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

Functional Genomics of Stress Tolerance
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provides access to a total of ~30,000 full length cDNA clones. More information regarding
these clones can be searched from the Knowledge-based Oryza Molecular Biological
Encyclopedia database (KOME; http://cdna01.dna.affrc.go.jp/cDNA). AGI provides
BAC and EST libraries, high density hybridization filters and clones on a cost recovery
basis. Databases dedicated to comparative cereal genomics include USDA Gramene
database (http:// www.gramene.org; Ware et al., 2002a, b) and John Innes Cereal Databases
(www.jic.bsrc.ac.uk). TIGR provides details of both rice and Arabidopsis genome
sequencing, the site also provides details of 13, 659 Tos17 insertion flanking
sequences mapped in silico to 2,448 rice PAC/BAC sequences. IRIS provides integrated
information on genetic resources and Oryzabase provides information on genetic
resources, genes, chromosome maps and general information on rice.
In 2000, with the completion of Arabidopsis genome sequencing, the
Arabidopsis research community planned The Arabidopsis 2010 Program. The aim was
to assign function to all the 25,000 Arabidopsis genes (Chory et al., 2000). Further, an
International Rice Functional Genomics Consortium (IRFGC) has been set up with the
goal of sharing knowledge, integrating the databases and functional genomics of rice
(http://www.iris.irri.org/IRFGC/) hand in hand with the rice genome sequencing
(Hirochika et al., 2004). IR64 deletion mutants developed at IRRI are accessible through
the International Crop Information System database (ICIS), both phenotypic and molecular
data related to the mutants are available at the site (Leung et al., 2001).
Besides the above, other mutant databases have also used the model plants
Arabidopsis and rice whose sequence data is already available. The two major resources
for Arabidopsis mutants generated through insertional mutagenesis are The
Arabidopsis Biological Research Center (ABRC) and Nottingham Arabidopsis Stock
Center (NASC) (Table 3). In fact, ABRC has the largest collection; it has more than
140,000 mutants generated through transposon and T-DNA tagging. Most of these
have been contributed by the Salk institute (http://signal.salk.edu/tabout.html). Of the
140,000 mutants available, sequence information of flanking sites is available for 50,256
lines. If a researcher is not able to find a knockout in the gene of interest in these two
databases for Arabidopsis then the other option would be to search in the The
Arabidopsis Knockout facility (Krysan et al., 1999). Another database, which serves to
integrate the data available from several projects on insertional mutagenesis, is the
Arabidopsis thaliana insertion database (ATIDB; http://atidb.cshl.org/). Through this
source more than 100,000 insertion lines can be accessed consisting of 196 defective
Supressor/mutator (dSM), 6113 Supressor mutator (SM) lines, 119 activation tagging,
1586 gene trap, 1289 enhancer trap and 94,947 T-DNA lines (Pan et al., 2003). Users can
search for T-DNA or transposon insertions in the sequence of interest and the stocks
can be ordered directly through NASC and ABRC. To establish a T-DNA tagged population
in which a T-DNA insertion can be found at a probability of ~99%, ~200,000
tagged lines of Arabidopsis and ~471,000 tagged lines of rice would be required (Jeon
et al., 2000). For Arabidopsis, such a resource is now available (Table 3) where T-DNA
tagging has been done on a genome-wide scale with more than 225,000 T-DNA inser-