1. The Breeding Management System
(BMS)
Product, Functionality and Users
An initiative of the CGIAR
Generation
Challenge Programme (GCP)
Mark Sawkins
2014 General Research
Meeting 7-11 October
Rayong, Thailand

2. Breeding Management System: the
key product of the IBP

3. Rationale for investing in the BMS
 Large private seed companies have successfully
implemented extensive suites of integrated informatics
tools to turbocharge their breeding programmes
 Implementation of this integrated informatics in public
programs lags behind, especially in developing countries
 Some tools have been developed at various CG centers, but
implementation has been uneven and they are not integrated
into a comprehensive system
 Most NARS programs still rely on rudimentary tools, from pen
and paper to Excel spreadsheets
 Small SMEs in developing countries typically do not have the
resources to acquire available commercial software or to
implement breeding IT systems on their own

4. Vision of the IBP
The IBP will provide a one-stop-shop where breeders can
access:
 high-throughput breeding services,
 logistics and data management tools,
 an intuitive analysis pipeline,
 breeding decision support tools,
 support to use these facilities and
 breeding communities of practice
in order to deploy molecular breeding technology for
sustainability and development.

5. Breeding Management System (BMS) –
Product Concept
 Simple and easy-to-use application containing all informatics tools needed
by a breeder
 Seamless flow of data between applications
 Accumulation, sharing and re-use of breeding data
 Targets routine breeding activities and will not replace research tools
 Will allow integration of users own tools into the system
 Implementable as a standalone system
 Access central and local database, as well as the BMS on a local PC
 Will also be implementable as a cloud-based system via iPlant cyber-
infrastructure
 For computationally intensive analyses or large data storage needs

6.  Breeding Planner
 tool for estimating duration of a breeding projects and resources required
based on crop parameters and breeding goals
 Phenotypic Crop Information System
 support selection of parental lines and management of phenotypic
information during breeding stage plan
 Seed Management System
 storage, distribution, planting and harvesting of seeds
 Field Book tool
 design and manage trials and nurseries
The nine key components of the BMS

7.  Breeding View
 statistical tool – for analysis of phenotypic and genotypic data
 Genotyping Data Management System
 support implementation of markers in breeding and new native trait
discovery projects
 Optimas
 Decision tool – to support selection of genotypes to be crossed or
advanced
 Genotyping visualization tools
 to make germplasm selection easier using graphical display
 Query tools
 for data search and quality control all along the system
The nine key components of the BMS

8. 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:

9. Product characteristics
The BMS is a flexible system with the guarantee
 New functionality can be added based on demand
 Individual BMS components and tools can be used ‘stand-
alone’
 The BMS runs on individual computer
 The BMS runs online through high performance cyber-
infrastructure
 Data privacy will be respected
 The majority of the tools and manuals will be available in
three different languages besides the current English version

10.  One on site support visit to familiarize and train users on how to use
BMS and migrate data
 Post implementation helpdesk for registered users
 Automatic updates and improvements to the BMS
 Discount service agreement for low-medium throughput genotyping
 Discount service agreement for sequencing provision
 Access to small genotyping grants (Genotyping Support Service) for
exposure to marker technologies
 Free access to seasonal private weather profile to better segment,
understand, analyze and interpret trial results
 Customization of the BMS to specific needs, including link to
customers’s existing databases or specific analytical tools
Support Services and supplementary
benefits

11. Genotyping data and applications
in the BMS and supported by GCP

12. Genotyping data in the BMS
 Typical IBP users may have little or no exposure to
molecular marker technology
 Are uncomfortable with using markers and may be
unfamiliar where and for what purpose markers can
be used in a breeding stage plan
 No ability or interest to invest in infrastructure to
support genotyping at their institute
 Provide access to preferentially priced genotyping
service for low to mid density SNP/SSR markers to
facilitate adoption and routine use of markers from
discovery to implementation

13. GCP Genotyping Services
 Access to third party commercial laboratories for
submission of genotyping projects at agreed
preferential prices supporting both discovery and
implementation projects
SNP – LGC Genomics
SSR – BecA & ICRISAT

14. GCP Genotyping Services
 SNP assays currently offered for 11 crops
 Range from 1-2k assays which are suitable for a range
of applications (genetic relatedness; MTA detection)
 New crops coming on board e.g. Lentil
Year Samples Datapoints Samples Datapoints
2010-2011 22848 4981920 41760 5317152
2011-2012 31720 3817150 12712 4066574
2012-2013 34787 4175378 9127 3388071
2013-2014 43093 3922150 14463 3039257
TOTAL 132448 16896598 78062 15811054
GCP (Direct) GCP (Indirect)

15. GDMS – Current functionality

16. Implementation of MAS in BMS
 MTA discovered in GCP projects
 Diagnostic markers available in public sector
 Can make readily available where SNP markers
are the same technology as our preferred
service provider (e.g. LGC Genomics)
 If another marker type (e.g., SSR) provide
information to users on KASPar markers
mapping closest to original MTA

