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ICARDA Generation
Genomic LIMS & GeMS |
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 With
the large amount of molecular data generated through
the commissioned research of the Generation
Challenge Program (GCP), it becomes imperative to
provide tools to the researchers to store, organize
and analyze the data and thus support decisions by
stakeholders. Integrating molecular and phenotypic
data is a step towards novel gene discovery for the
development of new crop varieties with better
adaptation to biotic and abiotic stresses and
improved yield capacities.
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ICARDA Generation Genome Management
System (IGGeMS):
ICARDA Generation Genome Management
System (IGGeMS) will manage classical genetic information and
molecular characterization in an analogous way to that described in
ICIS Chapter 18. The specific functions of IGGeMS are:
a) unique identification of
genetic variants including molecular polymorphisms, sequences
and traditional genes;
b) management of nomenclature of molecular variants;
c) identification of sources of different molecular variants;
d) identification of loci and alleles including molecular and
physical mapping positions;
e) linkage of genes to traits and products.
- Gene Management System:
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the convenient starting point
for managing Gene’s information.
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Integrated with ICIS Germplasm
Management System database.
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client / server web
application: Users can access the ICARDA Gene Management
System without any special programs, they need only an
internet browser (and any operating system on the client’s
side).
- users can specify several search
criteria:
- GEMS: Managing molecular data -
OBJECTIVES:
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Unique identification of genetic
variants (molecular polymorphisms, sequences and Traditional
genes).
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Management of molecular variants
nomenclature.
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Identification of sources of
different molecular variants.
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Identification of loci and alleles
including molecular and physical mapping positions.
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Linkage of genes to traits and
products.
- Molecular Variant Data:
Data are usually represented in two ways with gel based
detection method
(1) 0’s and 1’s
(2) frequencies / intensity
(3) Crop is a diploid - (0
for alleles not present, 1 one copy of the allele present, I.e.
heterozygote) or 2 (two copies of the allele present I.e a
homozygote)
(4) For Hexaploid –
(provision for presence of alleles up to six times
(5) For Sequencing PDs,
variants are scored as:
A (adenine), G(guanine),
C(cytosine), T(thymine), R (=G or A),Y(=C or T) or N(=A or C or
G or T)
- The Gene Management System
table structure in ICIS:
- REFERENCES:
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Bioinformatics for Dummies by
Jean-Michel Claverie and Cedric Notredame
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Wiley publishing, Inc.
Indianapolis, Indiana - 2003.
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