Genome Organization and Comparative Genomics - Wheat Science and Trade - page 322

the hexaploid T. aestivum (Allouis et al., 2003).
These large-insert libraries provided the oppor-
tunity to conduct comparative analyses at the
DNA sequence level between wheat and other
grass species, mainly the small-genome model
rice. Examples of such studies are comparisons
between orthologous rice, sorghum ( Sorghum
bicolor ), barley, and T. monococcum BACs selected
to contain WG644, a marker linked to verna-
lization response (Ramakrishna et al., 2002);
between a T. monococcum BAC clone carrying
the grain hardness loci Gsp-1 , Pina-A , and
Pinb-A and the orthologous region on rice
chromosome 12 (Chantret et al., 2004); between
fi ve regions on the short arm of chromo-
some 1A m S totaling some 1.5 Mb and identifi ed
by the markers BCD1434, low-molecular-weight
glutenins, and disease resistance genes SRLK ,
Lrk10 , and Lr10 and the orthologous genomic
sequence on the short arm of rice chromosome
5 (Guyot et al., 2004); between a 250-kb region
of hexaploid wheat and the orthologous regions
on rice and B. sylvaticum (Griffi ths et al., 2006);
and between the wheat Lr34 region and the
orthologous regions in rice and B. sylvaticum
(Bossolini et al., 2007). The main observations
from these studies are that (i) gene content and
order are relatively well conserved, but that rear-
rangements such as small deletions, duplications,
inversions, and/or translocations are common
evolutionary events (Fig. 15.2) and (ii) intergenic

regions are expanded in wheat relative to
the smaller rice and Brachypodium genomes. The
expansion is caused mainly by the amplifi cation
and insertion of retrotransposons in the wheat
genome.
The extent to which synteny is disrupted varies
with chromosome region. One factor that has
been shown to affect levels of colinearity is the
rate of recombination. Synteny between the
homoeologous wheat chromosomes is inversely
correlated with recombination rates (Akhunov et
al., 2003a). The higher recombinogenic distal
chromosome regions carry more nonsyntenic
markers than the more recombinational-inert
centromeric regions. This has also been observed
in wheat-rice colinearity studies (Akhunov
et al., 2003b; See et al., 2006). Another factor that
may infl uence the extent to which colinearity
between orthologous regions is conserved is the
type of genes that are present in the region under
investigation. For example, Guyot et al. (2004)
found that only 4 of 20 genes predicted to be
present in a 638-kb wheat 1A m S sequence were
found in colinear positions on rice 5S. However,
the genes that were present in non-colinear posi-
tions were mostly storage protein and disease
resistance genes. Both types of genes are highly
specialized and often appear in clusters of locally
duplicated genes that provide templates for rear-
rangements through homologous recombination.
Non-colinearity of storage protein genes, due to

Fig. 15.2 Gene distribution and microcolinearity with rice of the VRN-1 region in T. monococcum . Circles indicate genes.
The size of gene islands in T. monococcum is indicated. Microcolinearity between T. monococcum and rice is highly conserved.
The only break in colinearity is caused by a gene duplication present in T. monococcum .