Abstract
There is an ample genetic diversity of plants with medicinal importance around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, identification, characterization and documentation of the gene pool of medicinal plants are essential for this purpose. Genomic information of many a medicinal plant species has increased rapidly since the past decade and genetic resources available for domestication and improvement programs include genome sequencing, expressed sequence tags sequencing, transcript profiling, gene transmit, molecular markers in favor of mapping and breeding. In recent years, multiple endeavors have been undertaken for genomic characterization of medicinal plant species with the aid of molecular markers for sustainable utilization of gene pool, its conservation and future studies. Recent advancement in genomics is so fast that only some researches have been published till date and to a large extent documentation is restricted to electronic resources. Whole genome profiling of the identified medicinal plant species, carried out by several researchers, based on the DNA fingerprinting, is well documented in the present review. This review will facilitate preparing a database of the widely used, economically important medicinal plant species, based on their genomic organization.
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Introduction
In recent years, there has been a renewed awareness observed all over the world, concerning natural medicines that are extracted from plant parts. In this respect, 40 % or more of the pharmaceuticals used by the Western countries, at present, are the derivative of natural resources. Quite an impressive and substantial number of plant species have already been well described in detail, in Ayurveda, the original indigenous system of Indian medicine (Mukherjee and Wahile 2006). Amidst its diverse climatic zones, India has a wealth of medicinal herbs with immense diversity. The forests harbor a large number of plant species, but deforestation has been solely accountable for the rapid loss of the said natural wealth to such an extent that numerous important medicinal plants are now endangered and under the risk of extinction. Pharmaceutical companies rely mostly upon materials obtained from plants growing in their natural habitats that are being depleted in an alarming rate. It is well documented that, use of medicinal herbs and trees is increasing with a skyrocketing speed every day. A large-scale commercial utilization of these Genuses is speculated here and it calls for a proportionate involvement of modern day crop improvement methods for genetic betterment of the plants described earlier. It must be admitted that, modern day crop improvement is moving towards a new platform of genomics. The advantages of genomics have already been well harvested in different field crops. So, the present review has been documented and fashioned on the scope of genomics on genetic improvement of plants having medicinal value. There are several reports available on molecular markers of different medicinal plants. Genetic markers in plants consist of single-nucleotide polymorphisms (Hyten et al. 2010; Myles et al. 2010; Arai-Kichise et al. 2011; Barbazuk and Schnable 2011; Marroni et al. 2011) and microsatellites (SSR, simple sequence repeats; short tandem repeats) (Csencsics et al. 2010; Buehler et al. 2011; Delmas et al. 2011; Gardner et al. 2011; Michalczyk et al. 2011). These molecular markers are employed for genome mapping and the invention of disease-associated alleles, along with population mapping, and forensics, the analysis of germplasm, trait mapping, and marker-assisted selection in plant breeding and others (Appleby et al. 2009). Several assays have been developed for high-throughput genotyping in plants using these markers (Appleby et al. 2009; Jones et al. 2009). Genomic polymorphisms can also be wrapped up for validation of identity of species, devoid of prior sequence information, by means of sequence-independent array technology (Niu et al. 2011; Jayasinghe et al. 2009). Nonetheless, NGS is fast becoming the alternative technique for the characterization of genetic markers (Myles et al. 2010; Marroni et al. 2011; Elshire et al. 2011; Arai-Kichise et al. 2011; Deschamps and Campbell 2010) and the unambiguous detection of multiple alleles of homologous loci in polyploid plants (Griffin et al. 2011). Despite the escalating use of DNA sequence-based approaches, yet fingerprinting techniques persist to be exploited for genomic profiling of medicinal plants (Zhou et al. 2008; Kumar et al. 2007; Techen et al. 2010; Xue and Xue 2008; Qiu et al. 2009; Diao et al. 2009; Ruzicka et al. 2009; Tamhankar et al. 2009; Gupta et al. 2007; Huang et al. 2009; Li et al. 2009). A remarkable and unique progress is the utilization of real-time PCR for the quantitation of amplified markers (Xue and Xue 2008), which should facilitate the determination of the degree of adulterant contamination in primary samples.
