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

Breeding Management System: the key product of the IBP

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

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.

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

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

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

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:

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

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

Genotyping data and applications in the BMS and supported by GCP

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

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

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 Datapoints2010-2011 22848 4981920 41760 53171522011-2012 31720 3817150 12712 40665742012-2013 34787 4175378 9127 33880712013-2014 43093 3922150 14463 3039257TOTAL 132448 16896598 78062 15811054

GCP (Direct) GCP (Indirect)

GDMS – Current functionality

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

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

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

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

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

Future directions

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

IBP/BMS Users

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

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

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

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

IBP Phase II proposal

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

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

Challenges and perspectives

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?

♦ 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

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.

Thanks!