17. Implementation of MAS in BMS
 Requires additional features/functionality
Support individual plant sampling in fieldbook
Retrieve and visualize in relevant places of
the BMS diagnostic markers for easy
selection and ordering
After genotyping results received upload to
BMS and visualize “translated” genotypes in
the fieldbook for use in progeny selection

18. Applications using genotyping data –
what’s currently available in the BMS
 Breeding View (discovery)
 OptiMAS (Implementation)
 MBDT (Implementation)
 Others external to the system but potential for
some level of integration
 IciMapping
 ISMU2-GS Pipeline

19. Breeding View - QTL analysis
 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 sequential analysis
 QTL results for each trait combined
 Single Flapjack view for all traits

20. Decision support for marker implementation
 OptiMAS
 Developed at INRA, Le
Moulon
 Implementation of markers in a
MARS breeding scheme
 Identify and track favorable
alleles through cycles of
recombination and selection
 Molecular Breeding Decision
Tool (MBDT)
 Developed by team at
ICRISAT
 Implementation of markers in a
MAS and MABC context

21. Future directions

22. Future Directions
 Continuous improvement of UI based on user feedback
 Additional analysis methods for expanded experimental
designs and genetic analysis
 Seed inventory management system
 Cloud based deployment available in late 2014
 Data will be stored in a single shareable database with
user access roles
 Off-line capability will be supported by a data cache
which will synchronize when a connection is available
 Language support

23. IBP/BMS Users

24. IBP Users
 Primary target:
 NARS partners wanting to enhance the effectiveness of
their breeding programmes by integrating molecular
methods and end-to-end informatics pipelines
 All interested CGIAR breeding programmes and networks
 SMEs working in developing countries, without the in-
house capacity to build a breeding workflow system
 Secondary target:
 Basically anyone running breeding activities
 Both the public and the private sectors

25.  Can use the complete system from end to end,
but
 Able to select what parts of the system to use
 No requirement to dispose of existing working
solution to use BMS – can be accommodated
and customized
 Open source nature of BMS permits
customization/modification. Use at own risk
Users

26. Categories of users of the BMS
 Champion – a breeder already using BMS in
their breeding program on a daily basis
 Early adopters – those willing to take the risk to
try early versions of technology
 User community - have been informed about
the BMS but may not use it regularly
 Potential users in both public and private sectors
 Stuart Andrews presentation Friday “Commercial
plans”
 Community and media – the rest of the world

27. Soliciting feedback from users
 Champions and early adopters with email
exchange and regular calls
 CIMMYT as preferred partner/user
 GCP/IBP organized courses and workshops

28. IBP Phase II proposal

29. Objectives
 To provide modern pedigree, phenotype and inventory data
management, data collection and decision support tools for cultivar
development to breeding programs serving SA and SSA
 IBP team to support key users in adoption of, migration to, and
customization of the BMS
 Integrate molecular marker information and genomic composition in
parental selection and cultivar development
 Provide professional development resources for students and
practicing breeders to improve plant breeding skills
 Provide access to a BMS that facilitates data sharing and can be
fully integrated with external technologies via a published, openly-
accessible web service API
 Provide access to breeding programs to professional service
providers who support, customize and maintain the BMS in a
sustainable way

30. Linking the BMS with other initiatives
 Delivering a high-density genomics breeder’s toolkit
(Genomics back office project)
 Consortium of CGIAR Centers and Cornell University
 Development of pipelines for analysis to “Operationalize” GWS and
GWAS analyses and provide to breeders digested results that they
can rapidly implement in breeding
 Lukas Mueller – Presentation Friday morning “Back Office Project”
 DArT – access to analysis pipelines and sequencing database
 Development of an Interoperable API to facilitate connection
among different informatics platforms (data sharing and
access to tools)
 Collaboration among key players (IBP included)
 Regular calls and meetings

31. Challenges and perspectives

32. Challenges and Perspectives
♦ Access to suitable tools and analytical pipeline is often
not a key limitation today
♦ Tool and technology development relatively easy
♦ Capacity in most target countries is increasing
significantly
♦ One of the real challenges is adoption of the tool
♦ What prevents/dissuades users from adopting a
particular technology?

33. ♦ Most people are reluctant or resistant to change
♦ Most changes can be implemented only by:
♦ Strong bottom-up demand
♦ Mandatory top-down decision
♦ Need to be open and ready to:
♦ Change the way you do business
♦ Dedicate time to learn new things
♦ Requires the buy-in of upper management of user institutions
♦ Must apply a proactive promotion with kick-off meeting at user institutions
♦ Stepwise approach by starting with the population of the DB
♦ Support must be: reliable, quick, local and adapted to the user profile
♦ One size doesn’t fit all!
Challenge to adoption – Human behavior

34. The way forward
 Version 3 of BMS released last month a single user
application (central and local database implementation)
 Version 4 of BMS a LAN version (Q1 2015) for small
group of breeders in one location with enhanced
functionality (central and local database implementation)
 Version 5 of BMS (Q3 2015) full data synchronization
and offline working capabilities. Roles and permissions
and a single database implemented. Marker support
targeted.
 More details of functionality to come will be listed on our
new IBP website.

35. Thanks!