Impact of molecular marker techniques
Through the introduction of molecular markers, it is currently feasible to create straight inferences in relation to genetic divergence and inter-relationships amongst organisms at DNA level, devoid of the misleading environmental influences or imperfect pedigree accounts. Genetic assessment of plant populations and species, for taxonomic, evolutionary, and ecological research, has been immensely assisted from the advancement of a range of molecular marker systems. Even though every molecular marker system is derived from distinctive principles, yet their function is to expose the genome-wide variability. An evident difficulty that typically arises is as to how to select the apposite DNA marker amid the countless marker systems. Overall, the preference of a molecular marker system should be conciliated between consistency and simplicity of analysis, statistical rule, and assurance of exposing polymorphisms. Molecular systems are helpful in characterization of genetic divergence amongst several cultivars or species for the evaluation of genetic fidelity, identifying genes of commercial and agronomic interests, and enhancement via genetic transformation system. Su et al. (2008) reported the development of strain-specific sequence-characterized amplified region (SCAR) markers for strain detection and authentication of Ganoderma lucidum. Balasubramani et al. (2011) developed DNA markers from the genomic DNA through amplification and sequencing of the whole internal transcribed spacer region (ITS1, 5.8S rRNA and ITS2). They also established that the use of universal primers proved to be efficient and reliable in authenticating Berberis species. These primers are functional as a molecular pharmacognostic means in quality assessment of raw drugs. In an altogether different approach, Wang et al. (2012) employed the methylation-sensitive amplified polymorphism (MSAP) marker to appraise cytosine methylation difference in several regenerated plantlets and among organs of Clivia miniata. Wiriyakarun et al. (2013) reported the utilization of polymerase chain reaction restriction fragment length polymorphism (PCR–RFLP) to recognize plant origin of Pueraria candollei, Butea superb and Mucuna collettii. Nevertheless, to develop marker-assisted selection (MAS) breeding (for example in Catharanthus roseus) Chaudhary et al. (2013) reported the detection and mapping of QTLs, affecting pharmaceutical alkaloid contents in leaf and root. Some of the important achievements completed in medicinal plant species through molecular approaches are described in Tables 1, 2, and 3. Detection of genetic variation is also imperative for micropropagation and in vitro germplasm conservation to eradicate unwanted somaclonal variations. Somaclonal variations take place in reaction to the in vitro stresses and are manifested in the form of DNA methylation, chromosome reorganizations, and point mutations (Phillips et al. 1994). Therefore, a quality test for true-to-type planting material at an early stage of development is reflected to be helpful for in vitro culture. Molecular markers provide a significant tool to verify the genetic consistency and to test the true-to-type character of in vitro regenerated plants.
Application of RAPD
The root of RAPD method is the differential PCR amplification of genomic DNA. It infers DNA polymorphisms generated through “rearrangements or deletions at or between oligonucleotide primer binding sites in the genome” via short random oligonucleotide sequences (mostly ten bases long) (Williams et al. 1991). It can be utilized across species by means of universal primers because this approach does not entail prior information of the genome under analysis. The chief shortcoming of this approach is that the profiling is contingent on the reaction circumstances that may fluctuate amid laboratories and since a number of distinct loci in the genome are amplified by each primer, profiles are incompetent to differentiate heterozygous from homozygous members (Bardakci 2001). Nevertheless, due to the swiftness and effectiveness of RAPD analysis, high-density genetic mapping in loads of medicinal plant species such as Pueraria montana (Heider et al. 2007), Atalantia species (Ranade et al. 2009), Chlorophytum borivilianum (Samantaray and Maiti 2010), Swertia chirata (Balaraju et al. 2011), Withania somnifera (L.) Dunal (Rana et al. 2012) have been achieved. In Bacopa monnieri, Ramesh et al. (2011) used a RAPD fingerprinting approach to evaluate the genetic stability of 19 different micropropagated clones with the mother plant (wild type). Even though this study illustrates the sustained use of RAPD, relative assessment of a variety of DNA fingerprinting techniques indicate that this technique is less reliable and more complicated to implement consistently in comparison to AFLP, SSR, and ISSR (Pejic et al. 1998; McGregor et al. 2000). The details of RAPD markers used in molecular assessment of medicinal plants are being included in Table 1.
