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densities reaching 1 gene per 10-20 kb in the gene
islands.
The VRN-2 gene maps to the distal 13% of
chromosome arm 5AL, which has a RGD of 1.97
(Linkiewicz et al., 2004). Approximately 440 kb
of contiguous sequence for that region contains
eight genes and one pseudogene, indicating an
overall gene density of 1 gene per 55 kb. The
genes are organized in three islands, one with
three genes and the other two islands each con-
taining two genes. The three-gene island spans
15 kb, and the two-gene islands span 22 kb and
28 kb. The gene density within the islands is thus
in the range of 1 gene per 5-24 kb. The distance
between islands varies from 52 kb to 224 kb. The
highest gene density found in this region was
1 gene per 5 kb, and the lowest gene density
was 1 gene per 300 kb.
The VRN-1 gene is located interstitially on
chromosome arm 5AL in a segment defi ned by
fraction lengths 0.68 and 0.78 (Sarma et al., 1998).
The RGD in the larger 0.35-0.78 region is 1.18,
which is considered average (Linkiewicz et al.,
2004). Two overlapping BAC clones and three
individual BAC clones, comprising a total of 550 kb,
have been sequenced for that region. Nine genes
and one pseudogene have been identifi ed, resulting
in an average density of 1 gene per 61 kb. Seven of
the genes were organized in three islands with local
gene densities of 1 gene per 3.4 kb, 6.2 kb, and
9.6 kb (SanMiguel et al., 2002; Yan et al., 2003;
Fig. 15.2). The other two genes were found on
separate BAC clones. Thus, within the 0.2-cM
interval that spanned VRN-1 , gene densities varied
from being comparable to those in rice to what is
expected to be an average gene density in wheat.
While the VRN-1 , VRN-2 , and Lr10 regions
were selected because of their agronomic impor-
tance, this was not the case for the 4DL13 region.
The 4DL13 region is located on a segment of
chromosome arm 4DL defi ned by fraction lengths
0.56 and 0.71 and has a RGD of 1.57. The
sequenced region consists of nine BAC clones
totaling 1 Mb. Of the fi ve annotated genes, two
clustered in a 14-kb region. The three remaining
genes were separated by intergenic distances
of 140 and 190 kb (A. Massa, J. Dvorak, P.
Rabinowicz, and K.M. Devos, unpublished data).
The overall gene density for the region is 1 gene
per 200 kb.
To obtain representative examples of the gene
organization in proximal chromosome regions, six
BAC clones that mapped to centromeric bins on
different chromosomes and had been annotated
for gene content were randomly selected (K.M.
Devos, P. San Miguel, and J.L. Bennetzen,
unpublished data). The size of the bins varied
from 27% to 45% of a chromosome arm. Relative
gene densities were <0.8 in fi ve of the bins and
1.16 in the 7BS centromeric bin. Three of the
BAC clones contained no genes, and the other
three contained one gene each.
These studies confi rmed the overall trend seen
in RGD values obtained from deletion mapping,
that is, gene numbers decrease when moving from
the telomere toward the centromere. Lower gene
numbers are translated into fewer gene islands
and larger intergenic distances. In the distal chro-
mosome regions, most genes are clustered with
two or three genes occupying 40 kb or less. Gene
densities in these islands approach those observed
in the 400-Mb rice genome (International Rice
Genome Sequencing Project 2005). Relatively
fewer of these islands are seen in the interstitial
chromosome regions, and more genes are present
as singletons. When gene islands are present, gene
densities, however, remain in the order of 1 gene
per 5 to 20 kb, irrespective of the location in the
genome. In the proximal regions, gene islands are
largely lacking and genes are separated by large
intergenic distances.
Intergenic regions consist mainly of retrotrans-
posons that have inserted into one another in a
nested fashion, similar to the patterns found in
maize (Wicker et al., 2001; SanMiguel et al., 2002;
Gu et al., 2004; Kong et al., 2004; Fig. 15.4).
While retrotransposons have occasionally been
found in genes (Harberd et al., 1987; Martienssen
and Baulcombe 1989), most retrotransposons
insert into other repetitive sequences. This could
be an active selection mechanism, devised by the
plant to both preserve gene function and control
retrotransposon activity through the insertion of
new elements (Bennetzen 2000). On the other
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