Genetic diversity of high-elevation populations of an endangered medicinal plant

Genetic diversity and population structure analysis of Paris polyphylla Sm. revealed by SSR marker

Paris polyphylla Sm. is a vulnerable medicinal plant distributed in the Himalayan countries. This plant has numerous pharmacological benefits, including anticancer, anti-inflammatory, analgesic, and antipyretic properties. The distribution, conservation status, and traditional usage of this species are fairly known in Nepal. However, its diversity and population structure at the molecular level are unexplored. This study analyzes, the genetic diversity and population structure of 32 P. polyphylla germplasms collected from Central, Eastern and Western regions of Nepal using 15 simple sequence repeat (SSR) markers. All the SSR primers were polymorphic and amplified 60 alleles ranging from 50 bp to 900 bp. The polymorphic information content (PIC) value ranged from 0 to 0.75. The average value of the observed heterozygosity (Ho), expected heterozygosity (He), Shannon's information index (I), and total heterozygosity (Ht) were 0.63, 0.53, 0.92 and 0.32, respectively. The analysis of molecular variance (AMOVA), showed a maximum variation of 74% within the individual in a population and only 26% variation among the population. In the population STRUCTURE analysis two clusters were formed where Eastern germplasms (EN) were separated far from the Central and Western germplasms (CWN), this clustering was in complete correspondence to the unweighted pair group method based on arithmetic average (UPGMA) and principle coordinate analysis (PCoA). Furthermore, in the UPGMA and PCoA, germplasms collected from the same or relatively similar geographic origin were closer. These findings are critical for developing conservation policies, facilitating evolutionary research, sustainable utilization and commercial cultivation of this pharmacologically important and threatened species.

Genetic diversity and population structure of critically endangered Dactylorhiza hatagirea (D. Don) Soo from North-Western Himalayas and implications for conservation

Dactylorhiza hatagirea (D. Don) Soo is medicinally important herb, which is widely used in ayurveda, unani, and folk/traditional medicine system to cure diseases. Due to its immense ethno-botanical properties, the trade of D. hatagirea is estimated to be USD 1 billion/year in India. Unfortunately, due to overexploitation of the herb from the wild, has resulted in dwindling of its populations in their natural habitats, which has led to its critically endangered status. Molecular genetic studies are still scarce in D. hatagirea, therefore, in current study, genetic diversity and population structure analysis was carried out of 10 populations (48 individuals) collected from three cold desert regions (2527 m-3533 m amsl) of Himachal Pradesh. Mean observed heterozygosity (Ho) and expected heterozygosity (He) was recorded 0.185 and 0.158. The maximum values for Fst (fixation index) and Nm (gene flow) were recorded 0.945 at locus KSSR14 and 1.547 at locus KSSR 4 respectively. Mean genetic differentiation (Fst) coefficient was estimated to 0.542. Overall, low levels of genetic diversity was recorded in the populations of D. hatagirea, might be due to habitat specificity (alpine meadows ecosystem; humid laden undulating habitat), restricted distribution and high anthropogenic activities. However, two populations viz., Bathad and Rangrik were recorded with high diversity and largest number of private alleles, stipulates that these populations might have high evolutionary significance and response to selection. Dendrogram analysis revealed that the populations of D. hatagirea were clustered into four major clusters, which was supported by Bayesian based STRUCTURE predictions. Clustering pattern of majority individuals of different populations revealed consistency with their geographic origin. Outcomes of current study reveals the status of genetic diversity and population structure of endangered D. hatagirea, which can be futuristically utilised for appropriate planning of conservation strategies.

Genetic diversity and structure revealed by genomic microsatellite markers in Centella asiatica (L.) Urb., a plant with medicinal potential

BACKGROUND

Around the world, medicinal plants are utilised for various purposes. Centella asiatica is one of the important medicinal plants widely used in many medicinal systems. Nevertheless, analysis of the genetic diversity would pave the way for its most suitable utilisation.

METHODS AND RESULTS

The present study analyses the genetic diversity and structure of eighty C. asiatica accessions collected from the southern states of India, using ten genomic microsatellite markers. The mean Nei's gene diversity (0.46) indicates considerable genetic diversity. Analysis of molecular variance (82.48%) exhibited significant genetic variance between samples within the population. The cluster analysis brought out the structure of the analysed populations as three subpopulations based on the genetic differentiation.

