Integrated Breeding Platform - iPlant Pods

darkfryingpanΚινητά – Ασύρματες Τεχνολογίες

10 Δεκ 2013 (πριν από 3 χρόνια και 8 μήνες)

81 εμφανίσεις

Integrated Breeding

Platform (IBP)

Configurable Workflow System

Martha Narro, iPlant Collaborative

January 11, 2013


Slides from Xavier
Delannay

and Graham McLaren, CGIAR

Integrated Breeding Platform


IBP
-

a one
-
stop
-
shop where breeders can
access:


Databases (
germplasm
, pedigree, phenotypic,
genotypic and environmental)


A configurable workflow system (CWS)


Logistics and data management tools


Breeding planning and management tools


Analytical tools


Breeding decision support tools


High throughput breeding services


Support services to use these facilities


Scientific network

Integrated Breeding Portal

https://
www.integratedbreeding.net
/

IBP builds on existing tools already in
use by IRRI and other CGIAR breeders


Existing breeding management tools and related
DBs


ICIS Database schema and query tools


IRIS Crop Information System and Tools


IWIS
Genealogy Management & Int. Nursery System


Maize
Fieldbook

and Maize Finder Query Tool


ICRIS Molecular Biology Database


New Concepts: The IBP CWS will


be configurable for different crops and breeding strategies,


be workflow driven


leading users through breeding workflows,


h
ave a new user
-
friendly interface, and


will be available as stand
-
alone and as a web
-
based system.


Existing ICIS tools will continue to work with the CWS
until all functionality is replicated and improved

Who should be interested in
using the IB CWS
?


Starting late January 2013 the portal will be open
broadly to all scientists working in plant science, for
both the public and private sector


More specifically:


All CGIAR breeding programs and networks


NARS partners wanting to enhance the effectiveness
of their breeding programs by integrating molecular
methods


SMEs working in developing countries without the
capacity to build a breeding workflow system in
house

Breeding schemes

Project
planning

Population
development

Field trial
management

Statistical
analysis

Breeding
decision

Breeding with marker
-
assisted
selection (MAS)

Project
planning

Population
development

Field trial
management

Statistical
analysis

Breeding
decision

Genotyping

M
arker
-
assisted backcrossing
(MABC)

Project
planning

Backcrossing

Field trial
management

Statistical
analysis

Breeding
decision

Genotyping

M
arker
-
assisted recurrent

selection (MARS)

Project
planning

Population
development

Field trial
management

Phenotypic
analysis

Final
breeding
decision

Genotyping

QTL analysis

QTL
selection

Recombination
cycle

I
nventory of existing functionality

IB Database
V1


IB
Germplasm

database


Germplasm

nomenclature,
chronology
,

IP
and passport data


Pedigrees and breeding history


IB phenotypic database v1


Available for use as central database or local database


Databases crop
-
specific


Genotypic database (GDMS)
for management of low to
medium density genotyping data and MTA
data


Central database contains fingerprinting and MTA data for global use


Local database focuses on project
-
specific genotyping data


Germplasm and Phenotype Study
Browsers


Databases fully integrated into CWS workbench


I
nventory of existing functionality

Nursery and Trial Management


Breeding
M
anager
configured for
different crops


Includes crossing manager, nursery manager, pedigree recording


Focuses on breeding steps for 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 and data capture


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
CWS workbench


I
nventory of existing functionality

Analytical and breeding decision tools


Statistical tools available with the following options:


Access to
Genstat

while complete suite of tools is being developed


Temporary license to use cases while Breeding View is being developed


Breeding View

for user
-
friendly access to
Genstat

tools, focusing on
main functionalities needed by breeders and molecular breeders


R
-
based analytical suite


Most functionalities available now as standalone tools


To be linked together soon in Java
-
based R
-
AP user interface


Decision support tools:


R
-
based selection indices


OptiMAS

traces alleles by descent through breeding populations


Allows optimum recombination of lines with favorable alleles (MARS)


MBDT
-

MABC management tool

Tools to be integrated into the CWS by the end of
2012

Launching the workbench will display a splash screen.


