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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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to be syntenic at 30.2 Mb in the short arm of Bd2
(Supplementary Table 1). Therefore, this region may
contain centromere of Bd2.
1.2.2 Wheat consensus chromosome 2 (WC2)
Of the 214 wESTs belonging to WC2, matched with
two brachypodium chromosomes (Bd5 and Bd1). The
level of similarity was higher with Bd5 (smallest
chromosome) than with Bd1 (largest chromosome) as
48.6% were syntenic to Bd5 and 37.4% were syntenic
to Bd1, which is largely syntenous with WC4 (Table 1;
Figure 1). The remaining 14% were syntenic to the
remaining three brachypodium chromosomes (Bd4,
Bd2 and Bd3). The two small distal regions of
WC2S matched with Bd5 whereas the interstitial and
proximal regions were syntenous to Bd1. Except
proximal region C
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0.36 FL of WC2L, which matched
with Bd1 as well as Bd5, the remaining region of
WC2L had similarity with Bd5. The same region
(C
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0.36 FL) of WC2L also matched Bd5 for an equal
number of wEST suggesting that WC2 and two
brachypodium chromosomes (Bd1 and Bd5) might be
originated from a common ancestral chromosome and
still preserve a complex relationship. The syntenic
relationship between WC2 and these two brachypo-
dium chromosomes may be summarized as follows:
WC2S-C-WC2L = Bd5/Bd1
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C-Bd1/Bd5 (Figure 1).
The wEST BE442655 located in pericentro-meric
region of WC2S gave a hit at 51.8 Mb of Bd1 (Qi et
al., 2010) suggesting the probable position of Bd1
centromere (Supplementary Table 1).
1.2.3 Wheat consensus chromosome 3 (WC3)
Out of 212 wESTs belonging to WC3, 80.7% were
syntenous with Bd2 and the remaining 19.3% wESTs
were syntenous with other four brachypodium
chromosomes (Bd3, Bd1, Bd4 and Bd5) (Table 1).
Excellent synteny conservation of WC3 was observed
all along its two arms with Bd2 except few regions of
partial syntenies with other brachypodium chromo-
somes. The summary relationship of the WC3 with
the brachypodium chromosomes may be depicted as
follows: WC3S-C-WC3L = Bd2
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C-Bd2 (Figure 1).
The wEST BE404580 mapped near the centromere of
WC3L and showed synteny with long arm at 41.7 Mb
of Bd2 (Qi et al. 2010). High level of synteny between
WC3 and Bd2 suggest that both WC3 and Bd2
perhaps originated from a common specific ancestral
chromosome.
1.2.4 Wheat consensus chromosome 4 (WC4)
From a total of 170 wESTs belonging to WC4,
82.4% were syntenic to Bd1, the remaining 17.6%
being syntenic to the remaining four brachypodium
chromosomes (Bd4, Bd2, Bd3 and Bd5). Therefore,
WC4 is highly syntenous with a single brachypodium
chromosome (Bd1) (Table 1). The order of synteny
along the chromosome length was as follows:
WC4S-C-WC34L = Bd1
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C-Bd1 (Figure 1). The two
wESTs, namely BE497309 and BF202969 spanning
the pericentromeric region of WC4S and WC4L,
detected syntenic positions at 59.8 Mb and 60.7 Mb,
respectively in the chromosome Bd1, suggesting the
possible position of Bd1 centromere (Qi et al., 2010).
1.2.5 Wheat consensus chromosome 5 (WC5)
Of the 255 wESTs belonging to WC5, 56.1% were
syntenic with Bd4 and 29.4% were syntenic with Bd1
chromosome. Remaining 14.5% wESTs matched the
other three brachypodium chromosomes (Bd3, Bd2
and Bd5). Complete short arm of WC5 (WC5S)
matched Bd4 except the most terminal 2% region (FL
0.98
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1.00) that matched with Bd3. Approximately
76% of the long arm of WC5 (WC5L) also matched
with Bd4 while remaining 11% (FL 0.76
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0.78, 0.78
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0.79 and 0.79
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0.87) and 3% (FL 0.87
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1.00) matched
with Bd1 and Bd3, respectively. Interestingly, terminal
regions of both the arms of WC5 matched a segment
of Bd3 with only one wEST (Table 1). The syntenic
pattern between WC5 and the brachypodium chromo-
somes may be represented as follows: WC5S-C-WC5L
= Bd3/Bd4
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C-Bd4/Bd1/Bd3 (Figure 1). The wheat
EST BG314119 that mapped in the pericentromeric
region of WC5S may indicate the location of inactive
centromere of Bd4 (Qi et al., 2010).
1.2.6 Wheat consensus chromosome 6 (WC6)
Out of 194 wESTs belonging to WC6, a maximum of
78.8% matched Bd3 and only 21.2% matched with
segments of remaining four brachypodium chromo-
somes (Bd1, Bd2, Bd4 and Bd5; Table 1). The
relationship between WC6 and Bd3 was comparable
to that between WC3 and Bd2. Syntenic conservation
can be represented as follows: WC6S-C-WC6L =
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