Presentation Title Goes Here …presentation subtitle. International Crop Information System : Its Development and its Rice & Wheat Implementation Graham

Presentation Title Goes Here …presentation subtitle.

International Crop Information System :Its Development

and its Rice & Wheat Implementation

Graham McLaren and Arllet M. Portugal

Generation Challenge Program

aportugal

My presentation is mostly about my involvement in the development of ICIS and its implementation for rice and wheat

:: color, composition, and layout

Outline

• Importance of Data Management• ICIS Vision• What is ICIS?• Genealogy Management System• Data Management System• IRIS: Linking Islands of Information• IWIS3: Managing the Global Wheat Data• ICIS Development• Future Development through IBP

aportugal

I will discuss a brief introduction about what ICIS is all about and how it was developed during the time that I was in IRRI.What are the issues then about data management in IRRI that drives to the development and adoption of ICISHow IRIS or the Internationl Rice Information System was implemented as system that integrates the different islands of information in IRRIWhat are some of the deficiencies in the legacy IWIS?How IWIS3 or the ICIS-based International Wheat Information System as a system to manage the global wheat data?What are the issues about ICIS user friendliness and how we tried to address those issues?How ICIS will be improved through the Molecular Breeding Platform of the GCP?


Importance of Data Management

• Data that are properly managed are:

more accessible to other researchers more likely to be re-used in another purpose Available to assist in the development of

combined/mutli-methods/across-time data sets More likely to be preserved – important for historically

significant data

Debby Terryhttp://www.library.uq.edu.au/escholarship/DT_dmp.pdf


Importance of Data Management …

• Greater access to research data will lead to: Better science

o Driven by the capacity for data linkage, sharing, analysis, aggregation & transformation more sophisticated cross-disciplinary and cross-method

research

o Scientific method changes from: “hypothesize, design and run experiment, analyze results” to “hypothesize, look up answer in database”

Enhanced returns from publicly-funded research Benefits afforded by the capacity for national and

global sharing & linkage of dataDebby Terryhttp://www.library.uq.edu.au/escholarship/DT_dmp.pdf


The ICIS Vision

• Connecting Islands of datao Connecting germplasm to crop improvemento Integrating data across disciplines o Leveraging data sets to understand crop adaptationo Linking phenotype to genetics and genomics

• Enabling collaborationo Seed exchanged with informationo Leveling the information playing field

• Developing global information resourcs


What is ICIS?• ICIS is a computerized database system for general,

integrated management and utilization of genealogy, nomenclature, evaluation and characterization data for a wide range of crops.

• ICIS is a public open source collaboration involving a number of CGIAR centers and non-CG partners

• ICIS is an empty shell which must be implemented for each crop individually

ICIS

IWIS IMIS IVISICHIS ISCISIBIS …IRIS


Components of ICIS

• Crop Data Managemento Genealogy Management System (GMS)o Data Management System (DMS)o Inventory Management System (IMS)o Genetic Resources Information Management

System (GRIMS)• Genetics/Genomics (GEMS)


Genealogy Management System (GMS)

• GMS stores and manages information on genesis, genealogy, nomenclature and chronology of germplasm for a particular crop. It operates on the principle of unique identification of germplasm through system assigned Germplasm IDs

• It separates management of genealogy data from nomenclature so users are free to name germplasm as they like anf the genealogy is always ‘computable’


The GMS Data Model

has progenitors

Developed by

Called

Developed at

Developed by

With value of

Named by

METHODS

NAMES

LOCATIONS

USERS

USER-DEFINED FIELDS

ATTRIBUTES

Named at

GERMPLASM

Defined

property of

GENERATIVE GERMPLASM

DERIVATIVEAND MAINTENANCE

GERMPLASM has group

has source


Data Management System (DMS)

• DMS manages environmental data, germplasm characterization data and evaluation data for genetic resources and crop improvement projects.

• It is a data warehouse that accumulates and integrates data from a variety of sources.

• It handles any data structure and facilitates unambiguous annotation and linkage of data across studies via expandable controlled vocabularies


Data Model of DMS

The Effect of Fertilizer N on the yield of wheatYear: 2000Location: El Batan

Rep Main Plot Sub Plot Variety Fert Yield1 1 1 B 20 10.31 1 2 B 50 12.71 2 1 C 50 18.41 2 2 C 20 13.71 3 1 A 20 12.61 3 2 A 50 16.72 1 1 B 50 19.22 1 2 B 20 12.32 2 1 A 20 17.12 2 2 A 50 14.12 3 1 C 50 16.32 3 2 C 20 12.2

Filename: N2000DS.xlsStudy

Datum

Variate

Factor

Level

Observation

Unit


Data Model ...

