Transcript iMAS – Integrated decision support system for MAB

iMAS 1.9 – An Integrated
Decision Support System for
MAB
Abhishek Rathore1, Mallikarjuna, G.1, Manna, S.1, Hoisington, D1,
McLaren, G2, Davenport, G2, Crossa, J3
1International
Crops Research Institute for the Semi Arid Tropics, Hyderabad, India
2International Rice Research Institute, Manila, Philippines
3International Wheat and Maize Improvement Centre, Mexico
Contact: [email protected]
Click to Download iMAS
Few Acronyms Used
MABC
QTL
MAB
BLUP
-
Marker Assisted Back Cross
Quantitative Trait Loci
Marker Assisted Breeding
Best Linear Unbiased Prediction
iMAS
• iMAS is a single unified computing and decision support
platform
• Facilitate identification of trait-linked markers for use in
marker-aided selection and breeding
– Integrating and implementing the required computational
processes,
– Providing guidelines for correct application and interpretation of
computational tools
iMAS
• A Standalone system : Keeping NARS needs in mind
• Pipelining freely available quality software / statistical tools
• Biometrical Analysis
– IRRISTAT (G McLaren, IRRI, Philippines )
• Linkage and QTL Mapping
– GMendel (JL Holloway & SJ Knapp, Oregon State University, Oregon, USA)
– PlabQTL
(HF Utz & AE Melchinger, University of Hohenheim, Germany)
iMAS
• Visualization of Linkage and QTL Map
Linkage Map
– MapChart
(RE Voorrips, Plant Research International, The Netherlands)
Linkage Map & QTL
– GGT
(R van Berloo, Laboratory of Plant Breeding, Wageningen University, The
Netherlands)
– FLAPJACK (Iain Milne, Micha Bayer, Paul Shaw, Linda Cardle and David Marshal,
SCRI, Scotland)
• MABC Sample Size
• PopMin
(F Hospital, Ferme du Moulon, France)
• QUGene
(Scott Chapman, The University of Queensland, Australia) (Experimental)
iMAS Advantages
• Genotypic and phenotypic data analysis involves a number of
different software
• All have different input data format requirements
• Manual input file preparation
– Time-consuming
– Error-prone
• Which some time results in:
– Use of inappropriate methods
– Incorrect use of appropriate methods
Phenotypic
Data
iMAS
Genotypic
Data
Biometrical Analysis
Genotypic Data
Phenotypic Data
Linkage Map Building
QTL Analysis
MABC Sample Size
Visualization
iMAS - Modules
iMAS currently implements a mapping-population-based
approach to identify trait-linked markers
The system consists of six modules
- Data Validation module
- Phenotyping module
- Linkage Map Building module
- QTL Analysis module
- Genome / QTL Display module
- MABC Sample Size module
iMAS - Data Validation
The Data Validation module provides some facilities to
1. Check basic background information on your data
files
2. Gives an opportunity to correct your data files if
necessary, before starting to use iMAS.
iMAS – Phenotyping
Two sub-modules:
• Experimental Design
• Biometric Analysis
The Experimental Design sub-module helps you select
and generate a suitable experimental design for
phenotyping
The Biometric Analysis sub-module helps you perform
appropriate biometric analysis of resulting phenotyping
data to obtain accurate and precise average phenotypic
values
iMAS – Linkage & QTL Mapping
The Linkage Map Building module generates a linkage
map.
The QTL Analysis module undertakes QTL analysis
based on a linkage map and the average phenotypic
values.
The required linkage map and the average phenotypic
values could either be obtained from inside iMAS or from
some other software outside iMAS
iMAS – Genome Display
The Genome Display module facilitates graphical
display of genomic content of progenies
The MABC Sample Size module helps determine the
optimal sample size for marker-aided backcrossing
Biometrical Analysis
Data Validation
•Genotypic
•Phenotypic
Analysis
• Mixed Model
Biometrical Analysis
Data Validation - Phenotypic
Biometrical Analysis
Data Validation - Phenotypic
Biometrical Analysis
Data Validation - Phenotypic
Biometrical Analysis
Data Validation - Genotypic
Biometrical Analysis
Data Validation - Genotypic
Biometrical Analysis
Analysis - BLUPS
Biometrical Analysis
Analysis - BLUPS
Biometrical Analysis
Analysis - BLUPS
Biometrical Analysis
Analysis - BLUPS
Biometrical Analysis
Analysis - BLUPS
Linkage Map - GMendel
Linkage Map - GMendel
Linkage Map - GMendel
PLABQTL
QTL Mapping
•
•
By default Identified QTLs are visualized in Ghost View
However, for more appealing visualization GGT and
FLAPJACK can be used from within iMAS
GGT
iMAS - Visualization
FLAPJACK
iMAS - Visualization
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