The Workbench Dashboard will be displayed after a successful login.


The last opened project will be highlighted.



The Create New Project form allows the user to set the target Crop of the project.


The crop is then used to determine the central database for the project.


Users can set the Project Members, Methods and Locations used in the project.

A breeding workflow

Query Tools

At the outset of a
breeding cycle users
want to:


browse all germplasm
information


review existing
characterization and
evaluation


Project

Planning

Breeding Management

Query browsers

Germplasm browser

Study browser

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


make crosses,


develop populations,


track pedigrees,


track inventory,


characterize lines

Population

Development

Breeding Logistics

Breeding Management

Crossing Manager

Breeding Management

Nursery Manager

Breeding Management

Pedigree recording

Breeding Management

Inventory Manager

Field Testing

Once populations are
developed, the breeder
wants to:


select traits,


make lists of
germplasm
,


generate designs,


produce
fieldbooks
,


collect data,


check and store data.



Manage Field

Trials

Breeding Management

Trait Dictionaries

Measurement
Variate

Trait property

Reporting
units or scale

Measurement
method

Breeding Management

Trait Selector

Breeding Management

Germplasm List Manager

Breeding Management

IBP
Fieldbook

Breeding Management

Bar Code labels

Breeding Management

Tablet Devices

Fieldroid

Genotyping

To use molecular
technologies, the
breeder wants to:


select population,


select markers,


genotype population,


check and store
genotyping data.


Genotyping

IBP marker services


The new marker services concept based on high
-
throughput SNP genotyping was operational in 2011


Decision to focus on a single SNP genotyping provider
(
KBioscience
, UK)


SNP conversion to
KBioscience

platform almost complete


GCP funds the conversion of 1,000
-
2,000 SNPs for each crop of interest


Assays available to customers after that (between 8
-
10 cents/
dp
)


First set of genotypes fingerprinted as part of conversion process


SSR genotyping support still being provided by current labs as
needed


BecA


ICRISAT

Availability of SNP markers at GCP for genotyping (as of August 27, 2012)

Crops

Partners

No. of SNPs

Status

Maize

Converted by CIMMYT in early
2010

1250

Available for genotyping

Cowpea

University of California Riverside
-

Jeff Ehlers

1122

Available for genotyping

Chickpeas

ICRISAT
-

Rajeev Varshney

2068

Available for genotyping

Pigeonpeas

ICRISAT
-

Rajeev Varshney

1616

Available for genotyping

Rice

IRRI
-

Michael Thomson et al.

2015

Available for genotyping

Cassava

IITA
-

Morag Ferguson, P.
Rabinowicz

1740

Available for genotyping

sorghum

EMBRAPA
-

Jurandir

Magalhaes
,
CIRAD
-
Jean
-
Francois Rami

1503

Available for genotyping

common bean

USDA
-

Perry Cregan, CIAT


Stephen Beebe

1497

Available for genotyping

Wheat

CIMMYT
-

Susane

Dreisigacker


2428

Available for genotyping

Soybean

USDA
-

Perry Cregan; IITA
-

Melaku Gedil

1082

Available for genotyping

Groundnut

ICRISAT
-

Rajeev Varshney

91

Available for genotyping

Genotyping Data Management

Once the data is
collected, the breeder
wants to:


do single site analysis,


combined analysis,


Identify marker
-
trait
associations (MTAs),


Store results back to
GDMS


Analysis

Pipeline

The Analysis Pipeline

Analytical tools


Breeding View

Single site

analysis workflow

QTL analysis workflow

Configurable steps

Finally, the breeder
wants to:


select lines,


predict effect of next
crosses,


promote lines for
evaluation and
release


Decision

Support

Decision Support

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



Release Milestones


A first
prototype of the
CWS was demonstrated to
users
in Beijing in
June
2012


Broad opening of IBP Portal by January 2013, with CWS
(Configurable Workflow System) downloadable as single integrated
application


Thanks!