NITROGEN FERTILIZERPROPERTY

SCALE kg/ha

METHOD

Fert

Total Application

VariateFactor

Yield

GRAIN YIELD

t/ha

Adjusted Yield


Data Model ....

STUDY

FACTOR

Applied inApplied in

LEVEL

Level ofLevel of

OBSERVATION UNIT

Indexed byIndexed byRecorded Recorded fromfrom

DATUM

Measurement ofMeasurement of

VARIATE

Observed inObserved in

PROPERTY

Identified byIdentified by

SCALE

Expressed inExpressed in

METHOD

Measured/Applied byMeasured/Applied by


ICIS Applications: Standalone Tools

ICIS Workbook

SetGen

Inventory Tracker


GMS Applications

• Genealogy Display Tools• Pedigree Input Tools• Breeder’s Tools (Set Generation)• Breeder’s Tools (Field Books)• Analysis Tools (Coefficients of Parentage)


SETGEN

•GMS application for managing lists of germplasm for breeding, characterization or evaluation

o genealogyo nomenclatureo chronology


List Manager – germplam list generator


A. Add germplasm record


B. Generate a cross


C. Generate a Selection


D. Create a trial list – Import from Excel


ICIS Workbook • It is a macro in Excel that facilitates loading and

retrieving evaluation, nursery trial, crop improvement data and even molecular data.


Workbook File: Evaluation Data

Sample Workbook file for the Irrigated Breeding Program


Browse – pedigree analysis

Released lines

Coefficient of Parentage (COP)

Mendelgram of Yecora F 70 and Oasis F 86


IRIS: Linking Islands of Information

BREEDING

PROGRAM

SOIL STRES

S DATA

INGER

GRC

SHU

IR64 MUTAN

T DATAB

ASEGCP

DATA

GAMMA LAB

aportugal

Hence, we implemented ICIS for rice which is the International Rice Information System, linking scattered information in the institute and integrating data from the genebank, international trials and breeding programs


IRRIGATED RICE BREEDING

CENTRAL IRISDATABASE

IRB LOCALDATABASE

IRRIGATED RICEBREEDERS

Grain Quality

PBGB DATAMANAGEMENT

Cross Definition

Quality

Field Books for HB, F2, PN, OYT, RYT

Evaluation Data andPedigree Processing

Data

aportugal

The first breeding program that we moved to ICIS was the irrigated one because it was managed in mainframe then. We reimplemented the generation of the fieldbooks and data processing in the ICIS Retriever.There is a local database where data from a cycle is stored. The breeders will give the cross definction which the data management team will enter in IRIS. They will generate the fieldbooks, give it to the scientists and receive and enter the data in ICIS. Grain Quality data are provided using an ICIS template. After each cycle, the data from the local databsae is uploaded to the central IRIS.


Sample Field book with historical data

aportugal

This is the sample of the fieldbook used by the irrigated program. It contains historical data of the lines.Some traits are observed per entry, while others like yield and agronomic traits were measured by replication.


IRRI Rice Breeding Programs – fully managed in IRIS

PROJECT SIZE / CYCLE (Crosses, Lines)

IRRIGATED 500, 10000

RAINFED 500, 10000

HYBRID 1000, 2000

WIDE HYBRIDS 1000, 2000

UPLAND 100, 5000

COLD TOL. 100, 5000

PERENNIAL 500, 1000

aportugal

Here are the number of crosses and lines being generated by each of the IRRI breeding programs. They are now all managed in IRIS.


INGER: International Trials

>>

Trial Details

Field book

Rainfall

Promising entries

Weather

aportugal

The major use of ICIS in managing our international trials is the electronic fieldbook. We hired a consultant in IRRI then to create templates for each of the international trials. INGER then send this template to their collaborators.A template of the international trial typically contains the followsing: Trial details, the fieldbook, the rainfall data, the promising entries and the weather data.


