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(1 st September 2014) Appropriate Technologies and Innovative Approaches for Agriculture Knowledge Sharing-II Rajeev Varshney and PVNS Prasad ICRISAT Breeding Data Management Integrated Breeding Platform Breeding Management System (BMS)

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Page 1: ICRISAT Breeding Data Managementksiconnect.icrisat.org/wp-content/uploads/2014/09/day1... · 2014-09-06 · ICRISAT Breeding Data Management Integrated Breeding Platform Breeding

(1st September 2014)

Appropriate Technologies and Innovative Approaches for Agriculture Knowledge Sharing-II

Rajeev Varshney and PVNS Prasad

ICRISAT Breeding Data Management

Integrated Breeding Platform

Breeding Management System (BMS)

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ICRISAT uses Integrated Breeding Platform as its data management software

Open Source & Free

Available to NARS

A ‘one-stop-shop’ where breeders can access:

Databases (germplasm, pedigree, phenotypic, genotypic)

The Breeding Management System (BMS) • Logistics and data management tools • Breeding planning and management tools • Statistical analysis tools • Breeding decision support tools

High throughput genotyping services Electronic Data Capture Tools Breeders networks to share ideas and experience

Breeding Data Management

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Germplasm and phenotypic database

• Phenotyping database being redesigned for optimized breeding use

Crop information system and tools

Genealogy management & intl. nursery system

Maize Fieldbook and Maize Finder query tool (conversion of Excel-based tool to Java application)

GDMS genotyping database (Developed at ICRISAT)

Collaborative work with several partners involved (CGs, ARIs)

Multiple tools developed by CGIAR Centres

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https://www.integratedbreeding.net/

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Breeding Management System

Breeding Activities

Parental selection Crossing Population development

Germplasm

Management

Open Project Specify objectives Identify team Data resources Define strategy

Project

Planning

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

Administration Project conf.

Workbench

administration

&

configuration

Breeding

Management

System

Trial Fieldbook Environment characterization system

Field Trial

Management

System

Genotypic

Data

Management

System

Sample

management

Analytical

Tools

Sel. Indices Breeding App. MARS App. Cross Prediction Simulation

Decision

Support Tools

Breeding Applications Analytical Pipeline

Breeding mana. Genealogy mana. Query tools

Sample mana.

Data management Statistical analysis Molecular Genetic

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Simple and easy to use application containing all 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 DB on a local PC

Will also be implementable through the internet via iPlant

• For computationally intensive analyses or large data storage needs

BMS - Product Concept

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Installation of the BMS involves:

• Register for software

• Download and Install BMS infrastructure files

• Download and Install BMS Applications

• Download and Install Selected Crop Databases

• Download and Install Documentation Files

Download and Install the BMS

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Launching the workbench will display a splash screen while the

workbench starts Tomcat and MySQL.

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The Home screen of the BMS will be displayed after a successful login

where existing programs are displayed.

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The List Manager is at the center of all activities in the Breeding Management System:

• First screen you arrive at after opening your Breeding Program

• New left navigation menu provides direct access to all tools

• Easily build and work with the lists that are used in each stage of the breeding cycle

Key List Manager Features:

• Ability to browse and modify existing lists

• Ability to search for lists and germplasm entries

• Ability to create a new list dynamically by pulling from existing lists or germplasm search results

• Expanded ability to modify list contents

• Ability to export lists for use outside of the Breeding

Management System

List Manager Functionality

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List Manager allows to browse and search existing lists from the program and public databases. It also allows to create and save new germplasm lists to the program database

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Once the strategy and parental material have been identified, the breeder wants to:

• Make crosses

• Develop populations

• Track pedigrees

• Track inventory

• Characterize lines

Breeding Logistics

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Breeding Manager configured for different crops:

• Crossing manager, nursery manager, pedigree recording

• Focuses on population development and line selection

• Nursery advance and seed inventory tracking

IB Fieldbook:

• Focuses on field trial management for germplasm evaluation

• Trait selection, field design, labels and sample tracking

Android-based hand-held device:

• Optimized for use with Samsung Galaxy tablet for field data collection

• Other Android devices can be used if preferred

Breeding manager and Field books fully integrated into

BMS workbench

Nursery and Trial Management

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Once populations are developed, the breeder wants to:

• Select traits

• Make lists of germplasm

• Generate designs

• Produce Fieldbooks

• Collect data

• Check and store data

Field Testing

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Breeding Management

Trait Dictionaries

Measurement Variate

Trait property

Reporting units or scale

Measurement method

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Breeding Management - Trait Selector

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Select the desired Germplasm list from the program or public database or import a germplasm list from an external source

Breeding Management Upload Germplasm List

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Breeding Management - IB Fieldbook

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Specify the trial design from the drop down menu or import design from a layout file

Breeding Management Trial Design

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Breeding Management Tablet Devices

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At the outset of a breeding cycle users want to:

• browse all germplasm information

• review existing characterization and evaluation

• search for adapted germplasm

• perform head to head comparisons

Query Tools

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Select population

Select markers

Genotype population

Check and store genotyping data

Genotyping

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Example –

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Genealogy Management System (GMS)

• Germplasm nomenclature, chronology, IP and passport data

• Pedigrees and breeding history

Phenotyping Data Management System (DMS)

• Germplasm characterization and evaluation data

• Annotated with Crop Research and Crop Trait Ontologies

Genotypic Data Management System (GDMS)

• Medium density fingerprinting data

• Genotyping data for MAS and MABC

• Genotyping data for Marker-trait association analysis

Databases fully integrated into BMS workbench

Integrated Breeding Database

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Breeding View provides easy access to the high throughput analyses routinely required by breeders

The same interface can be used to access procedures in Genstat or R-scripts and allows analyses to be configured

Single site analysis is available for complete and incomplete block designs as well as row-column designs and spatial analysis. New designs are being added at each update,

Analyses can be run in batches over environments and traits,

Two-stage multi-site analysis is available for GxE and stability analysis with or without grouping of environments,

Single pass meta analysis of unbalanced site by season data is being incorporated.

Statistical Analysis of Phenotyping Data

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Analytical tools – Breeding View

Single site analysis workflow

QTL analysis workflow

Configurable steps

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Breeding Decision support –

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 MABC

context

Decision support for Marker

implementation

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Continuous improvement of UI based on user feedback

Additional analysis methods for expanded experimental designs and genetic analysis

Seed inventory management system

LAN and cloud based deployment

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

Future Directions

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Bioinformatics - Trushar Shah

Biometrics - Abhishek Rathore

User inputs - Breeders and Genomics @ ICRISAT

Collaborators - Mark Sawkins, Arllet Portugal, Graham McLaren, Xavier Delanney, Efficio

Funding - Integrated Breeding Platform (IBP), ACIAR and DBT, Government of India.

Acknowledgements

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Thank you!

ICRISAT is a member of the CGIAR Consortium