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In-Depth Information
high-throughput identification of mutations in
candidate genes have been published (Gady et al.
2009; Rigola et al. 2009). All of this is leading
to the capability of using contemporary com-
binatorial “omic” methods to achieve breed-
ing outcomes in tomato; whether or not prac-
tical tomato breeding outcomes will be obtained
and/or explicitly reported in the literature using
these methods remains to be seen.
not the time and expense required for such stud-
ies can be justified to the contemporary tomato
breeder.
Early Breeding Research and the S.
pennelliiLA716 Introgression Lines
The cultivated tomato,
S. lycopersicum
L., has
become a model system for quantitative genetic
studies for a variety of reasons. Tomato is a
diploid organism and a self-pollinator, seed-
to-seed generation time is as little as three
months, controlled hybridizations are easy to
conduct, wide phenotypic variation exists within
the available germplasm, and diverse genetic
populations are relatively simple to construct
(Foolad 2007a, b; Labate et al. 2007). The
body of work led by C. M. Rick and col-
leagues paved the way for tremendous genetic
improvement of tomato varieties using acces-
sions from the related wild tomato species (i.e.,
Solanum
sect. Lycopersicon species other than
S.
lycopersicum
). Based on collections and botan-
ical studies of wild tomato species as well
as isozyme surveys of genetic variation within
Solanum
sect. Lycopersicon, which indicated
extremely low genetic variability within the cul-
tivated species, it was determined that wild
germplasm held the key to the improvement of
many important agricultural traits in tomato (
see
Rick and Fobes 1974, 1975; Rick 1976a, 1978,
1979). As a result, some breeders and geneti-
cists delved back into the wild tomato germplasm
(accessions of botanically related, but undomes-
ticated tomato
Solanum
species) in order to
identify and transfer beneficial traits into breed-
ing lines. As early as 1982, molecular markers
(specifically isozymes) were being used to map
tomato genes involved with phenotypic char-
acters (Tanksley et al. 1982). These develop-
ments resulted in the creation of segregating
interspecific populations of tomato, and, com-
bined with collaboration between public and
private researchers, enabled the genetic anal-
ysis of various phenotypic traits (reviewed in
Foolad 2007a; b). Since then, a wealth of QTL
Key Advances Enabling
Genomics-Assisted Breeding
in Tomato
The tools required for genomics-assisted breed-
ing in tomato are available: the tomato genomic
sequence has become available for public
use, early proof-of-concept “omics” studies
have been conducted on genetic populations
of tomato, large-scale marker identification
projects have produced multitudes of markers for
use within the tomato cultigen, new TILLING
populations have been developed and character-
ized, and large, multi-faceted omics databases
have been constructed, which allow users to com-
pare multi-omics datasets in order to construct
correlational networks of genes. Yet, as in many
other crop species, single-gene MAS (mainly
for disease resistance) remains the most widely-
used molecular breeding technique in practice
for tomato, and the status of “genomics-assisted
breeding” of tomato in the literature remains
nascent at best. In fact, a literature search of
“genomics assisted breeding of tomato” cur-
rently returns a litany of review articles but scant
primary research reports. Nevertheless, the pil-
lars upon which a genomics-assisted breeding
scheme could be devised now exist for tomato.
In this section, we describe these resources
and some early examples from the literature
that have begun to bridge the gap between
basic genomics and practical breeding outcomes
related to tomato fruit quality. The challenge is
how to seamlessly incorporate these types of
analyses and selection methods into a practi-
cal breeding program, and determine whether or
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