1. Data Management for 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. Three Types of Data for IB
parents
1) Genealogy or pedigree data
unique identification of germplasm through Germplasm IDs (GID)
names

4. 3 Types of Data 2) Phenotypic data
observable characteristics or traits
3 Types of Data
2) Phenotypic data
environmental
data across studies are linked via controlled trait vocabularies / standard terms

5. 3 Types of Data 3) Genotypic data genetic composition
 usually with reference to a specific trait under consideration

6. Sh. A. R. P. Importance of Data Management
Data that are properly managed are:
Sh. A. R. P.

7. Sh = Shareable Importance of Data Management
Data that are properly managed are: Sh
more accessible to research partners
national and global sharing & linking of data

8. A Importance of Data Management Data that are properly managed are:
= Available
enables reliable analysis & conclusions
leads to better science & more sophisticated research

9. R Importance of Data Management Data that are properly managed are:
= Re-usable
more likely to be used again for different purposes

10. P Importance of Data Management Data that are properly managed are:
= Preservable
 important for historically significant data
 scientific method changed to: hypothesize , then look up answer in database

11. Sh A R P Importance of Data Management
Data that are properly managed are: Sh
areable A
vailable R
e-usable P
reservable

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

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

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

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

16. A Simple Workflow for the Cassava Tutorial
1. Search for Germplasm
Search a particular germplasm by name from the database
Understand the information about germplasm entries contained in the ICASS database.
2. Import Parental Lists
MALE2009
FEMALE2009
Set of 12 female parents and 12 male parents (some repeated) with high protein content and CMD Resistance
There were will be two lists created. One for female parents and another one for male parents
3. F1 Nursery
NR2009F1
( )
F1s planted
12 crosses made from the female and male parents
4. Clonal Propagation
NR2010C1
283 plants developed through clonal propagation
Derive 284 plants from the F1 through clonal propagation
5. Selected Clones
NR2011V1
25 selected from the initial list of clones
Select 25 individuals from the initial clones for traditional clonal increase
6. Field Trial
The selected clones will be tested in the field for evaluation
There will be 3 locations and 3 reps in RCBD

17. Running the Cassava Tutorial