine simultaneously chemical and functional parameters in different foods. Data fusion and multivariate data analysis techniques are also integrated into the analysis to increase the effectiveness of these approaches. The aim of this project is to evaluate the analytical methods based in vibrational spectroscopy (e.g. NIR, MIR) combined with multivariate data analysis to monitor the safety of BSFL raised on different diets.
Expected outcomes and deliverables:	The student will learn valuable techniques and strong skills in experimental design, non-destructive techniques (infrared spectroscopy), microbiology, statistics, chemometrics, preparing and writing a scientific report.
Suitable for:	This project is open to applications from students with a background in food sciences, animal sciences, microbiology, molecular biology or biotechnology. Highly suitable for Masters/Honours students.
Primary Supervisor:	Prof. Louw Hoffman, A/P Daniel Cozzolino and R Deidre Mikkelson
Further info:	Please contact louwrens.hoffman@uq.edu.au; d.cozzolino@uq.edu.au and d.mikkelsen@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	How to make antibiotics in pig feed redundant, naturally
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	The maternal-offspring relationship has been a major focus of research in humans, pigs, and other species. Sows communicate with piglets in an orchestrated flow of chemically-coded messages, a process referred to as vertical transfer. Some of the chemicals are originated in the maternal diet allowing piglets to acquire feed preferences and overcome neophobia (i.e. a reluctance to consume unfamiliar foods). In the wild, piglets and sows eat the same feeds. In contrast, commercial practices based on least-cost feed formulation and nutrient requirements have taken the diets of sows and piglets in different directions. The project aims to propose a rational adaptation of feed composition to pair sow and piglet diets while meeting the nutritional requirements of the two. The objective is to obtain optimal dietary intervention in sows based on aligning ingredient selection in sow and piglet feeds, to direct preferences, and enhance appetite and gut health without the need for in feed antibiotics in post-weaning piglets.
Expected outcomes and deliverables:	Scholars may gain skills related to animal handling, biological sample collection and processing, laboratory work and data/statistical analysis. The student will be particularly involved in the analysis of feed volatiles in pig’s blood and other body fluids of interest. There is a high possibility of generating a publication from the work that will be undertaken. It is anticipated that the scholar will participate in group meetings and animal experiments. In addition, the student is expected to produce a report and an oral presentation by the end of the project.
Suitable for:	This project is open to applications from students with a background in Animal Science, Veterinary, Biology, Molecular Biology and Chemistry. In addition, the applicant must demonstrate interest in working with pigs.
Primary Supervisor:	Marta Navarro
Further info:	Please contact m.navarrogomez@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Heat tolerance in lactating sows: dietary strategies, metabolic biomarkers and microbiome signature
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	Environmental hyperthermia is a main welfare and economic problem in livestock production particularly relevant in the tropical and sub-tropical areas of our planet Earth. Relevant to pig reproduction the rise in heat wave episodes together with the hyperprolificity of modern sows pose a paramount wellness risk for sows and piglets. This proposal aims to address the impact of heat stress in gestating/lactating sows by testing different nutritional interventions with complementary modes of action such as reducing metabolic and microbial heat production and increasing intra-cellular protection. In addition, the most heat-tolerant individuals will be selected and characterized in terms of blood and liver biomarkers (differential transcripts, proteins, and metabolites) and microbiome profiles associated with heat resilience. The proposal is the first ever studying heat tolerance metabolic biomarkers and microbiome signatures in gestating and lactating sows using a holistic approach under controlled environments.
Expected outcomes and deliverables:	Identify dietary supplements that increase heat tolerance in sows. Identification of individual metabolic variations associated with heat tolerance in lactating sows (metabolic and microbiome markers in resilient compared to the most vulnerable individuals). Scholars may gain skills related to animal handling, biological sample collection and processing, laboratory work and data/statistical analysis. The student will be particularly involved in the analysis of biomarkers in pig’s blood and other body fluids of interest. It is anticipated that the scholar will participate in group meetings and animal experiments. In addition, the student is expected to produce a report and an oral presentation by the end of the project.
Suitable for:	This project is open to applications from students with a background in Animal Science, Veterinary, Biology, Molecular Biology and Chemistry.
Primary Supervisor:	Marta Navarro
Further info:	Please contact m.navarrogomez@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.

Project title:	Exploring non-invasive and smart technologies to monitor and predict shelf-life in fresh foods
Project duration:	10 Weeks – Summer Program, 26-36 hours a week, applicant is required on-site for the project.
Description:	Most fresh foods (e.g. fruits, meat, seafood) are highly perishable product and must be stored under refrigerated conditions to control microbiological growth and other deteriorative changes. It is generally accepted that a food is past its shelf-life when it is no longer acceptable to the consumer. Changes in colour, flavour, texture, aroma or nutrient content have declined to the point that it is no longer acceptable to the consumer. It can also be when it becomes a food safety issue, where the food product may make consumers ill. Whilst shelf-life is usually equated with spoilage, in many cases the end of shelf-life might be reached before spoilage is evident. Recently, non-destructive methods and techniques based in vibrational spectroscopy such as near (NIR) and mid infrared (MIR) spectroscopy own intrinsic benefits such as being non-invasive, rapid, and almost no sample preparation required. These methods have being able to determine simultaneously chemical and functional parameters in different foods. Data fusion and multivariate data analysis techniques are also integrated into the analysis to increase the effectiveness of these approaches. The aim of this project is to evaluate the analytical methods based in vibrational spectroscopy (e.g. NIR, MIR) combined with multivariate data analysis to monitor food shelf-life.
Expected outcomes and deliverables:	The student will learn valuable techniques and strong skills in experimental design, non-destructive techniques (infrared spectroscopy), statistics, chemometrics, preparing and writing a scientific report.
Suitable for:	This project is open to applications from students with a background in food sciences, animal sciences, molecular biology or biotechnology. Highly suitable for Masters/Honours students.
Primary Supervisor:	A/Prof Daniel Cozzolino and Prof. Louw Hoffman
Further info:	Please contact d.cozzolino@uq.edu.au and louwrens.hoffman@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application.