Agriculture Reference
In-Depth Information
17,000 Mb for hexaploid wheat), the wheat, rice,
and maize genomes appear to be highly colinear.
Loci that map to non-colinear locations in differ-
ent genomes are usually detected by multicopy
probes and most likely represent paralogues rather
than orthologues. Furthermore, considering that
the grass ancestor has undergone a whole-genome
duplication some 70 million years ago, apparent
orthologues detected by single-copy probes may,
in fact, be paralogues if different gene copies were
deleted in different grass lineages, thereby com-
plicating comparative analyses (Paterson et al.,
2004). Breakdown of synteny tended to occur
mostly toward the distal chromosome regions
(Kurata et al., 1994).
While the early comparative maps relied on the
cross-mapping of RFLP markers, which meant
that only polymorphic loci could be mapped,
advances in genomics in both wheat and rice
allowed much more detailed comparisons to be
conducted. By 2004, wheat deletion maps con-
taining more than 16,000 loci had been con-
structed (Qi et al., 2004). The sequence of the rice
genome had also been completed (International
Rice Genome Sequencing Project 2005). Rice
orthologues for the mapped wheat ESTs and
their physical location could be identifi ed
in silico
from the rice genomic sequence. This showed
that the homoeologous group 1 chromosomes of
wheat (W1S-cent-W1L) corresponded to rice 5S
(R5S)-cent-R10-R5L, with 'cent' the centro-
mere position in wheat. Wheat group 2 chromo-
somes (W2S-cent-W2L) corresponded to
R4S-R7L-cent-R7S-R4L, W3S-cent-W3L to
R1S-cent-R1L, W4S-cent-W4L to the proxi-
mal part of R3L-R11-cent-R3S, W5S-cent-
W5L to R12L-cent-R9-distal part of 3RL,
W6S-cen-W6L to R2S-cent-R2L, and W7S-
cent-W7L to R6S-R8L-cent-R8S-R6L (La
Rota and Sorrells 2004). These relationships do
not take into account the complex translocation
involving chromosomes 4A, 5A, and 7B. The
effect of this rearrangement on the comparative
relationship with rice can be seen in Color
Plate 30.
Despite the clear evidence of syntenic blocks,
some 35% of wheat markers that appeared to be
single-copy in wheat mapped to nonsyntenic
positions in rice, suggesting that interchromo-
somal rearrangements involving small regions or
potentially single markers are commonplace.
Non-colinear markers were found across the
entire genome, but were particularly prevalent in
the satellite region on 1BS, the most distal bin on
chromosome 4AL, and the bin adjacent to the
6BS satellite (La Rota and Sorrells 2004).
Wheat-rice colinearity was also diffi cult to estab-
lish for the centromeric regions. No breakdown
in synteny was apparent in the distal chromosome
regions, as had previously been noted by Kurata
et al. (1994).
While the D genome of wheat is generally con-
sidered to be the most ancestral confi guration
within the Triticeae tribe, comparative analyses
demonstrate that the entire Triticeae lineage
underwent at least one gross chromosomal
rearrangement since its divergence from the
Aveneae-Poeae lineage. The structure of
Lolium
and fescue chromosome 4, which differs from
wheat and other Triticeae species by a 4S/5L
rearrangement represents, in fact, the ancestral
chromosome confi guration. Chromosomes for
which the region orthologous to the long arm of
the group 5 chromosomes in wheat (this break-
point is proximal to the 4L/5L translocation that
characterizes some Triticeae species) is fused to
the distal region of 4S show orthology to rice
chromosome 3 over their entire length (Color
Plate 30). Translocation of the distal region of the
short arm of the ancestral Pooid chromosome 4
to the long arm of chromosome 5 led to a break
in synteny with the long arm of rice chromosome
3 (Color Plate 30). The 4S/5L breakpoint is
also absent in
B. distachyon
, providing further
evidence that the absence of this rearrange-
ment represents the more ancestral chromosome
confi guration.
Colinearity at the DNA sequence level
Large-insert genomic library development in
wheat started in the late 1990s with BAC librar-
ies, fi rst of the diploid wheats,
T. monoccoccum
(Lijavetzky et al., 1999) and
Ae. tauschii
(Moullet
et al., 1999), and later of the tetraploid
T.
turgidum
ssp.
durum
(Cenci et al., 2003) and
