Novel genomic assessments for finding true DNA variants contributing to the difference in beef cattle fertility

Fertility is a key factor influencing productivity and profitability in beef cattle, yet it remains a major challenge in northern Australia, where weaning rates are below 40%. Improving fertility could significantly enhance genetic gains and economic returns for the beef industry. However, identifying genetic factors linked to fertility is complex, as it involves multiple genes with small effects.

This project aims to uncover the genetic basis of fertility traits in cattle by using cutting-edge long-read sequencing technology (Oxford Nanopore Technologies, ONT). Traditional genome-wide association studies (GWAS) have identified key regions associated with fertility, but the causal genetic variants remain elusive, particularly structural variants (SVs)—large genomic alterations (>50 bp)—which are often missed by short-read sequencing.

For the first time, this study will analyze structural variants in fertility-related genes, leveraging ONT sequencing and advanced bioinformatics approaches. By integrating gene expression data, fertility phenotypes, and genotypic information from over 28,000 cattle, this project will improve genomic selection models and enable the development of low-cost, high-accuracy sequencing strategies.

Students involved in this project will gain hands-on experience in genomics, bioinformatics, and computational biology, including long-read sequencing, GWAS, structural variant analysis, and genomic prediction modeling. The research is highly applicable to agriculture, animal breeding, and biotechnology, offering opportunities to contribute to real-world improvements in cattle fertility and genetic selection.

This project will be conducted within The University of Queensland (UQ), a world-renowned research institution consistently ranked among the top universities globally for agriculture and life sciences. The project is based at the Queensland Alliance for Agriculture and Food Innovation (QAAFI), a leading research institute dedicated to advancing genetics, genomics, and agricultural innovation.

The research environment offers access to cutting-edge facilities and expertise, including:

• High-Performance Computing (HPC) Infrastructure – Access to UQ’s HPC system for large-scale genomic data processing, imputation, and statistical analysis.
• Next-Generation and Long-Read Sequencing Facilities – Equipped with Oxford Nanopore Technologies (ONT) sequencing platforms for long-read genomic and transcriptomic studies.

This is an Fellowship support scheme scholarship project that aligns with a recently awarded Australian Government grant.

The scholarship includes:

• living stipend of $36,400 per annum tax free (2025 rate), indexed annually
• your tuition fees covered
• single overseas student health cover (OSHC).

Learn more about the Fellowship support scheme scholarship.

Your application will be assessed on a competitive basis.

We take into account your:

• previous academic record
• publication record
• honours and awards
• employment history

A working knowledge of genetics, bioinformatics, statistical genomics, GWAS, Nanopore sequencing, molecular biology and computational tools would be of benefit to someone working on this project.

You will demonstrate academic achievement in the field/s of genetics, genomics, and bioinformatics and the potential for scholastic success.

A background or knowledge of genetics, bioinformatics, statistical genomics, computational biology, and molecular biology is highly desirable.

This project requires candidates to commence no later than Research Quarter 3, 2026. You can start in an earlier research quarter.

You must submit an expression of interest (EOI) by the closing date for the research quarter (RQ) you want to start in:

Before you apply

1. Check your eligibility for the Doctor of Philosophy (PhD).
2. Prepare your documentation.
3. If you have any questions about whether the project is suitable for your research interests, contact Dr Loan Nguyen (t.nguyen3@uq.edu.au).

When you apply

To apply, submit an expression of interest (EOI) for the program. You don't need to apply separately for the project or scholarship. How to submit an EOI

In your EOI, complete the 'Scholarship/Sponsorship' section with the following details:

1. Are you applying for an advertised project: 'Yes'
2. Project: 'Fellowship project scholarship'
3. Scholarship Code Listed in the Advertisement: NGUYEN-280225
4. Link to Scholarship Advertisement: https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/novel-genomic-assessments-finding-true-dna-variants-contributing-difference-beef-cattle-fertility

Submit an EOI