The document discusses the Breeding View, a statistical analysis tool integrated into the Breeding Management System (BMS) developed by the CGIAR Generation Challenge Programme. It provides a user-friendly interface for conducting phenotypic and genotypic data analyses, addressing the complexities of existing software by offering standard analyses suited for breeders' routine needs. Ongoing updates will enhance functionality, include new field designs, and allow user contributions of R scripts.

1. The Breeding View:
Statistical analyses in the Breeding
Management System (BMS)
An initiative of the CGIAR
Generation
Challenge Programme (GCP)
Mark Sawkins
Plant and Animal Genome
2015
San Diego, CA

2. Breeding View – what it is?
 Simple graphical Interface to conduct statistical analysis of
phenotypic and genotypic data
 Can access procedures in Genstat or R-scripts and allows analyses
to be configured
 Integrated into the IBP Breeding Management System (BMS)

3. The Breeding Management System is a comprehensive, all-in-one suite of tools to
effectively manage your breeding activities throughout all development phases of
your programs, from project planning to final decision-making:

4. Breeding View – Rationale for
development
 Existing packages are complex
Many features that are not relevant
Steep learning curve
Focus on publication ready graphics
 Majority of Breeders have specific, routine
requirements
Standard set of analyses
Push lots of data quickly
 BV provides a choice of statistical engine
(Genstat or R)

5. Current analysis pipelines

6. Statistical Analysis of Phenotyping Data
 Single site analysis is available for complete and
incomplete block designs as well as row-column designs
and spatial analysis.
 New designs are being added at each update,
 Analyses can be run in batches over environments
and traits,
 Two-stage multi-site analysis is available for GxE and
stability analysis with or without grouping of
environments,
 Single pass meta analysis of unbalanced site by
season data is being incorporated.

7. Statistical analysis of Genotyping Data
 Single trait linkage analysis (QTL)
 Quality control phenotypes
(summary statistics)
 Quality control marker data
 QTL detection – genome wide scan
using single and composite IM
 Output includes profile plots and
tables
 Results available for automatic
viewing in Flapjack
 HTML report of QTL results
 Multiple trait & environment
sequential analysis
 QTL results for each trait combined
 Single Flapjack view for all traits

8. Accessing BV from the BMS

9. Accessing BV from the BMS

10. Accessing BV from the BMS

11. Accessing BV from the BMS

12. Accessing BV from the BMS

13. Accessing BV from the BMS

14. Running an analysis in BV

15. Output from BV

16. Saving output to the BMS

17. To Come
 Ongoing updates to the Genstat and R scripts to
support new field designs and analysis types as
they are added to the BMS
 Additional field designs (e.g. Augmented, P-rep)
 Line x Tester analysis
 All pipelines fully integrated in BMS
 Addition of new pipelines (e.g., multi-site/multi-
year analysis
 Incremental improvements to output and reports
 Improved documentation for all pipelines

18. To come
 Ability to add user/community developed R-
scripts to BV
 Want to know more?
www.integratedbreeding.net
 Questions about licensing?
s.andrews@cgiar.org

19. Thanks!