Integrative genomic models for Eucalyptus globulus breeding

Degree type

PhD

Closing date

31 October 2022

Campus

Hobart

Citizenship requirement

Domestic/International

Scholarship

$28,854pa for 3.5 years

About the research project

About the Research Project:

The breeding of plantation forest tree species is an important activity for providing a sustainable wood supply that does not increase the erosion of the native forest estate. Traditional breeding methods, based on field recording and measurement, are now being complemented with methods that utilise genomic data. An exciting opportunity exists for a student with strong mathematical skills to help integrate genomics into Australia’s forest industry.

The PhD project will include the development of mathematical models that determine the relative likelihood of various hypotheses regarding identity and true parentage of trees used in breeding arboreta and genetics trials conditional on field-based recording of pedigrees and DNA assays such as whole genome or targeted sequencing. A unique characteristic of the Australian programs is the direct knowledge of the foundation set (origin) of individuals on which breeding is initiated. Forest trees are diploid organisms and a copy (allele) of each gene is received from each parent. A complete reconstruction of the founder haplotypes (the alignment of alleles of the same parental origin along the chromosome) opens the opportunity to efficiently identify chromosome segments that are resistant to recombination.  Such segments that are identified as containing important genes are ultimately targeted in selection programs. Single nucleotide polymorphisms (SNPs), which efficiently tag segments, need to be identified for this. The student will then focus on imputation. Industry standard assays are low-density (contain relatively few SNPs) and a goal will be to create mathematical and statistical methods to estimate the allelic states of SNPs that would be found by expensive higher-density assays.

The student will be expected to work closely with Tree Breeding Australia, which is the national breeder providing genetic evaluation services to the main hardwood and softwood species grown in Australia. The student will mix deterministic modelling with stochastic simulation and must have strong programming skills.

Research Environment:

Candidates will work in within the Discipline of Mathematics at the University of Tasmania. Mathematics is the language that underpins technology, enables innovation, and describes all aspects of the natural world. Mathematics provides fundamental skills in problem solving, modelling, analysis and research; it utilises the most modern computing technology combined with expertise developed over centuries. The Discipline of Mathematics provides a stimulating academic environment, conducting world class research, teaching and learning.

This project is funded by the University of Tasmania in collaboration with the Growers Research Advisory Committee of Forest and Wood Products Australia and will have strong links with industry collaborators. Candidates will be expected to spend a proportion of their candidature working closely with industry.

Primary Supervisor

Meet Professor Michael Charleston

Funding

The successful applicant will receive a scholarship which provides:

  • a living allowance stipend co-funded with Forest and Wood Products Australia Limited of $28,854 per annum (2022 rate indexed annually) for 3.5 years
  • a relocation allowance of up to $2,000
  • $10,000 per annum support for project costs for 3 years
  • a tuition fees offset covering the cost of tuition fees for up to four years (domestic applicants only)
  • international applicants may receive a University of Tasmania Fees Offset for up to four years

The scholarship supporting this project is funded by the University of Tasmania, Forest and Wood Products Australia Limited and the Australian Government through the Research Training Program.

Eligibility

Applicants should review the Higher Degree by Research minimum entry requirements.

Selection Criteria

The project is competitively assessed and awarded.  Selection is based on academic merit and suitability to the project as determined by the College.

Additional essential selection criteria specific to this project:

  • the candidate will ideally have strong skills in bioinformatics

Application process

There is a three-step application process:

  1. Select your project, and check you meet the eligibility and selection criteria;
  2. Contact the Primary Supervisor, Professor Michael Charleston to discuss your suitability and the project's requirements; and
  3. Submit an application by the closing date listed above.
    • Copy and paste the title of the project from this advertisement into your application. If you don’t correctly do this your application may be rejected.
    • As part of your application, you will be required to submit a covering letter, a CV including 2 x referees and your project research proposal.

Following the application closing date applications will be assessed within the College. Applicants should expect to receive notification of the outcome by email by the advertised outcome date.

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