Physiology and Molecular Biology of Stress ... - KHAM PHA MOI

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A.K. Tyagi, S. Vij and N. Saini
tion lines available. Detailed analyses of 88,122 lines have revealed mutations in ~74%
of Arabidopsis genes (Alonso et al., 2003). On the other hand, though a database is
available for T-DNA tagging lines of rice, it is not saturated, representing less than 10%
the number of lines required (Jeon et al., 2000). A total of 13,450 lines of rice are also
available which can be used both for promoter trapping and activation tagging (Jeong
et al., 2002). Chen et al. (2003) also characterized over 1000 T-DNA tags in rice genome.
There are several other rice mutant resources developed by the international rice research
community (Hirochika et al., 2004). A large resource of Mutator (Mu) insertions
is also available for maize (May et al., 2003).
Several institutes and companies in Europe have formed consortia (European
Consortia for Functional Genomics; see table 3) for functional genomics. GenoPlante-
Info (GPI; http://genoplante-info.infobiogen.fr/); FLAG DB/FST database (Flanking
sequenced tags; ~10,000 sequences flanking T-DNA insertion sites); CATMA (Complete
Arabidopsis Transcriptome Micro-Array; 21,120 gene specific tags are available
at the site); GPI EST database (EST’s are available from Arabidopsis, rice, Sorghum
bicolor, Medicago truncatula, Zinnia elegans, wheat, rapeseed, sunflower and pea)
and The Plantgene database (collection of Arabidopsis full length cDNA’s) and SAGE
data (Samson et al., 2003).
Few databases have been described lately which are more specific, these
include PlantsP and PlantsT functional genomics database which specifically provide
information related to protein phosphorylation and membrane transport respectively
(Tchieu et al., 2003). Both these databases not only provide sequence related information
about protein kinases, phospahatases, and membrane transport proteins but also
data on experimental functional genomics. One major database dedicated to stress
genomics is the Stress Functional Genomics Consortium (http://stress-genomics.org/).
It contains a collection of stress responsive ESTs from Arabidopsis thaliana, Oryza
sativa, Mesembryanthemum crystalinum, Hordeum vulgare, Selaginella and
Dunaliella. A collection of Arabidopsis mutants altered in stress signaling and global
gene expression profiles of Arabidopsis, rice and ice plant under stress conditions can
also be accessed through the site. In future, it would be desirable to integrate information
spread over several databases.
7. CONCLUSIONS
Use of traditional approaches for studying gene function has given way to genomewide
approaches and as the sequencing data from more plants are becoming available,
the interest is shifting to see what lies beyond the ‘bases’. The task of identifying
the function of each gene and their inter-relationships is not going to be easy unless
more genome-wide approaches are employed. For instance, a large collection of insertional
mutant plants freely available through several databases, microarrays and their
modifications, proteome analysis and other techniques which have developed side by
side to the large scale sequencing programs of model plants such as Arabidopsis and
rice are now available. Expression profiling would give ready clues only about the