Low cost genotyping with ultra-low fold sequencing for tropical cattle

Very low fold genome sequencing offers a pathway to low cost and high density genotyping, when combined with imputation and extensive genome sequence reference data.  While this has been explored for temperate breeds, little work has been done on tropical cattle, particularly Bos indicus and Bos indicus derived cattle that make up the majority of cattle in tropical and sub tropical region of the world. This project will deliver a highly accurate and efficient genotyping of SNPs and structural variants from ultra-low fold coverage sequence data. The project will work with all types of sequence data, for example Illumina, Nanopore and PacBio.

This PhD project is part of the ARC Training Centre in Predictive Breeding, led by UQ. The student will be based within the Centre for Animal Science in the Queensland Bioscience Precinct at UQ's St Lucia Campus and will undertake a placement with Neogen for up to 12 months. All supervisors are CIs and PIs of the ARC Training Centre.

This project is supported by the Research project scholarship.

Learn more about the Research project scholarship.

You must contact the principal supervisor for this project to discuss your interest. You should only complete the online application after you have reached agreement on supervision.

Always make sure you are approaching your potential supervisor in a professional way. We have provided some guidelines for you on how to contact a supervisor.

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 familiarity with genomic prediction models such as GBLUP, as well as experience in handling large-scale genomic data, including SNP data would be of benefit to someone working on this project.

You will demonstrate academic achievement in the fields of quantitative genetics and genomic selection and the potential for scholastic success.

A background or knowledge of genomic selection methodologies, quantitative genetics and data analysis tech is highly desirable.

Before you apply

Before submitting an application you should:

1. check your eligibility for a Doctor of Philosophy (PhD)
2. prepare your documentation
3. contact Dr Mehrnush Forutan (m.forutan@uq.edu.au) to discuss your interest and suitability
4. submit your application by 4 December, 2024 4 December, 2024.

When you apply

You apply for this scholarship when you submit an application for your program. You don’t need to submit a separate scholarship application.

In your application ensure that under the ‘Scholarships and collaborative study’ section you select:

• ‘My higher degree is not collaborative’
• ‘I am applying for, or have been awarded a scholarship or sponsorship'
• ‘Other’, then ‘Research Project Scholarship’ and in the ‘Name of scholarship’ field enter TROPICALCATTLE-FORUTAN.

Apply now