Genetic Evaluation – Methodology Genomic Prediction

Development of new tools and methods to analyse genomic data for livestock genetic improvement.

Ph.D opportunity at Animal Genetics and Breeding Unit, University of New England

Project Information

For over 45 years, AGBU has been developing new tools and methods to analyse livestock genetics. AGBU is regarded as one of the world frontiers in implementing new methods for genomic evaluation at the commercial level, and currently analysing genomic data for thousands of individuals every month. The developed methods were implemented in the national genetic evaluation software BREEDPLAN, LAMBPLAN, and MERINOSELECT. More recently, multi-breed and crossbreed individuals have become a focal point of mainstream research at AGBU. Therefore, AGBU is required to modify the previous methods or create new ones to not only analyse such data, but also enable capacity to handle significantly larger datasets from various sources.

Questions to Address

This project aims to develop new algorithms and methods for the analysis of large genomics datasets of multi-breed and crossbreed livestock for use in genetic evaluations.

Proposal objectives

· New methods to analyse multi-breed and crossbred genomic and phenotypic data

  • New methods for phasing and imputation of missing genotypes
  • New methods to predict Estimated Breeding Values (EBVs) using pedigree, phenotypes, genomic data (including haplotypes) and new relationship matrices including the possibility of inclusion of putative causal variants / weighted regions.
Selection Criteria
  • Knowledge and motivation in the development and innovation of algorithms, especially for analysing genomic data
  • Strong programming skills, especially in R, C/C++, Python and FORTRAN
  • Knowledge of the Linux operating system
  • Familiarity with analysing large text datasets, especially for analysing genomic data
  • Experience working with databases and knowledge of object-oriented programming, functional programming and parallel programming in the above programming languages is desirable

Scholarship Information

This scholarship is offered to top quality international candidates who wish to enrol in a research degree with AGBU. The Scholarship provides an annual stipend of $28,854.00 (2022), course tuition fees and single Standard Overseas Health Insurance.

How to Apply

Applicants must meet UNE’s admission requirements for a PhD program. Please see the entry requirements.

To apply for the scholarship please review the relevant application guidelines and complete the application form attaching a cover letter and CV. All Scholarship and candidature applications can be submitted through AskUNE.

HDR Scholarship Application Guidelines

HDR Scholarship Application Form

General Enquires to Mohammad Ferdosi at mferdos3@une.edu.au

The Animal Genetics and Breeding Unit reserves the right to not fill this scholarship if no suitable candidate is found.

Additional Information:

Other key researchers are Natalie Connors and Stephen Miller (AGBU).

Scholarship ID S22-03.4