Functional Genomics for the Study of Fruit Ripening and Quality: Towards an Integrative Approach - Fruit Ripening: Physiology, Signalling and Genomics - page 310

The Tomato Genetics Resource Center
( http://tgrc.ucdavis.edu/; University of
California, Davis, CA, USA) maintains a
large collection of wild relatives and
monogenic mutants affecting many aspects
of plant development and responses such
as disease resistance.
The Solanaceae have adapted to diverse
niches with diverse phenotypes, but their
genome structure is relatively well
conserved. Tomato, as member of this
family, offers an opportunity to understand
the diversifi cation of these plants. The
genome sequence, recently obtained, is
expected to benefi t breeding and genetic
engineering programmes for solanaceous
crops and other fl eshy fruits. It is also of
interest for phylogenetic studies because of
its intermediate diversity between the rosid
and asterid clades.
Tomato was developed for use in model
DNA marker technology because line
populations are easy to develop by
interspecifi c introgression and to assess for
identifying quantitative trait loci (QTLs)
(Frary et al. , 2000). ESTs are currently used
to study functional genomics and as a
complement to genome sequencing (Rudd,
2003). Tomato has a large EST collection
(>298,000 entries) in the public domain.
This collection contains 18,051 unigenes
(unique consensus sequences), of which
~70% have homologues in the Arabidopsis
genome and the remaining 30% have
unknown functions. Continuing research on
Arabidopsis may speed up the tomato
functional genomics, while EST and full-
length cDNA sequencing should help to
predict the functions of the remaining
genes.

dbEST database ( http://www.ncbi.nlm.nih.
gov/dbEST/). Current and future large-scale
EST sequencing projects are likely to
increase the number of ESTs in the public
domain, providing additional opportunities
to compare intra- and interspecifi c genome
expression and expanding opportunities for
digital gene expression analysis. Progresses
in bioinformatics and biostatistics make it
possible to functionally analyse large-scale
EST data sets in a highly effi cient manner
(Ronning et al. , 2003).
Insertional mutagenesis is a powerful
tool for identifying gene function. Tran-
sposons have also been isolated for
promoter trapping, and E -glucuronidase is
used for enhancer trapping (Meissner et al. ,
2000). Transcriptional enhancers can also
be placed on a binary transformation
vector to induce genetic mutants by
expressing endogenous genes close to the
T-DNA insertion site. This method was
successfully used to generate 10,427
transgenic tomato lines, of which 1338 had
visually observable novel traits; virus-
induced gene silencing (VIGS) technology
was used to determine the function of
many of these unknown genes. Tran-
scriptome profi ling monitors, microarrays
with 30,000 gene probes, have been used to
study plant defence-related responses such
as fusicoccin-induced changes in gene
expression and systemic wound responses
(Strassner et al. , 2002). A widely used
tomato microarray with >150,000 ESTs and
12,000 unigenes (Tom1 Microarray, http://
ted.bti.cornell.edu/) has allowed broader
analysis of gene expression (Alba et al. ,
2004). Another genome array chip with
>10,000 unigenes is commercially
available from Affymetrix. Another recent
'omics' approach to dissect biological
systems is metabolomic analysis (Aharoni
et al. , 2002).

18.3 Functional Genomics Approaches
in Tomato

ESTs are created by partially sequencing
analysed transcripts that have been
converted into cDNA. Recent progresses in
'omics' technologies and advanced DNA
sequencing technology have allowed large-
scale EST sequencing. There are now
millions of ESTs in the NCBI public

18.4 Micro-Tom as a Model Tomato
Line

Small organisms such as the fruit fl y,
Drosophila melanogaster , are often used as
model systems in genetics studies.