2010 06 07-11 Integrated Breeding Platform Analysis Workshop

• Program
• Final Logistics for Zaragoza Workshop
• Appendix 1
• Appendix 2
• Presentations
• Group Picture
• List of Participants - Data Analysis Workshop

Data Analysis Workshop (DAWS)

GCP-IBP
Zaragoza, Spain
June 7-11, 2010
Fred van Eeuwijk & Marcos Malosetti

Objectives
The objective of the workshop is to establish statistical support network for the Integrated Breeding Platform. This will involve agreeing to a set of core statistical procedures to support molecular breeding, reviewing analytical tools and training material covering those procedures, setting out a workplan to fill gaps in methodology and training material, establishing a timetable for training users of the IBP in these procedures and mechanisms for supporting users. Staff from Biometrics (WUR) will present methodology and training material on QTL, GxE, QTLxE and Association analysis using the Genstat Statistical package. Participants should consult with breeders to understand their needs and bring detailed information on current systems being used in their own institutes and projects including information on available training materials.


Background
IBP project 3.2.4 aims at supporting IBP user cases in the field of statistics and quantitative genetics, as well as developing training material and tutorials to assist new users when they join the platform. The project includes training in data generation, handling, processing and interpretation, as well as experimental design from field planting to MAS and MAB schemes. It provides assistance with the 'translation' of the molecular context to the breeding context and it will take care that the methodology developed for design and analysis of breeding trials is rapidly available to the users.
At the last GCP-IBP launching workshop in Hyderabad, February 2010, the planning for project 3.2.4 was discussed. As a reaction to the presentation of the plans by WUR, the PI of 3.2.4, various quantitative researchers expressed a desire to be involved in the setting up of a training network for courses on quantitative aspects of breeding research. Such a network would on the one hand be part of 3.2.4, but on the other hand should transcend 3.2.4. After a fruitful discussion, it was decided to plan a next IBP workshop in which the joint development of training material and a training network would be further discussed. The Zaragoza meeting is the follow up to the discussions in Hyderabad. The objectives are described below.

Objectives of IBP Zaragoza Data Analysis Workshop

1. Defining the content of training courses supporting IBP user cases and activities
2. Decide on maturity and accessibility of methodological research/development in IBP project 2.2.1(Develop and deploy statistical and genetic analysis methodology for molecular breeding) for inclusion in teaching material
3. Decide on a course schedule for the near future supporting IBP user cases: topics, times, places, teachers

Activities
In relation to especially objective 1, Fred van Eeuwijk and Marcos Malosetti (WUR) will present lectures and practicals on QTL and association mapping. The DAWS attendants will act as students and judge the material as being suitable or not as a basis for teaching courses within the IBP. The attendants will evaluate the quality of the presentations, the written material, the software, the general didactics, the choice of topics, etc. The goal is to adjust the presented material so that it can be used by any of the DAWS attendants to serve as teaching material.
Another contribution to the content of teaching modules will be discussed on the basis of material to be presented by José Crossa (CIMMYT) on the phenotypic analysis of single and multiple trials, including the analysis of GxE. In relation to objective 2, José Crossa will also discuss material related to genome wide selection strategies. Further contributions on the evaluation of breeding strategies and simulation will come from Jiankang Wang (CIMMYT) and Scott Chapman (CSIRO). David Marshall (SCRI) will treat data visualization and exploration.
Any of the other DAWS participants who has teaching material on quantitative methods in relation to plant breeding and thinks that it may be useful to include part or the whole of that material in future IBP 3.2.4 courses is invited to prepare a presentation/demonstration. For the list of candidate topics, see Appendix 1.