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
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
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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)
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.
Aromatic rice; matK; Molecular phylogeny; Evolution