international crop information system : its development and rice & wheat implementation

Presentation Title Goes Here …presentation subtitle.

International Crop Information System :Its Development

and Rice & Wheat Implementation

Arllet M. Portugal and Graham Mclaren

GCP

aportugal

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

:: color, composition, and layout

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


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)


Historical Data from ChinaHistorical Data from China


APPLICATIONS -APPLICATIONS -BrowseBrowse


SETGEN

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

o genealogyo nomenclatureo chronology


List Manager: germplasm list generator


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 Development

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

Release of ICIShttp://cropforge.org/projects/iciscomm/

aportugal

The documentation about ICIS is available through cropwiki and its releases were posted in cropforge.


Why IRRI needs ICIS then?

• Data are scattered around the institute• No integration in the current systems• System was unshareable• The technology was obsolete


IRIS: Linking Islands of Information

BREEDING

PROGRAM

SOIL STRES

S DATA

INGER

GRC

SHU

IR64 MUTAN

T DATAB

ASEGCP

DATA

GAMMA LAB


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


Sample Field book with historical data


INGER: International Trials

>>

Trial Details

Field book

Rainfall

Promising entries

Weather


GRIMS: Integration of Genebank System with IRIS


SHU and SMTA Portal


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


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

Search for a germplasm

Pedigree Tree

Trial Study


Rainfed

DurumTriticale

IWIS3 for Wheat Breeding

Irrigated


Generate a cross

IWIS 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


Future Development through MBP

• Configurable Workflow• Better management of molecular and genotyping• Integration of genotyping and phenotyping data• Integration of ontology system• Integration with analysis tools• Not Operating System dependent


AcknowledgementGuy Davenport

ICIS Development TeamZeus Development TeamMBP Development Team

CRIL Staff

ACIAR and AIMBP collaborators

IRRI GRC, PBGB, INGER and SHU

CIMMYT Global Wheat Program and GRP

Graham McLarenGCP

international crop information system : its development and rice & wheat implementation

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