Population genetic structure and diversity of high value vulnerable medicinal plant Acorus calamus in India using RAPD and chloroplast microsatellite markers

Abstract

Acorus calamus is a highly valued medicinal plant with global distribution used in several drugs of health care systems. We evaluated the genetic diversity and population structure of 50 populations of A. calamus from different geographical regions in India through RAPD and chloroplast microsatellite markers. From the total screened 82 RAPD primers and 18 cpSSR primers, 10 RAPD and nine cpSSRs were found polymorphic. The selected 10 RAPD primers produced a total of 96 reproducible bands, out of which 65 were polymorphic (67.70%). Whereas, the selected nine cpSSR markers produced 26 alleles and all of them were polymorphic. The mean genetic diversity (H T ) among populations using RAPD (H T = 0.263) and cpSSR (H T = 0.530) markers was higher in comparison to the mean genetic diversity within populations. Mean coefficient of gene differentiation (G ST ) between the populations was also high for both RAPD (G ST = 0.830) and cpSSR markers (G ST = 0.735), whereas the estimated gene flow was very low for RAPD (Nm = 0.102) and for cpSSR (Nm = 0.179). AMOVA analysis revealed that more genetic variation resided among the populations than within populations. Significant differences (p < 0.001) were observed between the populations and individuals within the populations. Cluster analysis of RAPD and cpSSR data using UPGMA algorithm based on Nei's genetic similarity matrix placed the 50 populations into two main clusters. The implication of the results of this study in devising strategy for conservation of A. calamus is discussed.

High Levels of Diversity in the Phytochemistry, Ploidy and Genetics of the Medicinal Plant Acorus calamus L.

“…In populations that are adapted to distinct environments, the fitness of immigrants or hybrids may be reduced by natural selection [32], further facilitating genetic divergence [33] and reducing genetic exchange between populations. Our previous population structure study [34] using genomic RAPD and chloroplast SSR markers detected high levels of population differentiation. However, contemporary enhancements in newly developed statistical tools have led to the emergence of methods for evaluation of the landscape and environmental effects on the distribution of genetic and phytochemical variation in natural environments [26].…”

“…Haplotype analysis: We reanalyzed the previously published cpSSR data from Ginwal (34). In each individual, the cpDNA alleles for all the loci were combined into a 9-locus chloroplast haplotype (chlorotype).…”

Genetic drift in six cultivated populations of Terminalia arjuna

“…Therefore, it revealed that the used primers had sufficient potency for population studies and this is the first report, which accesses the genetic diversity among and within populations of T. arjuna. The occurrence of low genetic diversity at the population level was also reported in many plant species [35,36,37,38,39,40,41].…”

Characterization and development of chloroplast microsatellite markers for Gossypium hirsutum, and cross-species amplification in other Gossypium species

“…The number of alleles per locus in this study ranged from 2-7 (mean = 4.25), with a mean PIC value of 0.48. Compared with the alleles and PIC values in other plants described in previous studies, such as those by Yang et al, 2008 (alleles = 2-6); Ginwal et al, 2011 (alleles = 2-3); Wang, 2013 (alleles = 1-3), this higher number of alleles and PIC value were not unexpected, as the Gossypium accessions were natural populations, and the genetic bottleneck caused by human-mediated selection pressure to accumulate a particular type of alleles governing various traits has not yet been applied (Iqbal et al, 2001;Vigouroux et al, 2002).…”