Application of ISSR
Several research groups used inter-simple sequence repeat (ISSR) as a better alternative DNA fingerprinting technique to appraise the genetic framework and diversity of wild and cultivated medicinal plants. Qiu et al. (2009) used ISSR markers to portray the genetic variation in wild and cultivated Rhizoma corydalis, a Chinese herbal medicine. In southern regions of China, the wild population of a medicinal plant species, Corydalis yanhusuo W.T. Wang ex Z.Y. Su et C.Y. Wu (Fumariaceae), has significantly been depleted and it has nearly been extinct from several other locations, owing to human interference along with environmental corrosion. These authors reported that the average within-population diversity of ISSR markers was superior in wild than in cultivated populations and suggested that the existing wild populations should be given a high precedence for in situ conservation as they possibly will function as reservoirs of genetic diversity in the species in the face of extinction (Qiu et al. 2009). Lata et al. (2010) reported that in vitro generated plants of Cannabis sativa, over 30 passages in culture and acclimatization in soil for 8 months, were genetically constant when assessed through ISSR markers and revealed a similar cannabinoid profile. The genetic variation amongst wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae) was investigated using ISSR by Shi et al. (2008). They observed that the genetic diversity in wild and cultivated populations was largely similar but there was noteworthy genetic variation among the wild populations. Use of ISSR markers have been well documented in several other medicinal plants like Swertia chirayita (Joshi and Dhawan 2007), Tribulus terrestris (Sarwat et al. 2008), Pleurotus citrinopileatus (Zhang et al. 2012). The particulars of ISSR markers employed in molecular evaluation of such medicinal plants are described in Table 2.
Application of AFLP
To triumph over the restraint of reproducibility coupled with RAPD, an amplified fragment-length polymorphisms (AFLP) technology (Vos et al. 1995) was developed. AFLP has several advantages to consider it applicable in the estimation of genetic diversity, genetic mapping, and tagging. AFLP has now developed into a favored approach as it unites the advantage of RFLP with the agility of PCR-based techniques by ligating primer recognition sequences to the restricted DNA and selective PCR amplification of restriction fragments via a restricted set of primers. The AFLP approach produces fingerprints of any DNA despite of its source, devoid of any previous information of DNA sequence. The primer pairs employed for AFLP typically generate 50–100 bands per assay. “Number of amplicons per AFLP assay is a function of the number selective nucleotides in the AFLP primer combination, the selective nucleotide motif, GC content and physical genome size and complexity”. Most AFLP fragments match up to distinctive locations on the genome and, therefore, can be used as pointer in genetic and physical mapping. The system can be used to differentiate strongly associated individuals at the sub-species level (Althoff et al. 2007) and can map genes too. Zerega et al. (2002) examined the use of AFLP as an analytical means of identifying Actaea racemosa from three other closely related sympatric species. A total number of 262 AFLP markers were generated, and one unique fingerprint was identified for A. racemosa, whereas two, six, and eight unique fingerprints were identified for the closely related species A. pachypoda, A. cordifolia, and A. podocarpa, respectively. Two commercial black cohosh products were also subjected to AFLP analysis and shown to contain only A. racemosa. The results of their study suggested that AFLP analysis may offer a useful method for quality control in the botanical dietary supplements industry. Applications for AFLP in plant mapping include genetic mapping of the pollen genome of Echinacea purpurea ‘Magnus’ (purple coneflower) which was amplified by a modified primer extension pre-amplification (PEP) procedure subsequently AFLP analyses of individual pollen grains (Aziz and Sauve 2008).
