Functional Genomics for the Study of Fruit Ripening and Quality: Towards an Integrative Approach - Fruit Ripening: Physiology, Signalling and Genomics - page 312

experiments to compensate for variability
in signal intensity due to the char-
acteristics of an individual fl uorochrome.
The obtained data functionally analyse
subsets of genes during fruit development.
There were specifi c genes differentially
expressed for each developmental stage
and particularly an increased number of
genes were induced at the beginning of
ripening (Moore et al. , 2002). These genes
are involved in ethylene synthesis,
carotenoid accumulation and cell-wall
modifi cations. As these studies progress, it
may become possible to predict functions
for ESTs with little or no known homology,
based on expression patterns and relation-
ships to better-known genes. In particular,
comparisons of expression profi les with
the tomato proteome hold the promise of
identifying underlying genetic and mol-
ecular events contributing to fruit develop-
ment and ripening.

The INNER NO OUTER (INO) gene is
needed for ovule development in
Arabidopsis. Expression is observed only
at the initiation site and developing outer
(abaxial) cell layer of the ovule outer
integument (Meister et al. , 2004). INO can
induce parthenocarpy and signifi cantly
reduce seed number (Martinelli et al. ,
2009). Transgenic tomato plants were
obtained for each of four promoter-gene
combinations (INO or DefH9 promoter with
iaaM or rolB) to produce parthenocarpy
(see Plates 9 and 10). Among the transgenic
tomato lines expressing iaaM, close to one-
third of the fruits showed no seeds, while
slightly more than one-third had a few
seeds. The remaining fruits had greatly
reduced seed production. Similar results
were obtained for transgenic tomato plants
for rolB gene. The promoters of INO and
DefH9 regulated expression of iaaM or rolB
similarly and produced similar proportions
of seedless and reduced-seed lines.
Seedlessness did not appear to affect fruit
shape or quality, although in DefH9-rolB
transgenic tomatoes a decreased number of
seeds was linked to altered soluble solids.
The Affymetrix tomato array was
employed to compare the breaker stage of
wild-type and transgenic fruits on a large
transcriptomic scale and to determine
changes directly caused by transgene
expression. At this stage, the fruit has a
yellow colour. Although direct changes
induced by genetic transformation in both
the transcriptome and metabolome are
likely to occur at earlier developmental
stages, the high numbers of gene
expression changes at the breaker stage
emphasized the differences due to
transformation. Pairwise comparison (one-
way analysis of variance, P < 0.001) of the
highly expressed genes showed hundreds
of downregulated genes in rolB- and iaaM-
transformed plants (0.96 and 0.98% of all
genes represented on the microarray,
respectively). Fewer upregulated genes
were observed (0.13 and 0.21% of the
represented genes, respectively).
There was a large overlap in the
expression of 1748 differentially expressed

18.6 A Functional Genomics
Case Study: Gene Regulation in
Transgenic Parthenocarpic
Tomato Fruit

In tomato, seeds contribute to fl avour and
are not considered undesirable in fresh
market fruits. However, seedless fruits
would facilitate tomato processing. Seed
formation is an integral component of fruit
development: developing seeds promote
cell expansion via the synthesis of auxin
and other unknown molecules.
Parthenocarpy is the formation of fruits
without seeds. In some species, fruit can
develop without fertilization, indicating
that it is possible to separate fruit
formation from seed development. This
phenomenon has a genetic basis (Vardy et
al. , 1989) and can be induced artifi cially
with hormone applications of gibberellins,
auxins and cytokinins. Raspberry fruit
were genetically transformed with a
DefH9-iaaM gene construct to induce
parthenocarpic fruits (Mezzetti et al. ,
2004). Seedlessness is highly desired by
consumers in fresh citrus and grapes.