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will also affect the rate with which these new
gene arrangements are fi xed in the popula-
tion (Gaut et al., 2007). Advantageous genes
will be fi xed faster and deleterious genes will
be purged faster in the high- than in the low-
recombinant regions. So, through interplay of
rearrangements and selection, recombination
leads to an increase in the density of mostly
duplicated gene copies in the distal chromosome
regions. This is true for both tandem and
dispersed gene duplicates.
A corollary of the enhanced evolutionary rates
at the ends of chromosomes is that the levels of
colinearity between wheat and other grass
genomes will be lower in the distal than in the
proximal regions (Akhunov et al., 2003a; See et
al., 2006). If the duplication occurred in the
wheat lineage, then the duplicated gene copy will
not have a true orthologue in rice. If, on the other
hand, the duplication pre-dated the wheat-rice
divergence, distal paralogues will have a higher
chance than proximal copies to be differentially
deleted in the two species, again leading to a
disturbance of syntenic relationships that will
affect mostly distal regions. Distal genes that are
nonessential may also accumulate mutations
faster, simply because recombination is inher-
ently mutagenic. For essential genes, this will be
counteracted by natural selection, but duplicated
gene copies will be largely free from such a
constraint.
Retrotransposons, on the other hand, are
present at higher frequencies in the proximal com-
pared with the distal chromosome regions. The
uneven distribution of retrotransposons in the
wheat genome may be caused by the preferential
insertion of LTR-retrotransposons into other
repeats. As mentioned earlier, this may serve to
preserve gene function as well as to potentially
inactivate existing elements in the genome through
the insertion of new copies. Accumulation of ret-
rotransposons in low-recombinant regions may
also be facilitated by the fact that selection is inef-
fi cient in these regions. However, a study in rice
found that retrotransposon removal occurred
equally effi cient in centromeric versus euchro-
matic regions (Ma et al., 2007). At least in rice,
preferential insertion of retrotransposons thus
seems to be the main cause of the inverse relation-
ship between gene density and number of ret-
rotransposons. Wheat has a steeper recombination
gradient than rice, and we cannot exclude that, in
wheat, removal of retrotransposons in wheat is
affected by recombination.
TOWARD SEQUENCING
THE WHEAT GENOME
Great strides have been made in wheat genomics
over the past 10 years. Nevertheless, making a
quantum leap forward in our understanding of
wheat genome organization, gene function, and
evolutionary mechanisms will require sequenc-
ing of the wheat genome. While the international
wheat community is unifi ed in its goal of obtain-
ing a whole-genome sequence of wheat, the dis-
cussion is still ongoing on the most appropriate
sequencing strategies. Early discussions focused
on whether to sequence the hexaploid bread
wheat genome or a diploid relative such as Ae.
tauschii . Bread wheat is the economically most
important Triticeae species. A key question was
whether the gene content of the A, B, and D
genomes was suffi ciently different to justify
the fi nancial resources needed for sequencing
all three genomes. The development of cheap
sequencing technologies has shifted the challenge
from generating the sequence to assembling
the reads into a high-quality draft sequence. The
debate now focuses largely on which technology
or combination of technologies will give the
highest information content for the lowest cost.
The most complete genome sequence is
obtained when sequencing is done BAC by BAC,
following the construction of a physical map.
This approach has been used to sequence the Ara-
bidopsis genome (The Arabidopsis Genome Ini-
tiative 2000), has been used by the International
Rice Genome Sequencing Project to sequence
the rice genome (International Rice Genome
Sequencing Project 2005), and is also being used
to sequence the maize genome (http://www.
maizesequence.org/). Physical maps for both the
diploid Ae. tauschii (J. Dvorak and M.-C. Luo,
pers. comm.) and for hexaploid wheat (see section
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