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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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Therefore, considerable efforts and resources have
been invested in developing genomic resources of
brachypodium. These efforts led to the development
of 20 449 ESTs (Vogel et al., 2006), two BAC libraries
(Huo et al., 2006), 64 696 BAC-end sequences (Huo
et al., 2008) and the high-quality genome sequence of
brachypodium (International
Brachypodium
Initiative,
2010). Using some of the above genomic resources,
comparative genomics studies revealed a closer
relationship of Triticeae grasses with brachypodium
relative to that with either rice or maize (Huo et al.,
2009; Gu et al., 2009; Kumar et al., 2009). The
phylogenetic studies involving chloroplast genome
sequences of brachypodium also confirmed close
relationship with other members of the tribe Triticeae
(Bortiri et al., 2008). Orthologous relationships between
brachypodium genome and those of rice, sorghum,
barley, hexaploid wheat and
Aegilops tauschii
have
also been observed (International
Brachypodium
Initiative, 2010). Besides the above, putative position
of centromere in each brachypodium chromosome has
been identified using conserved centromeric gene
sequences (COS-C) of wheat and rice (Qi et al., 2010).
Keeping in view a growing interest in the brachypodium
genome as a model system for temperate grass species
such as wheat, we compared the bin-mapped wheat
ESTs (taken from individual wheat chromosomes)
with brachypodium genome to decipher the syntenic
relationships between these two species and also to
relate the derived information with the known
syntenic relationship between wheat and rice (La Rota
and Sorrells, 2004). The results of this study are
presented in this communication.
1 Results and Discussion
1.1 Matching of mapped wESTs with brachypodium
genome sequences
During the present study, a total of 8 210 mapped
wEST sequences distributed on all the 21 wheat
chromosomes were subjected to BLASTN, each against
the sequences of five brachypodium chromosomes
(Bd1 to Bd5) representing 8× coverage of ~271 Mb
genomic sequence of brachypodium. Using wESTs as
query sequences, the number of significant hits to
brachypodium chromosome sequences were found to
exceed the number of non-significant hits at very high
stringent conditions of BLASTN analysis that took
into account not only similarity of sequences (average
90% CIP) but also relative lengths of the sequences
matched (87.5% CALP). Out of 8 210 mapped wESTs,
5 208 (63.4%) ESTs showed significant hits against
brachypodium chromosomes, and included 4 804
(92.3%) wESTs that were earlier mapped to specific
bins of wheat chromosomes belonging to different
homoeologous groups (Table 1). Remaining 404 wESTs
were earlier assigned either to chromosomes or their
arms only, but were not assigned defined positions
involving known deletion bins.
Most of the 4 804 wESTs, which showed homology
with brachypodium (wheat/brachypodium homologs),
each had two or three homoeoloci involving homoeo-
logous chromosomes of the concerned group; the
physical order of these homoeoloci among three
chromosomes was also nearly similar, irrespective of
the size of individual chromosome within a homoeo-
logous group. Therefore, based on conserved syntenic
regions and extensive colinearity, the bin mapping
information of each of the three homoeologs of wheat
was integrated and consensus physical maps for each
of the seven homoeologous groups (total 7 consensus
chromosomes), namely WC1 to WC7 were generated
and used for study of synteny between wheat and
brachypodium genomes (see material and methods for
details; Supplementary Table 1). A total of 1 380 of
the 4 804 bin-mapped wESTs that gave significant
hits with brachypodium chromosomes could also be
assigned to the bins of wheat consensus chromosomes
WC1 to WC7 (Table 1). Majority of wESTs belonging
to an individual wheat consensus chromosome were
shared by one or two brachypodium chromosomes. For
instance, WC3, WC4 and WC6 exhibited a relatively
high level of synteny with Bd2, Bd1 and Bd3, respect-
ively. Similarly, WC1, WC2, WC5 and WC7 showed
composite synteny with Bd2/Bd3, Bd5/Bd1, Bd4/Bd1
and Bd1/Bd3, respectively. The results of the present
study extend the earlier work of Sorrells et al (2003)
and La Rota and Sorrels (2004), where syntenic
relationship between seven homoeologous groups of
wheat and twelve rice chromosomes were established.
Comparative analysis between the genomes of wheat
and brachypodium indicate that most individual
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