Using AFLP, He et al. (2009) investigated the population structure and genetic diversity of wild and cultivated populations of Magnolia officinalis subsp. biloba (Magnoliaceae) Plant. Principal coordinates analysis of AFLP data did not discriminate between wild and cultivated populations, which led the authors to conclude that alleles from the wild population were maintained in the cultivated gene pool. A sole report has been published in recent past by Agarwal et al. (2011) on development of sex-linked AFLP markers in jojoba (Simmondsia chinensis). Singh et al. (2002) reported application of AFLP markers for ascertaining clonal fidelity in tissue culture-raised progenies of a medicinally important plant, Azadirachta indica. AFLP markers are now being routinely employed for assessment of genetic variation in economically important plant species including chichory (Kiers et al. 2000), Withania sp. (Negi et al. 2000) (Table 3).
Use of microsatellite markers
“Microsatellite or short tandem repeats or simple sequences repeats (SSR) are monotonous repetitions of very short (one to five) nucleotide motifs, which occur as interspersed repetitive elements in all eukaryotic genomes” (Tautz and Renz 1984). However, strand slippage during DNA replication, where the repeats allow matching through excision or addition of repeats, results in disparity in the number of tandemly repeated units (Schlotterer and Tautz 1992). As slippage in replication is more expected than point mutations, microsatellite loci tend to be hypervariable. Microsatellite assays explain wide inter-individual length polymorphisms during PCR analysis of unique loci using discriminatory primers sets. High level of polymorphism and their co-dominant nature have made SSRs ideal markers for studying genetic diversity in plants (Plaschke et al. 1995). Hon et al. (2003) reported the efficiency of SSR markers in genetic authentication of two Panax species. Later on, Qin et al. (2005) employed SSR markers to identify and differentiate American ginseng and Oriental ginseng, cultivated and wild American ginseng. Huang et al. (2009) developed eight polymorphic microsatellite loci for the Chinese medicinal plant Artemisia annua L. (Asteraceae), useful for investigating the genetic diversity, genetic structure and gene flow within populations. Li et al. (2009) isolated polymorphic microsatellite loci and characterized them from an AC-enriched genomic library of Akebia trifoliate ssp. australis. A robust set of 17 polymorphic EST–SSRs were developed and used for evaluating 20 turmeric accessions (Siju et al. 2010). Eleven microsatellite markers were isolated and characterized from enriched genomic libraries of Channa argus (Gul et al. 2010). Rahimmalek et al. (2011) developed and characterized SSR markers for the first time from the genome of yarrow (Achillea millefoilum L.), using the slightly modified Hamilton protocol to allow the selection of desired genotypes rather than phenotypes and hence to accelerate the breeding programs. Microsatellite (GTG)5 were used to assess DNA polymorphism and genetic diversity in Allium ampeloprasum (Guenaoui et al. 2013). Likewise, Zhou et al. (2012) used 10 microsatellite (SSR) loci to investigate genetic diversity and differentiation in 16 natural populations of Saruma henryi Oliv. Use of cross-species SSR markers was reported in genetic diversity analysis of synthetic interspecific hybrid of Hibiscus which revealed a closer association of diploid genomes and high variability of tetraploid genomes (Satya et al. 2012). Most recently, Katoch et al. (2013) used DNA-based molecular marker techniques, viz. simple sequence repeats (SSR) and cytochrome P-450 markers to estimate genetic diversity in Picrorhiza kurrooa.
Use of single nucleotide polymorphism (SNPs)
“Single nucleotide variations in genome sequence of individuals of a population are known as SNPs”. They comprise the most copious molecular markers in the genome and are extensively distributed all through genomes even though their occurrence and allocation vary between species. Maize has 1 SNP per 60–120 bp (Ching et al. 2002). The SNPs are generally more ubiquitous in the non-coding regions of the genome. An SNP, within the coding regions, is either non-synonymous and results in an amino acid sequence alteration (Sunyaev et al. 1999), or it is synonymous and fail to modify the amino acid sequence. Synonymous changes can modify mRNA splicing, ensuing in phenotypic variations (Richard and Beckman 1995).
