Genetic diversity and population structure assessment using molecular markers and SPAR approach in Illicium griffithii, a medicinally important endangered species of Northeast India

Abstract

Background Illicium griffithii is an aromatic medicinal tree species that has been listed in the IUCN Red List as an endangered species. Dried seed pods of I. griffithii have a good market potential in the spices and pharmaceutical industries. Fruits are the potential source of shikimic acid and used for the production of oseltamivir (a drug against bird flu). However, in recent years, unscientific harvesting and rampant exploitation of the species has caused a negative and adverse effect on its natural population. Proper knowledge of genetic diversity and population structure is crucial to understand the population dynamics, adaptation, and evolutionary pattern of a particular species for conservation. It was from this view point that the present study was undertaken so as to compare the various types of DNA-based molecular markers namely RAPD, ISSR, DAMD, and SCoT by their efficiency and SPAR approach to evaluate the genetic diversity of I. griffithii as well as to analyze population genetic structure for conservation purpose. Result A total of 250 discernible bands were generated with 246 bands (98.40 %) being polymorphic in nature. All the primers in combination gave a mean polymorphic information content (PIC) of 0.81 and Rp value (resolving power) of 4.32. Nei’s, Gst, and AMOVA analysis showed similar values of genetic differentiation among populations (Gst = 0.396, FST = 0.30, respectively), revealing a low level of genetic differentiation among the eight sampled populations. I. griffithii with an estimated gene flow value of Nm = 0.761 was significantly low among populations. Clustering pattern obtained with Bayesian structure and PCoA diagram revealed that intermixing of genetic material across populations is only possible when the populations lie close to each other. This is further validated with UPGMA clustering method where a positive correlation of genetic variability with geographical distance among closely related populations could be clearly seen. Conclusion The result aids in the identification, collection, and preservation of diverse germplasm of I. griffithii from Arunachal Pradesh and Meghalaya of Northeast India. This would further help in understanding the population structure and genetic diversity among other Illicium species in order to formulate effective conservation strategies for the improvement of this endangered taxa.

Genetic Diversity and Population Differentiation of a Chinese Endangered Plant Ammopiptanthus nanus (M. Pop.) Cheng f.

“…Generally, it is believed that the genetic diversity of endangered plants is lower than that of ordinary species due to the small number of remaining plants, genetic drift caused by inbreeding or self-inbreeding, and an increase in homozygotes [5]. Studies on the genetic diversity of endangered species can reveal the mechanisms of their endangerment [6] and provide a scientific basis for conservation strategies [7]. Thus, this has gained increasing attention from conservation biologists [8,9].…”

“…It is only found in a limited area in Kyrgyzstan [16] and in the Wuqia County of China, at an altitude of 2000-2400 m [15,17], growing on sunny arid slopes with 138 mm of average annual precipitation, 2580 mm of annual average evaporation, a 35 • C extreme maximum temperature, and a −30 • C of extreme minimum temperature, and is considered a super-arid plant with outstanding biological properties of drought tolerance [18] and cold tolerance [19][20][21] as well as the ecological values of wind protection, sand fixation, and prevention of soil erosion; its flower number is large, and its yellow corolla and "explosive" opening pattern in a short time has high ornamental value (Figure 1); its stems and leaves are rich in alkaloids, flavonoids, and phenylpropanoids [22], which were traditionally used for medicinal purposes; and it also has important academic value in the study of paleoclimatic changes. gered species can reveal the mechanisms of their endangerment [6] and provide a scientific basis for conservation strategies [7]. Thus, this has gained increasing attention from conservation biologists [8,9].…”

“…The most frequently used molecular markers are inter-simple-sequence repeats (ISSR) [29]. The main advantages of using this method is that it is highly efficient, quick, inexpensive, robust, reproducible, highly polymorphic, randomly distributed throughout the genomes, and widely applicable to any genome [7]. The method has been effectively used for estimation of the genetic diversity and population genetic structure of plant resources [30][31][32].…”

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean

“…For this purpose, various types of molecular markers were developed and applied to assess the genetic diversity among the genotypes [17]. In the different marker systems, numerous Polymerase Chain Reaction (PCR)-based markers were proven to be efficient for the investigation of genetic variability in collections of plant species [18], including the common bean. Many molecular markers, including RAPD [19][20][21], AFLP [22][23][24], ISSR [25,26], SSR [27][28][29], and SCoT [30,31], were successfully applied in the molecular variability analyses of the common bean.…”

Genetic similarity among Dendrobium species from Indonesia using RAPD markers

“…Compared to traditional methods, DNA-based molecular marker approaches are considered more advanced due to their high authenticity and consistency. However, the selection of suitable techniques and markers should be based on the nature of the genetic structure of the species (Borah et al 2021). According to several publications, the RAPD method has been widely used to determine the genetic relationships in different orchid species, such as Vanda coerulea (Manners et al 2013), Rhynchostylis retusa L. (Permatasari et al 2018), D. chrysotoxum Lindl (Tikendra et al 2019b), Rhynchostylis gigantea (Duangrath and Sumontip 2020), Spathoglottis plicata (Auvira et al 2021), Coelogyne (Hon et al 2021), and Phalaenopsis amabilis (Mursyidin et al 2022).…”