Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny
- 182 Downloads
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.
- 5.Borah RL, Sharma GC (2012) Systematic survey of Zingiberaceae of Dibrugarh district, Assam, India. Indian J Fundam Appl Life Sci 2:365–373Google Scholar
- 9.Roy J (1998) Karyophotometrical analysis and exploration of major oil constituents of Zingiberaceae. Mahatma Gandhi University, KottayamGoogle Scholar
- 14.Wang Y, Sun E, Wang W et al (2016) Effects of habitat fragmentation on genetic diversity and population differentiation of Liposcelis bostrychophila badonnel (Psocoptera: Liposcelididae) as revealed by ISSR markers. J Stored Prod Res 68:80–84. https://doi.org/10.1016/j.jspr.2016.04.008 CrossRefGoogle Scholar
- 18.Drummond A, Ashton B, Buxton S et al (2010) Geneious 5.5Google Scholar
- 20.Rohlf FJ (2000) NTSYS-pc—numerical taxonomy and multivariate analysis system. Exeter Publishing, Ltd., New YorkGoogle Scholar
- 22.Yeh FC, Yang RC, Boyle TBJ et al (1997) POPGENE, the user friendly shareware for population genetic analysis. Biotechnology 7(2):104–110Google Scholar
- 24.R Development Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
- 28.Zhao R, Zhang H, An L (2018) Anthropogenic disturbances affect population size and biomass allocation of two alpine species from the headwater area of the Urumqi river, China. Pakistan J Bot 50:199–209Google Scholar
- 37.Vukov D, Ilić M, Ćuk M et al (2018) Combined effects of physical environmental conditions and anthropogenic alterations are associated with macrophyte habitat fragmentation in rivers—study of the Danube in Serbia. Sci Total Environ 634:780–790. https://doi.org/10.1016/j.scitotenv.2018.03.367 CrossRefPubMedGoogle Scholar
- 38.Chen K-X, Wang R, Chen X-Y (2008) Genetic structure of Alpinia japonica populations in naturally fragmented habitats. Acta Ecol Sin 28:2480–2485Google Scholar
- 39.Guo W, Hussain N, Wu RUI, Liu BAO (2018) High hypomethylation and epigenetic variation in fragmented populations of wild barley (Hordeum brevisubulatum). Pak J Bot 50:1379–1386Google Scholar