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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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0.24
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0.55, indicated a consensus bin or map position
within the fraction lengths 0.45
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0.55 on the short arm
of group 3 chromosomes (see Supplementary Table 1).
In case of non-availability or anomaly in bin-mapping
information due to one of the three homoeologues,
location of wEST consistent with the remaining two
homoeologs was used to construct the consensus map
for that individual homoeologous group. Wheat ESTs,
which were earlier mapped only on one of the three
homoeologous chromosomes of a group could not be
placed on the consensus map, but were still utilized in
the present study for improving wheat-brachypodium
synteny.
3.4 Identification of centromere location
Wheat ESTs that were previously mapped to the
pericentromeric regions and had homology with
specific individual brachypodium chromosomes were
used as query against the putative centromeres of
brachypodium identified by Qi et al. (2010).
3.5 Estimation of EST density
EST density ratios were calculated by dividing the
observed number of ESTs in a particular bin by the
expected number of ESTs. Expected number of ESTs
between the short and long arms was based on arm
ratio data. The arm ratios for individual wheat
chromosomes were earlier reported by Gill et al.
(1991) from physical measurement of C-banded
mitotic metaphase chromosomes of Chinese Spring.
3.6 Estimation of nonsynonymous vs. synonymous
substitution rates (Ka/Ks)
The sequence divergence between wheat and brachy-
podium matching pairs of sequences were estimated
by computing the rate of nonsynonymous versus
synonymous substitutions (Ka/Ks) using DnaSP v5.10
software (Librado and Rozas, 2009; http://www.ub.es/
dnasp/). A total of 153 homologs, having high quality
matching (85
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92% CIP and CALP) were aligned
using MUSCLE program in MEGA v5 software
(Tamura et al., 2011) and results of the sequence
alignments were saved in mega file format (.meg).
These files were then analyzed for synonymous and
nonsynonymous substitution rates by DnaSP v5.10.
Authors' Contributions
SK participated in the design of the study, performed analysis
and drafted the manuscript. HSB and PKG participated in the
design and supervision of the study and preparation of the final
manuscript. All authors have read and approved the final
manuscript.
Acknowledgements
The authors are thankful to the Department of Science and
Technology, New Delhi, India, for the financial support to
carry out this study. Thanks are also due to Professor B.
Ramesh, Head, Department of Genetics and Plant Breeding, Ch.
Charan Singh University, Meerut for providing necessary
facilities. PKG held a position of NASI Senior Scientist during
the tenure of which this study was completed.
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