IBP Simulation Tools WorkshopWageningen, June 2nd 2011

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Simulation Tools – Workshop4 Report

Structure of Workshop

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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?

Summary of Responses

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Use-friendly

Intuitive

Functional

Suitable

Recommend Use

0 10 20 30 40 50 60 70 80 90 100

NOYES

Proportion of responses (N = 16; Blank =“NO”)

Comments from participantsBest Features

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“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”

Comments from participantsBest Features

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“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”

Comments from participantsWeakness

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“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”

Comments from participantsOther comments

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“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”

Summary

Simulations Tools

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Interface

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Familiar Windows-like environment, graphics and links to pipeline

BUT complex and not-necessarily intuitive

Usability

10

Most participants recognized that simulation:Enhance understanding of GE system and programCan evaluate multiple optionsImprove efficiency of breeding programsAnd tools had significant and powerful functionality

However:Complex inputs make difficult to specify simulationsImproved tools are required to document breeding

strategiesComputing power maybe limitation

Other comments

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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

Future…

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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 simulationsLinkage with costs to evaluate strategies both in terms of

genetic gain and costWork with Use-Cases to apply simulation tools to answer

strategic and tactical questions about design and implementation of breeding programs.

Roles of simulation team

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Undertake ‘strategic’ simulation analysese.g. Assessing potential of marker-assisted

selection in different types of trait, gene, environment systems

Provide service to use case scientistsPut results of QTL analyses into a simulation formatHelp use-case scientists to design and evaluate

options forDesign 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