CONCLUSIONS

The study showed significant intra-population variation, predominant inbreeding and population differentiation in C. asiatica. The findings will help better understanding of the genetic structure and gene pool of the plant.

Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: an endangered medicinal plant

Gloriosa superba L., an endangered medicinal plant with global interest due to presence of colchicine, an important alkaloid used in formulations of Indian and Traditional medicine. The plant has become endangered due to its unscientifically exploitation and high medicinal values. In the Present study 10 randomly amplified polymorphic DNA (RAPD) and 6 ISSR markers were employed to assess genetic divergence among micro propagated, wild and field cultivated plants of Gloriosa superba collected from different parts of India. In RAPD analysis, all the 10 accession with 10 RAPD primers amplified 466 fragments, with 96.43 % polymorphism and with an average of 46.6 bands per primer. The size of amplicons varied from 1656 to 100 bp. While, ISSR primers produced 328 fragments of which 298 were polymorphic with an average of 49.7 bands per primer with 91.83% polymorphism. The size of amplicons ranges from 2395 to 181 bp. RAPD, ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes, Average PIC value for RAPD, ISSR and combined RAPD + ISSR markers obtained was ≤ 0.50 suggesting the informativeness of markers. Jaccard's coefficient ranges from 0.18 to 0.75 (RAPD) and 0.17 to 0.61 (ISSR) and 0.21-0.52 for pooled ISSR and RAPD markers. The clustering pattern based on UPGMA analysis of the genotypes in the combined analysis revealed that the majority of the genotypes remained similar to the ISSR dendrogram, while the RAPD-based dendrogram showed some variation in the clustering of genotypes. The result of PCA scattered plot obtained were in agreement with the UPGMA dendrogram, which further confirms the genetic relationships explain by cluster analysis. Results confirmed that the genotype studied had good genetic diversity and can be used for identification, conservation, and future breeding program of Gloriosa species and consequently for the benefit of the pharmaceutical industries.

Amplified Fragment Length Polymorphism: Applications and Recent Developments

AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.

Molecular analyses of genetic variability in the populations of Bergenia ciliata in Indian Himalayan Region (IHR)

Bergenia ciliata is an important medicinal plant species of Indian Himalayan Region (IHR). Genetic variability and population genetic structure of B. ciliata sampled from IHR was studied using two single primer amplification reaction (SPAR) methods (DAMD: Directed Amplification of Minisatellite region DNA; ISSR: Inter Simple Sequence Repeats). To provide a reasonable scientific basis for management and conservation of B. ciliata populations in IHR, genetic diversity analysis of 11 populations with 24 SPAR markers (15 ISSR and 9 DAMD) revealed significantly high level of (90.03%) polymorphism at species level. However, genetic variability was low at population level and KUL and BWS populations showed maximum while SHM population revealed least genetic diversity among the 11 populations. Analysis of molecular variance revealed highest percentage of variation (73%) within populations, followed by 17% among populations and least (10%) among the Himalayan regions. Clustering pattern obtained from UPGMA dendrogram was supported by STRUCTURE and principal coordinate analysis, segregating all the 11 natural populations of B. ciliata into two genetic clusters: Eastern and Western Himalayan populations. The clustering patterns of all the three statistical methods indicated that populations of B. ciliata have structured in response to the local micro-climates of the habitats in IHR, and therefore, it can be concluded that genetic variability is in congruence with the geographical diversity.

Molecular analysis of genetic diversity and population genetic structure in Ephedra foliata: an endemic and threatened plant species of arid and semi-arid regions of India

