1. IBP Simulation Tools Workshop Wageningen, June 2 nd 2011 1 Simulation Tools – Workshop4 Report

2. Structure of Workshop 2 Roles of simulation team within IBP? Brief introduction to plant breeding simulation using the QuGene platform (this talk) Tutorials/examples: Phenotypic selection with 1 gene, 1 trait, 1 environment Selected examples of simulation applications in breeding program Questions?

3. Summary of Responses 3 Proportion of responses (N = 16; Blank =“NO”)

4. Comments from participants Best Features 4 “Ability to simulate and estimate different population requirements and visualize results graphically. ” “A very powerful tool … it makes it possible for one to predict the outcomes of breeding” “User friendly” “The tool is great because it allows you to review your breeding strategy, taking in consideration of critical information from other research units in the program” “Integrated with other tools” “Very robust and flexible”

5. Comments from participants Best Features 5 “Flexible in the breeding design” “Graphics” “Best user interface … but not intuitive” “Comparing breeding strategies – helps with design for better genetic gain” “Improves understanding of the GE system”

6. Comments from participants Weakness 6 “Complex inputs” “The learning curve is steep” “Additional guides are necessary” “Complex” “Definition of the breeding program” “Requires a better understanding of the breeding procedure” “Large number of simulation cycles require more powerful computers to reduce time”

7. Comments from participants Other comments 7 “A very promising tool, however time allotted for this workshop was insufficient for good demonstration” “Go ahead with the breeding program design tool” “Breeding program design tool looks easier way to build [strategy] than the text editor” “Economic integration for good assessment in financial terms” “Time limitation/constraints for workshop presentation to grasp procedures ” “Too much information in a short time”

8. Summary Simulations Tools 8

9. Interface 9 Familiar Windows-like environment, graphics and links to pipeline BUT complex and not-necessarily intuitive

10. Usability 10 Most participants recognized that simulation: Enhance understanding of GE system and program Can evaluate multiple options Improve efficiency of breeding programs And tools had significant and powerful functionality However: Complex inputs make difficult to specify simulations Improved tools are required to document breeding strategies Computing power maybe limitation

11. Other comments 11 Insufficient time to adequately cover material in the workshop Links to tools to allow economic evaluation of breeding strategies would be useful Inclusion of templates for standard breeding methods

12. Future… 12 Integration with GenStat output via FlapJack currently allows importation of much of the information required to specify genetic-environment system Require better tools to aid description and definition of breeding programs (may be useful per se) Development of templates Explore options for integration with iPlant infrastructure to allow large simulations Linkage with costs to evaluate strategies both in terms of genetic gain and cost Work with Use-Cases to apply simulation tools to answer strategic and tactical questions about design and implementation of breeding programs.

13. Roles of simulation team 13 Undertake ‘strategic’ simulation analyses e.g. Assessing potential of marker-assisted selection in different types of trait, gene, environment systems Provide service to use case scientists Put results of QTL analyses into a simulation format Help use-case scientists to design and evaluate options for Design of breeding programs (BPDTool) Assessing simulation results, given different assumptions about genetic models controlling ‘unknown’ QTL effects (Excel template and GenStat/FlapJack tools) Contacts: Adrian Hathorn, Scott Chapman, Jiankang Wang, Mark Dieters