Rice Genomics and Genetics 2015, Vol.6, No.1, 1-8
3
found that the sequences of all genotypes were
muted during evolution and showed number of
changes such as substitution, insertion and deletion
in the cultivars (data not given). The number of
substitution
Figure 1 Amplification of 10 aromatic rice cultivars employing
matk
gene specific primer.
Note: Ladder= Low range DNA ruler plus; Name of cultivars
represents in the lower of the gel; Numbers on the right side
of margin represents molecular weight marker DNA in base
pairs (bps) and Number on left side represents size of
amplified fragments in bps
was higher between the 1110 bps to 1270 bps which
might be the crucial during evolution. Similarly,
Kron et al
.
(1999) was also found the insertion and
deletion in
mat
K of Epacrids and vaccinioids.
Meanwhile MSA of ten aromatic rice genotypes
along with wild relatives of rice and grasses revealed
that the conserved nucleotide sequences as well as
nucleotides changes during evolution of aromatic
rice as compared to wild relatives and grasses under
family Poaceae. The key mutational changes such as
substitution ‘G’ to ‘C’ and ‘A’ was found in cultivars
except ‘Banikunja’ and ‘Basaomati (Paikanapua)’
viz. ‘Basnasapuri’, ‘Basnaparijat, ‘Basumati
dhan’,‘Chatiamaki - 1’, ‘Dhoiabankoi’, ‘Ganjam
local - 2’, ‘Gatia’ and ‘Kalikati - 1’ at position 1352
bp respectively. Whereas, most variable nucleotide
sequences was present in all aromatic rice genotypes
at position 1389 to 1384 (Figure 2A) and complete
deletion of nucleotide ‘T’ was observed at position
1761 and 1769 in all ten aromatic rice genotypes
(Figure 2B). Relevant to these issues is also
indicating that a gene is not a homogenous population
of nucleotides since different parts of the gene
assume different functional responsibilities and
some sections might lack a function. Consequently,
rates of nucleotide substitution can vary along the
entire coding, or even the noncoding regions of a
gene (Sastri et al., 1992; Clegg et al., 1994; Clark et
al, 1995).
Phylogenetic tree for
matK
gene based on nucleotide
sequences for both aromatic rice genotypes along
with wild relatives and grasses under family Poaceae
based on the alignment dataset was constructed by
neighbour joining statistical method of bootstrap test
with 1000 bootstrap replications in MEGA 6.
Phylogenetic tree of ten aromatic rice genotypes
showed one outgroup and two sub-clusters. Genotype
‘Banikunja’ was an outgroup, whereas genotypes
‘Basnasapuri’, ‘Ganjam local-2’, ‘Basumati dhan’,
‘Gatia’ and Basnaparijat’ were placed in cluster-IA
and ‘Dhoiabankoi’, ‘Chatiamaki-1’, ‘Basaomati
(Paikanapua)’ and ‘Kalikati-1’ was in cluster-IB
(Figure 3). Divergence time scale from ‘Basnasapuri’ to
‘Banikunja’ was estimated which was found
maximum for genotype ‘Banikunja’ i.e 0.015 and
minimum for ‘Gatia’ and ‘Dhoiabanki’ i.e. 0.009.
The maximum 47 and minimum 9 bootstrap values
were observed. Evolutionary divergence between the
sequences were estimated by using pair wise
distance matrix for aromatic rice cultivars it was
found that genotypes of ‘Banikunja’ and ‘Ganjam
local-2’ was distantly related with maximum
divergence value of 0.0296. whereas, Basumati dhan
and Gatia was closely related with minimum
divergence value of 0.0190 (Table 1).
Phylogenetic analysis of aromatic rice along with
related sequences was performed in order to find out
the relationship between aromatic rice, wild relatives
and grasses under family Poaceae in MEGA 6
program. Phylogenetic analysis of 41 other rice
species and grasses along with ten aromatic rice
genotypes were subjected to study the evolutionary
pattern of aromatic rice. It observed that there are
two main groups evolved from common ancestor.
Phylogenetic tree was categorized into two main
groups cluster-I and cluster-II. Cluster-I was further
divided into two sub-clusters IA and IB and aromatic
rice genotypes was placed in sub sub-cluster IA
1
which indicates the aromatic rice was evolved after
cultivated rice viz.
Oryza sativa
indica and japonica
group. Similarly cluster-II was also divided into two
sub clusters IIA and IIB. The 12 wild relatives of
Oryza
group was completely separated during
evolution and placed differently in sub sub-cluster-
IIB
1
(Figure 4). These 12 wild relatives of
Oryza
group might be evolved from closely related grasses
such as
Maltebrunia letestui
,
Prosphytocloa prehensilis
and
Leersia oryzoides
. Whereas domesticated rice
