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that influence ripening, nutrient acquisition, and
photosynthetic productivity.
Studies focusing on the application of con-
temporary genomics information to tomato
breeding for the purpose of modulating
carotenoid levels have been conducted. A TILL-
ING approach was employed by Gady and col-
leagues (2012) in order to identify and describe
two different mutations in the
PSY1
gene that
exhibited significant phenotypic effects. Using a
mutagenized population described in Gady and
colleagues (2009), the researchers identified M2
individuals with point mutations in the
PSY1
sequence and produced tomato lines with null
and weak alleles of
PSY1
that resulted in altered
carotenoid accumulation (Gady et al. 2012). This
study is an example of the utility of TILLING for
applied breeding objectives. Now that rapid and
cost-effective identification of mutants is pos-
sible, it is expected that TILLING approaches
will be employed by pre-breeders to generate
novel genetic variation in more genes that are
involved in fruit color, carotenoid accumulation,
sugar accumulation and content, ripening, and
more.
Concurrently, forward genetics approaches
are still routinely employed to mine existing
genetic variation in closely related wild species
of tomato. One recent multi-year QTL study
identified two QTLs, stably inherited from a
S. pimpinellifolium
accession, that significantly
increased fruit lycopene content in a recom-
binant inbred line (RIL) population (Ashrafi
et al. 2009, 2012). This research was followed
up with a marker-assisted backcross (MABC)
experiment to simultaneously verify the QTL
effects, fine map the QTL regions, and develop
near-isogenic lines useful for breeding purposes
(Kinkade 2010; Kinkade and Foolad, unpubl.
results). In this case, a large number of molecu-
lar markers were required to execute the MABC
breeding and fine mapping experiments effec-
tively; therefore, new simple sequence repeat
(SSR) markers were developed utilizing avail-
able tomato genomic BAC end sequences physi-
cally located near the QTL regions. Field exper-
iments were conducted using BC
2
and BC
2
F
2
populations segregating for different QTL inter-
val sizes, and fruit lycopene content was mea-
sured by high performance liquid chromatogra-
phy (HPLC). As a result, the phenotypic effect
of one QTL (
lyc12.1
) was verified as stable in
the genetic background analyzed (Kinkade 2010;
Kinkade and Foolad, unpubl. data). In addition,
lyc12.1
was delimited to a
0.3cMregionof
chromosome 12, near-isogenic lines (NILs) with
lyc12.1
in a relevant cultivated tomato genetic
background were developed, and tightly-linked
co-dominant markers for tracking the QTL were
produced (Kinkade 2010; Kinkade and Foolad,
unpubl. data). The results of this research were
made possible in part by the availability of
tomato genomics resources, which were success-
fully employed to translate findings from a QTL
study into a validated breeding tool for increasing
lycopene content. Further, this series of studies
indicates that current tomato genomics tools are
useful enough to develop tiny introgressions con-
taining useful alleles from wild accessions and
transfer them to cultivated genetic backgrounds
with minimal linkage drag. However, more high-
throughput techniques are required to develop
correlational networks and identify MAS targets
for carotenoid regulation from large populations
in an efficient manner.
Omic-scale identification of carotenoid reg-
ulatory mechanisms in segregating populations
has just begun to be conducted, and some of
the necessary tools have been developed for the
tomato system. Fraser and colleagues (2007b)
demonstrated that high-throughput metabolic
profiling techniques based on MALDI/TOF-
MS (matrix-assisted laser desorption/ionization
time-of-flight mass spectrometry) could be
employed to evaluate tomato populations seg-
regating for carotenoid accumulation level and
carotenoid profile using crude extracts. Because
quantifying the various species of carotenoids
in large populations is laborious and expen-
sive, this has tremendous utility for genomics-
assisted breeding for increased carotenoid con-
tent.
∼
Although
it
has
not
been
definitively
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