Project number: 2008-328.16
Project Status:
Completed
Budget expenditure: $8,760.00
Principal Investigator: Sonja Dominik
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 31 Aug 2012 - 28 Feb 2013
Contact:
FRDC

Need

Strong foundations have been developed by CSIRO Food Futures Flagship for breeding programs in Atlantic salmon, hybrid abalone, Pacific oysters and Black Tiger Prawns. The next step is to draw on some of the high density molecular marker (SNP) technology to overcome challenges to further increase genetic gains, in particular for the enhancement of difficult to measure or lowly heritable traits. For Atlantic salmon, the evaluation by CSIRO of using selection approaches based on SNP markers (genomic selection) for the improvement of AGD resistance is about to conclude, and in the other industries, the molecular technologies for enhanced management strategies, are being developed.

Already in these first stages of dealing with SNP marker data, the need for efficient data processes has been recognised due to the volume of data. The risk of data mismanagement is high.

The Centre of Integrative Genetics (CIGENE) in Norway has been a leader in the development of tools for data processing and analysis to assist the agriculture and aquaculture sectors.

CIGENE has implemented their data processing pipeline in Galaxy, a scientific workflow software. Galaxy enables scientists with little programming skills to handle data of large volume efficiently, extract subsets and analyse data. The specific application of Galaxy for the purpose of genetic improvement is rare and CIGENE has expert knowledge in this area.

This Bursary for Prof Sigbjorn Lien, will enable the direct transfer of knowledge and skills to leading Australian researchers, and the discussion of the future of the technology with key industry stakeholders.

Objectives

1. To support a three week research and training visit to Australia by Prof Sigbjorn Lien of CIGENE
2. To review and asses the needs in SNP data handling, processing and analysis in Atlantic salmon and black tiger prawn breeding programs
3. 3) To transfer knowledge to researchers on the development a bioinformatics pipeline in Galaxy for SNP data in Atlantic salmon and black tiger prawn
4. 4) To provide industry with an overview of the use of molecular technologies in aquaculture breeding programs in Europe

Related research

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Industry
Environment