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Objective 2.2 Applications of the CWS

Functionality Table for the Integrated Breeding workflow System (IBWS)

Breeding Activity Applications Tools
Integrated Breeding Workflow Management
The Integrated Breeding workflow system is a stand-alone
information management system comprised of the
IB Database and the Workbench which supports six major
 kind of breeding activities, each consisting of several
applications with corresponding tools that support those
breeding activities from project planning to decision making.
IB WorkBench - Administration
Installation of public crop databases. Set up and
management of private local data bases and IB
Workbench with access control and project
management.

  IB Workbench - Project Configuration
For each breeding project defined in a particular
workflow installation, specify and manage the
breeding workflow, breeding and testing locations,
team members, naming conventions, breeding
methods, trait templates, and specific
application settings.

  Database access and workflow management
Underlying infrastructure of the workflow
system supporting data storage and
connectivity between applications.

1) Project Planning
Breeders can compare breeding strategies for different
breeding situations and query historical germplasm
characterization and evaluation data to select parents,
donors and recipients
Breeding Planner
Interactive tools to compare breeding strategies
for genetic gain and well as resource requirements.
  • Compare breeding strategies
  • Timelines and resources
  Query Manager
Query tools to facilitate review of historical
data by germplasm, nursery and trail and by
filtered queries across all evaluation records.
2) Breeding Management
Breeders manage the logistics of population development
and capture characterization data, pedigree information
and seed inventories.

Germplasm information including origin, pedigree,
nomenclature, breeders' rights and IP restrictions is
managed and accessible so that it can be used for
diversity analysis and improved phenotypic predictions.

Breeding Manager
Applications to facilitate population development
including hybridization, characterization through
nurseries, selection and population advancement.

  Seed Inventory Manager
Seed inventory data captured during population
advancement or trial harvests in managed through
 an inventory management system supporting
acquisition, reservation and disbursement,
shipping and quality testing.

  • Seed acquisitions
  • Seed reservation
  • Shipments
  • Quality assurance
  Geneaology Manager
Pedigree information for imported germplasm
can be added to the database. Pedigrees of
breeding lines can be connected to imported
lines and edited when new information is available.
Coefficients of parentage can be calculated
and analysed.

3) Field Trial Management
Breeders can prepare entry lists and checks and merge
these with trait templates and field lay-outs to produce
fieldbooks for single site and multi-environment germplasm
evaluation. Environmental conditions can be recorded
and used in the interpretation of evaluation trials.
IB Field Book
A user friendly wizard interface merges germplasm
lists with trait templates and field lay-outs to
produce fieldbooks. Collected data is imported,
checked and stored in the IB Database for
analysis and interpretation.

  • Trial Entry List preparation
  • FieldBook preparation
  • Experimental Design
  • Label preparation
  • Data Collection
  • Seed Inventory tracker
  Data Collection
Fieldbooks can be exported for data collection
by printing or transfer to a variety of hand-
held devices.
  • Report generator for printed fieldbooks
  • Export to a variety of hand-held device options
  Environment Characterisation
Site and environmental characterization data
available for interpretation of GxE interaction
and identification and demarcation of Target
Populations of Environments.
  • Site Characterisation
  • Soil Data
  • Climate Data
  • Socioeconomic Data
4) Genotypic Data Management
Breeders have access to fingerprinting data for potential
parents connected to genetic maps showing marker-
trait associations.

Breeders manage genotyping data for marker assisted
breeding, quality control and diversity analysis.

Sample Management
Germplasm and marker lists are merged to
produce Labbooks which ensure rigorous
sample tracking for requesting marker analysis.
Data is imported from completed Labbooks
and connected to the correct sample records.

  Marker Queries
Users can review polymorphic markers for
parental sets and select marker sets for
population evaluation and trait integration.
For a given trait select diagnostic markers.
5) Analytical Pipeline (overview)
The IBP CWS provides three separate ways for breeders
to analyse data generated as part of their experiments
(see below). The full integration of the analytical pipelines
 into the CWS will allow the seamless flow of data from
the databases to the statistical applications and from
those to the breeding decision tools without needing a
manual intervention by the breeder.
   
5a) Analytical Pipeline - Breeding View
Breeding View results from a collaboration between
the IBP and VSNi, the company behind the development of
GenStat. It provides access to the main statistical
functions available in GenStat, but via a simplified,
breeder-friendly interface arranged along an analytical
workflow. Following an initial free period, access to
Breeding View will require a license for some of the users
of the IBP CWS (to be further defined).
Phenotypic analysis
The phenotypic analysis part of the Breeding
View analytical workflow handles all the
typical statistical functions expected by
the breeders to analyse their phenotypic trials.
  • Quality control phenotypes
  • Derived and transformed variables
  • Single site phenotypic analysis
  • Single site mixed model analysis
  • Two stage Multi-site phenotypic analysis 
  Molecular genetic analysis
The molecular genetic analysis combines
the results of the phenotypic data with
corresponding marker data to perform a
QTL analysis to identify genomic regions
affecting key breeding traits. This is one
of the key steps for implementation of
marker-assisted recurrent selection (MARS)
in a breeding program.
  • Quality control genotypes
  • QTL analysis (SIM & CIM)
  • QTL x E
5b) Analytical Pipeline - R-scripts
The R-script analytical pipeline (R-AP) combines R-based
statistical functions developed by various collaborators
 into a comprehensive single application that provides
all the analytical options necessitated by the breeder.
It is based on open-source code and is meant to be
freely accessible as part of the IBP CWS. At this time,
the R-scripts are available as individual tools usable
by the breeders. They will be fully integrated into
the RAP Menu Interface by June 2013.

