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differential copy numbers or complete absence of
the genes, has been shown for maize zein genes
(Song et al., 2002) and the wheat prolamins (Gao
et al., 2007). Disease resistance genes have also
been shown to undergo rapid rearrangements,
leading to non-colinearity of these genes in cross-
species comparisons (Gallego et al., 1998; Leister
et al., 1998; Brueggeman et al., 2002).
Disruption of colinearity is evident in both
wheat—rice and wheat— Brachypodium compari-
sons. The effi cacy of a model organism tends to
decline with increasing phylogenetic distance.
Brachypodium is therefore expected to be a better
model for wheat than rice. However, this is not a
given as, for yet unknown reasons, some genomes
are much more prone to rearrangements. The rice
genome is generally considered to be a very stable
genome (Ilic et al., 2003). Others, such as the
maize and pearl millet ( Pennisetum glaucum )
genomes, seem to undergo rearrangements much
more frequently (Devos et al., 2000; Ilic et al.,
2003). The stability of the Brachypodium genome
has, so far, been investigated in the tetraploid
B. sylvaticum and is underway in the diploid B.
distachyon . Griffi ths et al. (2006) analyzed gene
colinearity across the Ph1 region of wheat, and
orthologous regions in B. sylvaticum and rice. Of
the 34 genes identifi ed in this region in wheat, fi ve
were missing in both rice and B. sylvaticum , seven
were missing in rice but not in B. sylvaticum , and
one was missing in B. sylvaticum but was present
in rice. In a similar study across the Lr34 region
by Bossolini et al. (2007), 11 and 10 of 15 wheat
genes were present in conserved locations in B.
sylvaticum and rice, respectively. An inversion
was identifi ed that differentiated the Pooid
genomes from rice. Sequence similarity was
greater between B. sylvaticum and wheat than
between rice and wheat, dating the phylogenetic
distance between Brachypodium and wheat at
35 MY. Preliminary comparative analyses at
the DNA sequence level between wheat and B.
distachyon also indicate that colinearity is often
disrupted (K.M. Devos, unpublished data). Inter-
estingly, there is also some indication that colin-
earity between rice and B. distachyon might be
more extensive, at least in some regions, than
colinearity of either with wheat. Based on this
limited data, it would appear that B. distachyon
will be a useful, but by no means a perfect, model
for wheat genomics.
MAP-BASED CLONING
Isolation of the fi rst plant gene using a map-based
cloning approach that involved chromosome
walking was achieved in Arabidopsis thaliana in
1992 (Arondel et al., 1992; Giraudat et al., 1992).
Chromosome walking, however, is fraud with dif-
fi culties when applied to large-genome species.
Because of the high content of repetitive DNA—
more than 80% in wheat (Flavell et al., 1974)—
most probes isolated from the ends of large-insert
clones are repetitive and cannot be used to gener-
ate contigs that span a gene of interest. The actual
chromosome walking step can be omitted if fl ank-
ing markers for the gene of interest are identifi ed
that span a physical distance smaller than the
average insert size of a large-insert clone. This
approach has been termed chromosome landing
(Tanksley et al., 1995) and was fi rst applied in
tomato (Martin et al., 1993). The chromosome
landing approach shifted the challenge in map-
based gene isolation from the walking step to
fi nding markers that are tightly linked to the trait.
Typically, this requires mapping populations of a
few thousand gametes to achieve the necessary
resolution and the ability to develop markers for
the region of interest. Targeted marker develop-
ment is facilitated by comparative information as
it allows orthologous regions in other species to
be tapped for markers. In the current era of
whole-genome sequencing, including the com-
pleted genomes of rice, sorghum, maize, and B.
distachyon , sequence information is the most
important source of markers for fi ne-mapping in
wheat.
The fi rst successful map-based cloning experi-
ments in wheat were concluded in 2003, some 10
years behind Arabidopsis. The lag was due to the
large size of the wheat genome, which made con-
struction of large-insert libraries and chromo-
some walking diffi cult. After all, constructing a
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