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Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny

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Abstract

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.

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Abbreviations

accD :

Acetyl-CoA carboxylase-D

atpF–atpH :

ATP synthase subunit b–ATP synthase subunit c

cob :

Apocytochrome b

cox1 :

Cytochrome oxidase subunit 1

ISSR:

Inter simple sequence repeats

PCA:

Principle component analysis

PIC:

Polymorphic information content

PCR:

Polymerase chain reaction

psbK–psbI :

Photosystem II reaction center protein K–Photosystem II reaction center protein I

RAPD:

Random amplified polymorphic DNA

rbcL :

Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

rpoC1 :

RNA polymerase C

rpoB :

RNA polymerase B

UPGMA:

Unweighted pair group method with arithmetic mean.

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India

    Supriyo Basak, Ishani Chakrabartty, Vivek Hedaoo, Rahul G. Shelke & Latha Rangan

  2. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China

    Supriyo Basak

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Correspondence to Latha Rangan.

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Supplementary Fig. 1

The multiple sequence alignment of three populations of Guwahati city, Northeast India. arpoC1, bcob. The genes rpoC1 and cob were characterized by no mutation. It showed that all the three populations were A. nigra (TIF 1602 KB)

Supplementary Fig. 2

The multiple sequence alignment of the three populations of Guwahati city, Northeast India showed no mutation in the sequence. arpoB1, brbcL. This study confirmed that all the accessions are of A. nigra (TIF 1364 KB)

Supplementary Fig. 3

The multiple sequence alignment of the three populations of Guwahati Assam showed no mutation in the sequence. aaccD, bmatK. This study confirmed that there was no taxonomic ambiguity in our experimental design (TIF 1602 KB)

Supplementary Fig. 4

The multiple sequence alignment of inter-genic regions for three populations of Guwahati Assam showed no mutation in the sequence. aatpF-atpH, bpsbK–psbI. This study confirmed that all the accessions are of A. nigra (TIF 1797 KB)

Supplementary Fig. 5

The multiple sequence alignment of mitochondrial region (cox1) of the three populations of Guwahati Assam showed no mutation in the sequence. This study confirmed that all the accessions are of A. nigra (TIF 1067 KB)

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Basak, S., Chakrabartty, I., Hedaoo, V. et al. Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny. Mol Biol Rep 46, 177–189 (2019). https://doi.org/10.1007/s11033-018-4458-3

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