S.D. Tanksley
Cornell University
My lab is interested in the evolution of genome structure and gene function
(especially related to domestication) in plants. In the past years, we
have developed the strategy by which the genomes from divergent plant
species are related to each other using comparative mapping strategies.
The approach has been to utilize conserved genes as probes on genomic
southerns to create comparative maps. Using this protocol, my lab and
others have now reconstructed the macrosyntenic relationships among many
species in the family gramineae and species in the family solanaceae (nightshades).
As a result, it is now possible to define conserved genome segments and
genes among species within the same family. These data reveal that gene
order and, in many cases, gene function is conserved within plant families.
More recently, my lab has begun reconstructing genome evolution across
plant families. As a starting point, we are defining both the macro and
micro syntenic relationships between arabidopsis (family brassicaceae)
and tomato (solanaceae). Rather than relying on southern hybridization
(which is ineffective for more the divergent gene sequences observed across
family boundaries) we are using a computational or in silico approach.
Approximately 80,000 ESTs (expressed tag sequences) have been generated
for tomato, corresponding to at least 15,000 unique genes. Each of these
genes is being compared against the translated tiling path of the arabidopsis
genome. ESTs are being selected which have a single, highly conserved
match in the arabidopsis genome. Thus far 1000 such highly conserved orthologs
have been identified and we are now in the process of mapping these in
the tomato genome. In addition, we are sequencing selected regions of
the tomato genome for comparison of micro synteny with arabidopsis. These
data suggest that, at the micro level (eg. 100 kb segments), chromosomal
rearrangements (e.g. inversions, translocations) have been only a minor
factor in the divergence of genome organization among plants. Rather,
the dominating factors have been repeated rounds of large-scale genome
duplication followed by selective gene loss. We hypothesize that these
processes have led to the network of synteny revealed between tomato and
arabidopsis and predict that such networks of synteny will be common when
making comparisons among higher plant taxa (Ku et al. 2000). As a collaborator
on the RCN project, we hope to be able to extend the tomato:arabidopsis
work to other plant families in order to better understand genome and
gene evolution in higher plants.
The second focus of our lab is understanding how domesticated plants
have come to produce large, variable shaped, edible fruit now associated
with modern agriculture. Over the past 15 years we have conducted a series
of QTL mapping experiments using small-fruited wild tomato species and
large-fruited cultivated types. These studies indicate that approximately
25 QTL (quantitative trait loci) have been involved in the evolution of
fruit size and shape in tomato (Grandillo et al. 1999). We are currently
cloning the genes responsible for these QTL. One QTL (fw2.2) has already
been cloned and is a member of a new gene family in plants which, in carpels/fruit,
controls cell division (Frary et al 2000). The encoded protein also has
predicted structural similarity with the RAS family of oncogenes in mammals,
suggesting an ancient and common origin of cell division control in both
plants and animals (Frary et al. 2000). As participants in the RCN project
we would hope to explore the evolution/function of fw2.2 and other genes
in higher plants involved in the domestication of fruit bearing species.
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