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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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retained and the centromeres of the remaining seven
chromosomes (A5, A7, A10, A3, A11, A2 and A9)
were lost in brachypodium (Qi et al., 2010; International
Brachypodium
Initiative, 2010).
1.7 Wheat ESTs uniquely mapped to specific bins
in wheat and their use for inferring relation with
brachypodium genome
It may be recalled that as many as 793 (16.51%) wESTs
(out of 4,804 bin-mapped wESTs) were mapped each
to single bins; perhaps these ESTs represent each a
single copy gene (Supplementary Table 5). These
wESTs were not used for the construction of wheat
consensus chromosome maps during the present study,
although these may be utilized for deriving syntenic
relationship between wheat and brachypodium in a
manner similar to their use in determining wheat-rice
synteny (Sorrells et al., 2003; La Rota and Sorrells,
2004; Singh et al., 2007). During the present study
each of the single copy wESTs matched with a unique
sequence of the brachypodium genome. A majority of
ESTs belonging to individual chromosomes of the
seven homoeologous groups (HGs) of wheat matched
with sequences of either one or two brachypodium
chromosomes (e.g. HG1 ESTs with Bd1 and Bd2;
HG2 ESTs with Bd1 and Bd5; HG3 ESTs with Bd2;
HG4 ESTs with Bd1; HG5 ESTs with Bd1 and Bd4;
HG6 ESTs with Bd3 and HG7 ESTs with Bd1 and
Bd3). These results of syntenic relationship between
wheat and brachypodium chromosomes inferred using
single copy ESTs are in agreement with the syntenic
relationship determined using multi-locus wESTs.
1.8 Comparison of wheat-brachypodium synteny
with previously reported wheat-rice synteny
It may be noted that wheat EST data set used for
analyzing the syntenic and structural relationship
between wheat and brachypodium during the present
study was also used in similar earlier studies involving
wheat and rice (Sorrells et al., 2003; La Rota and
Sorrells, 2004). Therefore, the three-way comparison
involving wheat, brachypodium and rice may help to
identify the patterns of synteny relationship among the
three species. A summary of this comparison is given
in Table 2. We noted that WC3, WC4 and WC6 had
comprehensive synteny with brachypodium chromo-
somes Bd2, Bd1 and Bd3, and with individual rice
chromosomes R1, R3 and R2, respectively. Thus,
WC3 matched with Bd2/R1, WC4 matched with
Bd1/R3 and similarly WC6 matched with Bd3/R2.
Therefore, it appears that the above three chromo-
somes of wheat, brachypodium and rice may have
originated form common individual specific ancestral
chromosomes as proposed in some earlier studies
(Salse et al., 2008; Luo et al., 2009; Qi et al., 2010;
International
Brachypodium
Initiative, 2010).
Further, each of the remaining four wheat consensus
chromosomes (WC1, WC2, WC5 and WC7) in
general showed syntenic relationship with two to three
specific brachypodium chromosomes and also with
two to three specific rice chromosomes (Table 2).
Therefore, during the course of speciation, new
chromosomes might have evolved through fusion
mechanism involving at least two chromosomes.
While conducting comparative genomic study involving
Ae. tauschii
, rice and sorghum, Luo et al (2009)
proposed that the chromosomes 2D and 7D of
Ae.
tauschii
evolved by chromosome fusion events. A
detailed comparison of the wheat-brachypodium
structural synteny reported during the present study
and the previously reported wheat-rice synteny may
help in exploring a detailed history of genome
evolution in grass lineage.
2 Conclusions
Mapped wESTs may be successfully used to examine
the synteny conservation and colinearity among wheat,
brachypodium and rice. Besides chromosomal rearran-
gements via chromosome fusion that were responsible
for alteration in chromosome number, extensive
synteny throughout the entire length of three wheat
and brachypodium chromosomes was also discovered.
It was further demonstrated that wheat brachypodium
Table 2 A summary of the prominent features of chromosome relationship among wheat, brachypodium and rice
Brachypodium chromosomes
2 & 3
1 & 5
2
1
4, 1 & 3
3
1 & 3
Wheat consensus chromosome
1
2
3
4
5
6
7
Rice chromosomes
5 & 10
7 & 4
1
3
3, 9 & 12
2
6 & 8
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