Rice Genomics and Genetics 2015, Vol.6, No.8, 1-8
1
Research Article Open Access
Molecular Phylogeny of Indian Indigenous Aromatic Rice Based on Sequence
Diversity of the Chloroplast-encoded
matK
Gene
Rahul G. Patil, Kundansingh R.Jadhao, Kailash C.Samal, Gyana R. Rout
Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture & Technology, Bhubaneswar-751003, Odisha, India.
Corresponding author email:
Rice Genomics and Genetics, 2015, Vol.6, No.8 doi:
10.5376/rgg.2015.06.0008
Received: 30 Jul, 2015
Accepted: 11 Sep., 2015
Published: 22 Sep., 2015
Copyright
©
2015
Patil R.G. et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Patil R.G., Jadhao K.R., Samal K.C., and Rout G.R., 2015, Molecular Phylogeny of Indian Indigenous Aromatic Rice Based on Sequence Diversity of the
Chloroplast-encoded
matK
Gene, Rice Genomics and Genetics, Vol.6, No.8 1
-
8 (doi:
10.5376/rgg.2015.06.0008
)
Abstract
Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene
matK
for 10 aromatic rice
cultivars and its wild relatives along with the progenitor’s grasses families. Multiple sequence alignment (MSA) of 10 genotypes
revealed higher number of substitution between the 1110 bps to 1270 bps which might be the crucial during evolution of aromatic
rice. Similarly MSA of all related sequences with aromatic rice cultivars showed substitution and deletion in aromatic rice cultivars.
The deletion of ‘T’ at position 1761 and 1769 was crucial nucleotide changes in aromatic rice as compared to its progenitors. The
aligned sequences were used for molecular phylogenetic analysis by neighbor-joining methods with 1000 replication of bootstrap test.
Phylogenetic tree of aromatic rice cultivars showed cultivar ‘Banikunja’ was outgroup whereas cultivars ‘Basumati dhan’ and ‘Gatia’
was more closely related. Similarly phylogenetic tree of aromatic rice with its wild relatives and grasses progenitors showed that
aromatic rice was more closely related to
Oryza sativa
japonica group. The genus
Oryza
was divided into two main clades and
evolved from completely different group of grasses families.
Oryza brachyantha
has high affinity for grasses and should be treated as
a progenitor for wild
Oryza
species.
Keywords
Aromatic rice;
matK
; Molecular phylogeny; Evolution
Introduction
Aromatic rice constitute a small but special group of
rice, which are considered best for aroma and have
occupied a prime position in society for aroma and
cooking qualities (Ahuja et al. 1995). A large number
of aromatic rice has already been disappeared and
many are at the verge of extinction. Therefore, there
is a utmost necessary to conserve the germplasm. The
chloroplast maturase K gene (
matK
) is one of the
most variable coding genes of angiosperms and has
been suggested to be a “barcode” for land plants. A
'barcode' gene that can be used to distinguish between
the majorities of plant species on earth has been
identified. However,
matK
exhibits low amplification
and sequencing rates due to low universality of
currently available primers and mononucleotide repeats.
In plant systematic,
matK
has recently emerged as an
invaluable gene because of its high phylogenetic
signal compared with other genes used so far (Muller
et al., 2006).The 1500 bp
matK
gene is nested in the
group II intron between the 50 and 30 exons of
trnK
in the large single copy region of the chloroplast
genome of most of the green plants (Sugita et al.,
1985; Steane, 2005; Daniell et al., 2006; Turmel et
al., 2006). Phylogenetic analysis of a data set
composed of
matK
,
rbcL
, and
trnT
-F sequences
from basal angiosperms demonstrated that
matK
contributes
more
parsimony
informative
characters and significantly more phylogenetic
structure on an average per parsimony-informative
site than the highly conserved chloroplast gene
rbcL
(Muller et al., 2006). Sequence information from
matK
alone has generated phylogenies as robust
as those constructed from data sets comprised of
2-11 other genes combined (Hilu et al., 2003).
Further, the molecular data generated from
matK
has
been used to resolve phylogenetic relationships at
taxonomic levels (Johnson and Soltis, 1994;
Hayashi and Kawano, 2000; Hilu et al., 2003;
Cameron, 2005). The
matK
gene stands out among
plastid genes used in plant systematic for its distinct
mode of evolution. The rate of substitution in
matK
is three times higher at the nucleotide level and six
times higher at the amino acid level than that of
rbcL
which denoting it as a rapidly evolving gene
(Johnson and Soltis, 1994; Olmstead and Palmer,
1994; Soltis and Soltis, 2004). Various scientist have
been studied the plant evolution, and able to solve
