1. Data Flows in Integrated
Breeding
Graham McLaren

2. Principles of DM for Integrated
Breeding (IB)
 IB requires high standards of sample and
pedigree identification,
 it requires integration of field and lab data,
 and quality is of paramount importance.
 Data collected during breeding processes
has immediate value for breeders and
 it also has cumulative value over years and
populations.

3. Information Cycle for Crop Improvement
Genetic Genomics
Resources Public Crop Information and
Information accessible via internet Genetics
Systems Databases
Crop Lead Centers
Curation, integration and publication
Community of Practice
Breeding Informatics
of Public Crop Information
Institutional National Project Private
CIS CIS CIS CIS
Shared Information management Practices
ARI NARS Networks SMEs
Local CIS Local CIS Local CIS Local CIS

4. Compatibility of DM Schemes
 Users may have existing DM systems which
need to be accommodated.
 DM needs to be compatible across all members
working on the same project.
 Use of analysis and decision support tools and
sharing of data with partners requires data to be
formatted and stored in defined ways.
 Training and support in DM and analysis is
essential for IB projects

5. Breeding Data Flows
Breeding Partner 1 Breeding Project 1
Breeding Partner 2 Breeding Project 2
Breeding Partner 3 Breeding Project 3
Breeding Partner n Breeding Project n Public
Project data Crop
Breeding management Information
data Copy of Project database
management Project shared Crop lead Center n
Database Public Central database
Breeding Partner 1 < shared and published >
Database
Local Project Public Crop
Breeding Data Central
Data Update to project
database Database
Data manager (DM): Project data curator: Central DB curator:
•Database management •QA for project data •QA for public data
•Breeding logistics •Curation and integration •Curation and integration
•Fieldbook preparation •Distribution to partners •Distribution to projects
•Data entry/checking •Project Trait Dictionary •Publication on Internet
•Data management •Fieldbook Templates •Global Trait Dictionary
•Update to public DB •Catalogue of Templates
•Download of public DB •Training of DMs and
•Training of partner DMs Curators

6. Interaction of breeding workflow and platform elements
LIMS MSL High density
GRSS ST genotyping
Genetic Resources FDM TSL
Phenotypic
Key characterization
Information System A&DS
Choose parental material based on haplotype
Sample Parental Material
ST values, known genes, traits and adaptation
Tracking
Develop crossing scheme based on genotype
Breeding Information system
PIM Pedigree
Information A&DS and phenotype compatibility
Public Crop Information
LIMS Laboratory Crossing Block Pedigree information updated
Information PIM
FDM Field Data High density
Analysis & LIMS MSL genotyping
A&DS Decision ST
Nursery 1 FDM TSL Phenotypic
Support
Platform Services evaluation
Genetic Selection of lines based on QTL analysis /
Resource A&DS estimation of marker breeding values
GRSS Service
Nursery 2 Pedigree information updated
PIM
Marker
MSL Service n cycles of selection Marker
ST LIMS MSL
and recombination genotyping
TSL Trait
Service
A&DS Selection on index of marker values
Evaluation Trials Multi-location
GRSS ST FDM TSL
testing
Selection of improved lines based on trait
Cultivars A&DS improvement and adaptation
and
Improved Lines Pedigree information updated
breeding lines PIM

7. The IBP Configurable Workflow System
Breeding Activities
Project Germplasm Germplasm Molecular Data Breeding
Planning Management Evaluation Analysis Analysis Decisions
Open Project Quality Assurance
Parental selection Experimental Design Marker selection Selected lines
Specify objectives Trait analysis
Crossing Fieldbook production Fingerprinting Recombines
Identify team Genetic Analysis
Population Data collection Genotyping Recombination
Data resources QTL Analysis
development Data loading Data loading plans
Define strategy Index Analysis
Breeding Field Trial Genotypic Data Decision
Breeding Project Analytical
Management Management Management Support System
Planning Pipeline
System System System
MB design tool, MABC
Cross prediction Breeding nursery Trial field book Lab book, Statistical analysis MAS
and Strategic and pedigree and environment quality assurance applications and MARS
simulation record characterization and diversity selection indices GWS
management system analysis
Breeding Applications

8. The Breeding Management
System
Breeding
Management
System
Genotypic Data
•Nursery Management Management
•Characterization lists System
ST •Pedigree maintenance
•Evaluation lists Field Trial
•Seed Inventory Management
System

9. Sample
ST
Tracking

10. Genotyping Data Management
System
Genotypic Data
Breeding Management
Management
System
System
Characterization •Planting list
lists
•Sample list
Analytical
ST LIMS Pipeline
•Genotyping Data Data Transformation
-Genotyping Database
•Quality Assurance -Application file formats

11. Tracking Genotyping
ST
Samples

12. LIMS Genotyping order form

13. LIMS Genotyping results:

14. Field Trial Management
System
Field Trial
Breeding Management
Management Analytical
System
System
Pipeline
Evaluation lists •Fieldbook Experimental
design and
preparation randomization
CWS Data Collection
Configuration -Hand-held devises
System -Automatic measurement
Trait templates •Environmental
characterization Data Transformation
-Phenotyping Database
•Quality Assurance -Application file formats
•Phenotyping data