SHU and SMTA Portal

aportugal

I think one of the greatest advantage of having most of the pedigree and evaluation data in IRIS was when IRRI decided to track the incoming and outgoing seeds because of IP issues. At that time, we didn't need to make a major development to handle the material transfer agreement. We just added it as an attribute of the germplasm in IRIS. There is a local DB to create list of entries for export and another local DB for imported lines. All lines or germplasm to be exported have to be in the central IRIS database. When the SMTA was agreed to be used, we didn't make major development to comply with the requirement of international treaties. Because IRRI already tracks its incoming and outgoing seeds before the adoption of SMTA, there was minimal disruption to the processing of incoming and outgoing seeds. IRRI was able to provide the information needed to be shared about the germplasm in compliance to the treaty. I think IRRI was the very first institution to comply with the treaty's requirement.


SMTA Document

aportugal

IRRI was able to generate an SMTA document specifiying materials under development because the information about the MTA and pedigree is all stored in IRIS. The document contains a URL to the SMTA portal to get further information about the entries of the list.I considered this integration of the Seed Health Unit and the compliance to the international treaty as one of my achievements in IRRI. Its success does not relay on me. But this was the task where all of us: CRIL, plant breeding, genebank, international trials and seed health unit and other divisions have to work together. This was also one of my most draining experience in IRRI as I was the one who usually coordinate the activities and meetings.


IWIS3: Managing the Global Wheat Data

International

Nursery Trials

IWIS2

Genebank

Accessions

ICARDA

Wheat Breeding

IWIS3NARS

Punjab Agricultural University

Directorate of Wheat Research, India

Advanced Research Institute

SPARC-AAFC

Univ. of Sydney

UQ

CIMMYT

Breeding Data

Durum/ Triticale

Irrigated

Rainfed

aportugal

This is how we vision IWIS3: as a system to handle global wheat data.


IWIS3 websites• CIMMYT http://iwis.cimmyt.org/

Search for a germplasm

Pedigree Tree

Trial Study


IWIS3 websites• Australia- India Wheat Molecular Breeding

http://iwis.nrcpb.org/

http://icis.camden.usyd.edu.au:81/IWIS/

http://gwis.lafs.uq.edu.au/


Rainfed

DurumTriticale

IWIS3 for Wheat Breeding

Irrigated

aportugal

How are we now implementing ICIS for the wheat breeding?First, we established a local database for each breeding program, moving their breeding trial lists from the legacy IWIS.This is rainfed local DB ... durum ... triticale and bread wheat irrigated.However, the key to adoption of ICIS for wheat breeding relies heavily on making ICIS easier to use for them which involves some customization of the tools.


Generate a cross

IWIS Cross

aportugal

We have a special way of assigning cross name or BCID in our wheat breeding program. It was such a special naming convention that requires the location of the female parent. This kind of naming convention can not be handled by SetGen, the application that generates crosses and selections. Breeders usually specify the trial ID and entryid of the female and male parents in a cross plan file.What I did was I created a macro that will fill up the GID based on the given trialid and entryID and generate the BCID for that cross.


Generate a Selection

• Run IWIS Selection• Retrieve the list of entries to

advance to next generation• Fill up the Description sheet of the

template• Enter the number of plants

selected in the NSEL• Enter outstanding trait, if there is

any.• Load the study• Generate the lines using SetGEn

IWIS Selection


Entering data using handheld

FieldLog


E. Generating Fieldbook Report• Run the IWIS Retriever• Click “Print Labels and

Fieldbooks”• Select Germplas list• Click Generate Fieldbooks• Click the type of the Field

book you wish to generate

Generate Field book for cross

Generate Field book for selection


ICIS Development

• Documentation• Management of the codes and its releases• Feature Request• Error-fixing• Workshops and Training


ICIS Development

Documentation of ICIShttp://www.cropinfo.org/icis/index.php/Main_Page

Code management and release of ICIShttp://cropforge.org/projects/iciscomm/


Future Development through IBP

• Configurable Workflow• Better management of molecular and genotyping

data• Integration of genotyping and phenotyping data• Integration of ontology system• Integration with analysis tools• Not Operating System dependent


Acknowledgement

ICIS Development Team

Zeus Development Team

IBP Development Team

CRIL Staff

Documents

Presentation Title Goes Here …presentation subtitle. International Crop Information System : Its Development and its Rice & Wheat Implementation Graham