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at a molecular level has yet to be definitively
elucidated.
of today's processing tomato cultivars (Fridman
et al. 2000; Schaffer et al. 2000; Causse et al.
2004; Foolad 2007a). The use of reverse genet-
ics approaches, such as “targeting induced local
lesions in genomes” (TILLING), for applied
breeding purposes has, until recently, been hin-
dered by the considerable time, labor, and cost
required to produce and screen mutant popula-
tions. Recently this approach has been used in
tomato to produce novel disease resistance (Piron
et al. 2010) and fruit quality traits (Gady et al.
2012). With the advent of high-throughput point
mutation detection schemes utilizing cheap next-
generation sequencing technologies and novel
bioinformatic pipelines, mutation breeding has
re-emerged as an attractive approach to gen-
erating new genetic variation in tomato breed-
ing material (Gady et al. 2009; Rigola et al.
2009).
In this chapter we look beyond the heav-
ily reviewed QTL analyses that have dominated
tomato literature until recently. Although many
QTLs have been identified for various fruit qual-
ity traits in tomato, extremely few are actively
used in today's commercially grown tomato
cultivars (Foolad 2007a; Kinkade 2010). There
are several legitimate reasons for this discrep-
ancy. Many detected QTLs and their associ-
ated molecular markers are based on interspe-
cific mapping populations of tomato, and thus
may be specific to those populations. Subse-
quent verification of such QTLs, their individ-
ual effects, and associated markers in breeding
populations is a time-consuming, expensive, and
risky task. This is especially true when the QTLs
are originally described in genetic populations
distantly related from or irrelevant to a given
breeder's germplasm and/or in different agricul-
tural environments from a given breeder's tar-
get climatic region. Also, the lack of a univer-
sal set of high-throughput marker assays that
can be utilized to discriminate between geno-
types within the cultivated tomato germplasm
has hindered the widespread use of genomics
information to assist the breeding process. In
tomato,
Practical Breeding Considerations
One of the goals of pre-breeding research in
tomato is the discovery of novel genetic ele-
ments that could be used by tomato breed-
ers to modulate important traits in a practical
manner. Since transgenic approaches for tomato
genetic improvement have remained generally
unacceptable to consumers, new genetic varia-
tion has either been introgressed into the culti-
gen from closely related wild species or gen-
erated via mutagenesis. Due to the fact that
most tomato fruit quality traits, such as soluble
solids content (SSC), viscosity, and carotenoid
accumulation, exhibit complex inheritance and
interact with the environment, the quantitative
trait locus (QTL) approach to identifying useful
genetic variation has been utilized extensively
for pre-breeding purposes. This technique also
has allowed researchers to develop mapping pop-
ulations and identify QTLs within the context of
germplasm improvement. With the development
of publicly available molecular maps and core
sets of markers, numerous quantitative genetics
studies have been conducted using various types
of intra- and interspecific populations of tomato,
and hundreds of putative QTLs affecting fruit
quality traits such as SSC, carotenoid content,
fruit size, acidity, firmness, and taste have been
reported and extensively reviewed elsewhere
(Foolad 2007a, b; Labate et al. 2007). Concur-
rently, much of the commercial-scale tomato
breeding capacity shifted from public to pri-
vate institutions. Thus, published results from
subsequent verification of identified QTLs in
relevant genetic backgrounds and environments
has been limited, with a few notable exceptions
(e.g., Lecomte et al. 2004; Yates et al. 2004;
Chaıb et al. 2006; Kinkade 2010). Further, most
detected QTLs have not been used for practi-
cal breeding purposes, with a few exceptions,
such as QTLs LIN5 and LS1, which purport-
edly increase fruit SSC and are found in some
these
concerns
and
roadblocks
are
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