Rice Genomics and Genetics 2015, Vol.6, No.1, 1-8
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various anomalies in the taxonomic levels by using
the chloroplast genes such as
matK
and
rbcL
. The
matK
gene has two unique features that emphasize
its importance in molecular biology and evolution. It
is characterized by its fast evolutionary rate and
putative function as a group II intron maturase. It
is a chloroplast encoded gene nested between the 5’
and 3’ exons of trnK, tRNA-lysine in the large single
copy region of the chloroplast genome (Sugita et al.,
1985).
Molecular sequence data has revolutionized
evolutionary studies and enhanced the revolution of
phylogenetic trees immensely. Genes used in plant
systematic display different trends of evolution.
Slow evolving genes such as
rbcL
and
atpB
, have
high sequence conserve among plant groups. This
high sequence conservation allows a good resolution
that has been confined to the family level, but cannot
solve the intricacies below this level (Goldman et al.,
2001). The
matK
gene is considered to be fast
evolving due to the fact that it has a high rate of
substitution and more variable sites compared to
other genes (Olmstead and Palmar, 1994). Some of
the researchers reported that the
matK
has been
considered as a pseudogene because they contain
stop codons within the ORF, bear indels that create
frame-shift mutations and display an equal level of
substitution for all three codons position (Kores et
al., 2000).Additionally, frame-shift mutations found
in the 3’ region of
matK
of the family Poaceae,
which could also alter or destroy the reading frame;
appear to be limited to the very 3’ region of this gene,
not affecting the functionally of domain X (Hilu and
Alice, 1999).
The genus
Oryza
, which includes rice and closely
related wild relatives, has emerged as a powerful
system to study the modes and mechanisms of
genome evolution (Ammiraju et al., 2008). The
genus
Oryza
comprises approximately 23 species
that have been grouped into six diploid (AA, BB,
CC, EE FF, GG) and four allotetraploid genome
types (BBCC, CCDD, HHJJ and KKLL) (Lu et al.,
2009). All
Oryza
polyploids are wild and contain
important phenotypic traits that have the potential
for use to improve the cultivated rice (Brar and
Khush, 1997). In the present study implies the
understanding of major evolutionary relationships of
aromatic rice under the family, genus and species
level by using the chloroplast derived
matK
gene.
Results and Discussion
Among the various approaches used in molecular
systematic, DNA sequencing has become one of the
most widely utilized, particularly above the genus
level. Sequence variation in the coding and spacer
regions of a number of chloroplast, mitochondrial,
and nuclear genes has been utilized, with some
genes more widely used, like the
mat
K,
Adh
1,
Adh
2
and
rbcL
, and both coding and intergenic spacer
region (ITS) of the ribosomal DNA (Clegg et al.,
1994; Hsiao et al., 1994; Clark et al., 1995). The
sequence data are cumulative, the potential sizes of
informative data sets are immense, and the data are
available in public computer databases. The
matK
gene is emerging gene as potential contributions to
plant molecular systematic and evolution (Johnson
and Soltis, 1994, 1995; Steele and Vilgalys, 1994;
Liang and Hilu, 1996). This gene has been used
effectively in addressing systematic questions in the
number of families i.e. Polemoniaceae (Johnson and
Soltis, 1995), Poaceae or Gramineae (Liang and
Hilu, 1996), Orchidaceae tribe Vandeae (Jarrell and
Clegg, 1995) and Myrtaceae.
In this investigation, sharp and bright bands of 1500
kbs of plastid
matK
gene fragment from template
DNA of ten aromatic rice varieties were amplified
by using
matK
specific primers (Figure 1). For the
sequencing large scale amplification was done and
amplified fragments were separated in 2.5% low
agarose gel electrophoresis and subsequently used
for elution though Gel Extraction Kit (Genei
TM
). The
ten eluted fragments of rice varieties were sequenced
with an ABI 3730 XL genetic analyser with a
BigDye terminator cycle sequencing kit (SciGenome,
Kerala, India). For correctness of the sequences,
DNAs isolated from independent varieties were
analyzed for each genotype.
All nucleotide sequences from ten aromatic rice
genotypes were subjected tomultiple sequence alignment
(MSA) in Muscle program. The conserved region was
identified in all aromatic rice genotypes and found
very little changes in the conserved region. With
close observation of all ten genotypes sequences, it was