15. The Trial Template

18. Analytical Pipeline
Genotypic Data
Analytical
Management Pipeline
System
Decision Support
Tools
Genotyping data •Genotyping QA
•Diversity analysis Diversity scores
•Genetic mapping Pedigree trees
COP matrices
Field Trial •Phenotyping QA Phenotype means
Management
System •Single site analysis Genotype BLUPS
Stability measures
•Multi site analysis Adaptation scores
Phenotyping data •GxE Analysis Marker scores
Genetic distance
•QTL Analysis Genetic maps
•QTLxE Analysis QTL estimates

19. LIMS Genotyping scores:

20. Decision Support and
Simulation
Breeding
Decision Support Decisions
Tools
Analytical
Pipeline Germplasm lists for
characterization
•MBDT Foreground markers
Diversity scores •Breeding indices Background markers
Pedigree trees Target genotypes
COP matrices •OptiMas Donor germplasm
Phenotype means Recipient germplasm
Genotype BLUPS Ranked germplasm
Stability measures Selection lists
Adaptation scores Simulation Parental lists
Marker scores Tools Crossing schemes
Genetic distance
Genetic maps Population sizes
QTL estimates Selection intensity
Marker densities
•QuLine Crossing schemes
•QuHybrid Selection schemes
Genetic models
GE systems •QuMARS
Trait selection
Breeding methods •QuGene GE targeting
Optimal breeding
systems

21. ICIS COP matrix
Lower Triangular part of Coefficient of Parentage Matrix
ROWID COLID ROWNO COLNO COP Optional Labels
50533 50533 1 1 0.9577 "IR 64" "IR 64"
70125 50533 2 1 0.2231 "IR 72" "IR 64"
70125 70125 2 2 0.9896 "IR 72" "IR 72"
11105 50533 3 1 0.1872 "IR 36" "IR 64"
11105 70125 3 2 0.5108 "IR 36" "IR 72"
11105 11105 3 3 0.9478 "IR 36" "IR 36"
Lower Triangular part of Inverse Coefficient of Parentage Matrix
ROWID COLID ROWNO COLNO INV-COP Optional Labels
50533 50533 1 1 1.1113776 "IR 64" "IR 64"
70125 50533 2 1 -0.1900738 "IR 72" "IR 64"
70125 70125 2 2 1.4324875 "IR 72" "IR 72"
11105 50533 3 1 -0.1170834 "IR 36" "IR 64"
11105 70125 3 2 -0.7344297 "IR 36" "IR 72"
11105 11105 3 3 1.4739708 "IR 36" "IR 36"

22. Flapjack QTL Information File
Compulsory Fields
QTL
Chromosome
Position
Minimum
Maximum
Trait
Experiment
Optional Fields
AddEffects
AddSE
Minlog10(P)
%VarExplained
PosMinFM
PosMaxFM
LFM
RFM

23. Flapjack Map Data
The map file should contain
information on the markers,
the chromosome they are on,
and their position within that
chromosome. The markers do
not need to be in any particular
order as Flapjack will group
and sort them by chromosome
and distance once they
are loaded.

24. Breeding program designer
Blue/gray – strategy + add new object at next level
Green – Generation X delete object
Yellow – selection round clone object
Pink/red – trait selection step
• To start, open ‘BreedingProgram.jar’
• Can create/drag/drop any new objects anywhere
• Use left mouse click to drag any piece and drop on higher hiearchy
• Use centre mouse click to zoom
• Edit in list/value boxes to set parameters
Scott Chapman

25. Available breeding simulation
tools
 QuLine, a computer software that simulates
breeding programs for developing inbred
lines
 QuHybrid, a computer software that
simulates breeding programs for developing
hybrids
 QuMARS, a computer software that
simulates marker-assisted recurrent
selection and genome-wide selection
Jiankang Wang

26. What can QuLine do?
 Comparison of genetic gains from different selection
methods
 Change in population mean
 Change in gene frequency
 Change in Hamming distance (distance of a selected
genotype to the target genotype)
 Comparison of cross performance
 Selection history
 Rogers’ genetic distance
 Number of lines retained from each cross
 Comparison of cost efficiency
 Number of families
 Individual plants per generation
 Validation of theories
Jiankang Wang

27. Integrating the applications of the Configurable Workflow System
Field Trial Genotypic Data
Breeding Genotypic Data Management Analytical Decision Support
Management
Management Management System Pipeline Tools
System
System System
•Genotyping QA
•Planting list •Fieldbook •Planting list •MBDT
•Diversity analysis
•Sample list preparation •Sample list •Breeding indices
•Genetic mapping
•OptiMas
LIMS •Phenotyping QA
•Nursery Management Data Collection •Single site analysis
•Characterization lists -Hand-held devises •Multi site analysis
•Pedigree maintenance •Genotyping Data -Automatic •GxE Analysis Simulation
•Evaluation lists •Quality Assurance •Genotyping Data Tools
measurement •QTL Analysis
•Seed Inventory •Quality Assurance
•QTLxE Analysis
•Environmental
•QuLine
characterization
•QuHybrid
•Quality Assurance
•QuMARS
•Phenotyping data
•QuGene
GMS DMS GDMS