Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny
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Genetic structure was evaluated among wild Alpinia nigra (Gaertn.) B.L. Burtt, populations. The information of genetic relatedness was developed using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and barcoding loci (plastid and mitochondrial). The order (high to low) of Shannon’s information index (I) and Nei’s gene diversity (h) from the populations was: “IIT Guwahati” > “Amingaon” > “Saraighat”. Genetic diversity decreased and genetic differentiation increased among the three populations. We observed no isolation by distance thus lower amount of gene flow was observed. Narrow range of genetic distance among the three populations and appearance of two distinct clusters strengthened the geographical isolation in dendrogram and principal component analysis. No mutation among the three populations was observed for seven plastid loci and two mitochondrial tested suggesting the taxonomic homogeneity. The phylogeny based on nine barcoding loci supported our observation that individuals of IIT Guwahati were partially isolated from the outside populations. Our study will provide a backbone for developing strategies to resist habitat fragmentation of Zingiberaceous plants.
KeywordsAlpinia nigra Genetic diversity DNA barcodes Habitat fragmentation ISSR marker Population differentiation RAPD marker
ATP synthase subunit b–ATP synthase subunit c
Cytochrome oxidase subunit 1
Inter simple sequence repeats
Principle component analysis
Polymorphic information content
Polymerase chain reaction
Photosystem II reaction center protein K–Photosystem II reaction center protein I
Random amplified polymorphic DNA
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
RNA polymerase C
RNA polymerase B
Unweighted pair group method with arithmetic mean.
SB, IC and RGS thank MHRD for fellowship. LR thanks the Department of Biotechnology (DBT) Government of India for funding the project by way of DBT Twinning Programme for NE (BT/33/NE/TBP/2010) and Biosciences and Bioengineering Department, IIT Guwahati for providing all necessary infrastructural support.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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