Program 2: New molecular technologies

Program Leader: Dr Mike Francki Aims Develop whole genome and recombination-based breeding strategies. Develop and evaluate association mapping as a marker identification selection strategy. Develop procedures and tools to graphically visualise genotypes to design ideal varieties with the optimum combinations of gene blocks. Develop improved breeders' software for cross outcome prediction. Develop and implement bioinformatics tools and systems allowing integration, analysis and access of complex and heterogenous databases for molecular plant breeding. Develop candidate gene-associated SNP markers for key target traits in crops and pastures. Develop highly multiplexed marker screens for low-cost and high-throughput implementation.

Outcome Major shifts in breeding methodology, tools and strategies leading to significant increases in rate of genetic gain in cereal and pasture plant improvement. A new generation of molecular breeding technologies will be delivered to breeding programs to provide major improvements in new varieties using non-GMO techniques. Outputs SNP molecular markers using a candidate gene-based approach, and high throughput low-cost SNP analysis systems. Increased efficiency in the application of protein and DNA markers in breeding programs. New marker technologies and systems. New strategies for effective molecular breeding in cereals and pastures. These will include association mapping to identify new molecular markers, and graphical genotyping to manage the whole genome in breeding. An Integrated Genetic and Genomic System (IGGS) in bioinformatics. Software to assist breeders make decisions on crosses and breeding strategies Subprogram 2.1: Developing candidate gene-based marker technologies Subprogram Leader: Prof John Forster 2.1.03 Development and implementation of candidate gene-based molecular markers in outcrossing forage species (J Forster) 2.1.04b Low cost analysis - solid phase diagnostics for DNA markers 2.1.05 Rice-wheat-barley comparative genomics for key agronomic traits Subprogram 2.2: Whole genome and recombination-based strategies Subprogram Leader: Dr Ken Chalmers 2.2.02 Plant breeding scholarship (K Chalmers / S Jefferies) 2.2.03a Association mapping and data management (K Chalmers) 2.2.03c Whole genome-based selection in backcross families in wheat and barley (K Chalmers) 2.2.04a Novel marker systems - developing new technologies and delivering to breeding programs (K Chalmers) 2.2.04b Novel marker systems - multiplex PCR technologies to accelerate the use of SSRs in cereal breeding and genetic research (M Hayden) 2.2.07 Map-based cloning of quality loci in barley (K Chalmers) Subprogram 2.3: Bioinformatics and biological computing for plant breeding Subprogram Leader: Prof Matt Bellgard 2.3.01 Bioinformatics and biological computing for plant breeding (M Bellgard) 2.3.01b Curation of molecular plant breeding data (D Mather) 2.3.01c AWCMMP: Curation of wheat and barley maps 2.3.01e Bioinformatics systems for molecular plant breeding (T Sawbridge) Subprogram 2.4: Breeders' software Subprogram Leader: Dr Howard Eagles 2.4.01a Breeders' software - tactical tools (H Eagles) 2.4.01b Breeders' software - strategic tools (H Eagles)

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