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mapping studies has been conducted using the
tomato system (reviewed in Foolad 2007a and
Labate 2007), which has subsequently sparked
in-depth transcriptomic and metabolomic stud-
ies, in addition to sequencing the tomato genome
(Mueller et al. 2009). Combined with the tomato
genome sequence, such information can now
be leveraged in the search for candidate genes
underlying detected QTLs, or in the search for
new QTLs. As a result, researchers have used
segregating interspecific populations to iden-
tify new alleles affecting various traits and
to subsequently clone and characterize them
(reviewed in Foolad 2007a). A majority of stud-
ies has been conducted using most widely known
tomato population, the
S. pennellii
-based intro-
gression lines [ILs; (Eshed and Zamir 1995)].
Many other tomato “immortalized” mapping
populations with useful traits have been con-
structed (see Foolad 2007b; Ashrafi et al. 2009)
and are expected to be heavily utilized in
future for both strategic and applied breeding
research.
Although more time-consuming to develop
than many other mapping populations, IL pop-
ulations can be more useful for QTL mapping
and phenotyping, since any significant differ-
ence(s) between an IL and the recurrent par-
ent is due to a single introgressed segment of
the donor
S. pennellii
genome. However, once
QTLs are detected, the physical size of the
genomic bin in which each QTL resides may
be quite large; therefore time saved by remov-
ing background wild genomic intervals prior to
QTL analysis may be moot, as further backcross-
ing, marker mapping, recombinant selection, and
validation experiments are still required prior
to practical application. Thus we posit that the
overall “work” required to identify and trans-
fer QTLs to elite germplasm using ILs is simi-
lar to other population types (see Barone et al.
2009). Nevertheless, in tomato, the
S. pennellii
-
based IL population has been the foundation of
many genetic discoveries and continues to be
a useful tool for contemporary omics experi-
mentation in the public sector (Liu et al. 2003;
Rousseaux et al. 2005; Schauer et al. 2005;
Schauer et al. 2006; Fraser et al. 2007a; Lipp-
man et al. 2007; Bermudez et al. 2008; Schauer
et al. 2008). QTLs for altered soluble solids
content, yield, fruit size, metabolic traits, and
many others, have been identified using the
ILs, and some of these QTLs are actively used
by commercial breeding programs (Rousseaux
et al. 2005; Lippman et al. 2007). This popula-
tion has also been used for metabolomic stud-
ies (Schauer et al. 2006; Fraser et al. 2007a;
Lippman et al. 2007; Bermudez et al. 2008;
Schauer et al. 2008), which will be discussed
later in this chapter. In addition, markers devel-
oped using the interspecific populations con-
structed for quantitative genetics studies helped
form the basis of the tomato genome sequencing
project.
Sequencing of the Tomato Genome
The tomato genome sequencing project offi-
cially began in 2004 as an international col-
laboration among ten countries (Mueller et al.
2009). A BAC-by-BAC approach, beginning
with physical mapping and BAC (bacterial arti-
ficial chromosome) tiling followed by “golden
path” sequencing, was initially proposed, and
as sequencing technology advanced rapidly
during the 2000s, this approach was utilized
to buttress next-generation sequencing datasets
(Mueller et al. 2009). A formal report on
the genome sequence and insights into the
evolution of tomato has recently been pub-
lished (Tomato Genome Consortium 2012). An
FTP site within the Solanaceae Genomics Net-
work (SGN;
http://solgenomics.net)
for mass
data download has also been developed for
researchers wishing to conduct their own anno-
tation and/or sequence investigation (such as
repeat masking, transposon detection, gene iden-
tification, etc.; Mueller et al. 2009). Gene identi-
fication using the raw sequence and the MAKER
annotation tool (Cantarel et al. 2007), fol-
lowed by track visualization using Apollo (Lewis
et al. 2002), is now possible and has been
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