Studies on the genetic diversity and structure in endangered and threatened species are of utmost importance to design and promote effective conservation and management programs. Ephedra foliata, an endemic and threatened species growing naturally in arid and semi-arid regions of north western India, was investigated to estimate genetic variability and population structure using inter-simple sequence repeats (ISSR) and directed amplification of mini-satellite DNA (DAMD) markers. Twenty-five (ISSR 15; DAMD 10) markers produced 449 fragments, of which 382 were polymorphic in nature, revealing 84.59% polymorphism. ISSR markers revealed higher levels of polymorphism, polymorphic information content, marker index, diversity index and effective multiplex ratio than DAMD markers. Higher values of polymorphism, genetic diversity and Shannon information index at species level than at population level revealed that E. foliata possess high genetic diversity. AMOVA revealed much higher variance within populations than among the populations. The three clustering approaches viz., UPGMA, PCoA, and STRUCTURE, grouped the eleven investigated populations into two clusters revealing two genetic populations and the patterns of clustering of populations was in accordance with their geographic distribution, suggesting that these populations have evolved in response to their local environments. The high level of genetic differentiation (G _ST  = 0.31) and moderate gene flow (N _m  = 1.11) among populations could be due to geographic isolation, regional climatic conditions, over-exploitation and improper seed setting. To the best of our knowledge, this study is the first endeavour to estimate genetic diversity and population structure of E. foliata using molecular markers.

Bacterial endophytes modulates the withanolide biosynthetic pathway and physiological performance in Withania somnifera under biotic stress

Despite the vast exploration of endophytic microbes for growth enhancement in various crops, knowledge about their impact on the production of therapeutically important secondary metabolites is scarce. In the current investigation, chitinolytic bacterial endophytes were isolated from selected medicinal plants and assessed for their mycolytic as well as plant growth promoting potentials. Among them the two most efficient bacterial endophytes namely Bacillus amyloliquefaciens (MPE20) and Pseudomonas fluorescens (MPE115) individually as well as in combination were able to modulate withanolide biosynthetic pathway and tolerance against Alternaria alternata in Withania somnifera. Interestingly, the expression level of withanolide biosynthetic pathway genes (3-hydroxy-3-methylglutaryl co-enzyme A reductase, 1-deoxy-D-xylulose-5-phosphate reductase, farnesyl di-phosphate synthase, squalene synthase, cytochrome p450, sterol desaturase, sterol Δ-7 reductase and sterol glycosyl transferases) were upregulated in plants treated with the microbial consortium under A. alternata stress. In addition, application of microbes not only augmented withaferin A, withanolide A and withanolide B content (1.52-1.96, 3.32-5.96 and 12.49-21.47 fold, respectively) during A. alternata pathogenicity but also strengthened host resistance via improvement in the photochemical efficiency, normalizing the oxidized and non-oxidized fraction, accelerating photochemical and non-photochemical quantum yield, and electron transport rate. Moreover, reduction in the passively dissipated energy of PSI and PSII in microbial combination treated plants corroborate well with the above findings. Altogether, the above finding highlights novel insights into the underlying mechanisms in application of endophytes and emphasizes their capability to accelerate biosynthesis of withanolides in W. somnifera under biotic stress caused by A. alternata.

Assessment of genetic diversity in Costus pictus accessions based on RAPD and ISSR markers

Costus pictus, belonging to the family Costaceae, is one of the valuable medicinal plants with its anti-diabetic property. Despite ever-increasing demand from the pharmaceutical industry, this species is being less exploited at molecular level. Hence, an effort has been made in the present study to characterize the 15 accessions of C. pictus collected from different geographical regions of India through random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers. A total of 25 RAPD and 20 ISSR primers were used in the present study. The RAPD analysis generated 343 loci, of which 124 were polymorphic with an average of 4.96 loci per primer. While, ISSR primers produced 177 loci, of which 77 were polymorphic with an average of 3.85 loci per primer. The similarity coefficients ranged from 0.86-0.99, 0.84-0.95 and 0.86-0.96 for RAPD, ISSR and combined RAPD-ISSR, respectively. The UPGMA dendrogram generated using these data showed low level of divergence among the accessions from South and West regions. Further, accession-specific bands were also revealed by RAPD and ISSR markers which might be contributed to specific trait. This investigation was an understanding of genetic variation within the C. pictus accessions. The present finding indicates that both the marker tools RAPD and ISSR combined or individually can be used in determining the genetic relationship between the accessions. It may be concluded that data of hereditary differences appeared among the C. pictus accessions could be utilized for their conservation and reproducing programs.

Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

The endangered Aquilaria malaccensis,is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

PLANT BIOCHEMISTRY. Fighting cancer while saving the mayapple

The genes required for synthesizing a plant-derived anticancer compound are identified [Also see Report by Lau and Sattely ]