Phenotypic Data Analysis
The phenotypic analysis part of the R-AP
workflow handles all the typical statistical f
unctions expected by the breeders to
analyse their phenotypic trials.

  Molecular genetic analysis
The molecular genetic analysis combines
the results of the phenotypic data with
corresponding marker data to perform a
QTL analysis to identify genomic regions
affecting key breeding traits. This is one
of the key steps for implementation of
marker-assisted recurrent selection
(MARS) in a breeding program.
5c) CIMMYT R-scripts in Fieldbook
In response to requests by CIMMYT breeders, the IBP is
 integrating existing R-scripts that are currently part of
the CIMMYT maize fieldbook into the IB Fieldbook so
that statistical analysis can take place directly from
the fieldbook if the breeder desires, rather than through
the separate analytical pipeline. Depending on the needs,
either option may make sense and the final choice is
left to the breeder.
Phenotypic analysis
The IB Fieldbook R-scripts will only
handle phenotypic analysis of the
type currently needed by the
CIMMYT breeders.
  • Single site mixed model analysis
  • Single site mixed model analysis
  • Multi site mixed model analysis
  • Multi site mixed model with spatial adjustment 
  • Line X tester mixed model analysis
6) Breeding decision
The breeding decision tools help the breeder decide
which next steps to take in his project based on
the information generated from the previous
activities.
Selection Indices
With selection indices, breeders can
quantify the consequences of their
choices using different selection strategies.
Phenotypic: (Smith selection index, Restrictive
Kempthorne & Nordskog selection index, Eigen
Selection Index and Restrictive eigen selection
index)
Molecular: (Lande and Thompson selection index
and the Molecular Eigen Selection Index

  MARS application
The OptiMAS application allows the
 breeders to select the best individuals
to recombine in a marker-assisted
recurrent selection scheme based on
the QTLs that they want to recombine
to generate superior progenies.
  • Prediction of molecular value
  • Selection of "best" individuals
  • Identification of best crosses
  ISMAB (Marker Assisted Backcrossing tool)
The MBDT application helps the breeder
in selecting, based on marker data,
the optimum plants to cross at each
generation of a marker-assisted backcrossing
project in order to quickly transfer a target
trait into a recipient parent.
  • Import a list of germplasm
  • Create a target ideotype
  • Identify recurrent and donor parent
  • Select background and foreground markers
  • Numbers of individuals to be genotyped 



Color Key

  • Currently available tools
  • Tools projected to be available by Dec 2012
  • Tools projected to be available by June 2013
  • Tools with no specific timeline for development at this time.

Old Applications page

Activity 2.2.1 IB Workbench
Activity 2.2.1 Tool 1.2 Backup
Activity 2.2.1 Tool 1.2 Upload
Application 2.2.1 Tool 2.4 - Breeding Methods
Application 2.2.1 Tool 2.5 - Naming Conventions
Application 2.2.1 Tool 2.7 - Trait Dictionaries for Fieldbook Development
Application 2.2.1 Tool 2.10 - Database
Application 2.2.1 Tool 2.11 - Middleware
Application 2.2.1 Tool 2.11 - Workflow Management
Application 2.2.1 Tool 2.12 - Data Exchange Protocol
Application 2.2.2 Breeding Manager
Application 2.2.2 Tool 3.1 Germplasm Browser
Application 2.2.2 Tool 3.2 Study Browser
Application 2.2.2 Tool 3.4 Table Viewer
Application 2.2.2 Tool 3.5 Breeders Queries
Application 2.2.2 Tool 4.1 - Germplasm Import
Application 2.2.2 Tool 4.1 Pedigree Import Tool
Application 2.2.2 Tool 4.2 Pedigree Editor
Application 2.2.2 Tool 4.3 - Seed Inventory
Application 2.2.2 Tool 4.4 - Germplasm Lists
Application 2.2.2 Tool 4.5 - Crossing Block
Application 2.2.2 Tool 5.2 - Nursery Book
Application 2.2.3 Tool 5.3 IB Fieldbook
Application 2.2.4 - Progeny Selector
Application 2.2.4 Tool 6.3 - Genotyping Data Manager
Application 2.2.5 Analytical Pipeline
Application 2.2.5 Tool 7.0 AP Menu
Application 2.2.5 Tool 7.0 Derived Variables
Application 2.2.5 Tool 7.0 Phenotypic Data Analysis
Application 2.2.5 Tool 7.8 Genetic Map Construction
Application 2.2.5 Tool 7.10 QTL Analysis
Application 2.2.5 Tool 7.13 Molecular Selection Indices
Application 2.2.5 Tool 7.13 Phenotypic Selection Indices
Application 2.2.5 Tool 7.13 Selection Indices
Application 2.2.6 Simulation Tools
Application 2.2.6 Tool 8.0 ISMAB
Application 2.2.6 Tool 8.2 Molecular Breeding Design Tool
Application 2.2.6 Tool 8.5 - OptiMAS
Application 2.2.6 Tool 8.7 Cross Predictor Tool
Objective 2.2 Applications of the CWS Old Page
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