Advancement in sequencing technology and accessibility of an escalating number of expressed sequence tags (EST) sequences has made direct analysis of genetic variation at the DNA sequence level achievable (Buetow et al. 1999; Soleimani et al. 2003). “Prevalence of SNP genotyping assays are based on one or two of the following molecular mechanisms: allele specific hybridization, primer extension, oligonucleotide ligation and persistent cleavage” (Sobrino et al. 2005). High-throughput genotyping methods counting DNA chips, allele-specific PCR, and primer extension approaches make SNPs especially attractive as genetic markers. They are apposite for automation and are employed for a variety of purposes, including rapid detection of crop cultivars and construction of ultra high-density genetic maps. Ginger (Zingiberofficinale Rosc), a well-known plant for its medicinal applications, was successfully applied for the development of high-throughput methods for the detection of SNPs and small indels (insertion/deletion). In that study, 64026 SNP sites and 7034 indel polymorphisms with frequency of 0.84 SNPs/100 bp were found and among the three tissues from which the EST libraries were generated, rhizomes had high frequency of 1.08 SNPs/indels per 100 bp whereas the leaves had lowest frequency of 0.63 per 100 bp and root showed relative frequency of 0.82/100 bp (Chandrasekar et al. 2009). Work has been done for authentication of medicinal plants by SNP-based Multiplex PCR, where highly variable intergenic spacer and intron regions from nuclear and cytoplasmic DNA have been used for species identification (Lee et al. 2012). Noncoding internal transcribed spacers (ITSs) located in 18S-5.8S-26S, and 5S ribosomal RNA genes (rDNAs) were the target region for this purpose. In this context, noncoding regions from two cytoplasmic DNA, chloroplast DNA (trnT-F intergenic spacer region), and mitochondrial DNA (fourth intron region of nad7 gene) were also successfully applied for the proper identification of medicinal plants and SNP sites obtained from the amplification of intergenic spacer and intron regions were properly utilized for the verification of medicinal plants in species level using multiplex PCR. Dendrobiumofficinale is used as a crude drug in traditional Chinese medicine (TCM) having tonic efficacy. For crude drug quality control and authentication of different populations the sequences from its chloroplast, nuclear, and mitochondrial genes and the method of genomic DNA (gDNA) suppression subtraction hybridization (SSH) were successfully used. In that experiment, six populations were authenticated successfully by nine SNP sites and six pairs of diagnostic primers. Amplification refractory mutation system (ARMS) was also designed to identify six populations on the basis of SNPs (Ding et al. 2008).
Expressed sequence tags of medicinal plants
Expressed sequence tags (ESTs), identified by the single-pass sequencing of randomly selected clones from the cDNA library, are molecular tools that are reasonably useful in defining an expressed gene, and also specify the profusion of transcripts. Large-scale EST databases offer a multitude of information concerning the complexities of gene expression patterns, the functions of transcripts, and the development of SNPs (Yang et al. 2004). In plant, large-scale EST databases have been recognized, and an array of ESTs procured from different tissues, developmental stages, and stress-treated cDNA libraries have been compared with model plants and crops. In most of the medicinal plants, nevertheless, the complete genome and draft sequences are yet to be established. Consequently, EST assay represents the most rational system for the study of the genome of the plants with medicinal importance; hence, several attempts have been made in this aspect by a number of research groups. Monoterpene indole alkaloid (MIA) pathway genes were identified from random sequencing of C. roseus cDNA library which revealed 3,655 unique ESTs, comprising 1,142 clusters and 2,513 single tons. A number of novel MIA pathway candidate genes were recognized by the cloning and functional characterization of loganic acid O-methyletransferase implicated in secologanin biosynthesis. Biochemical pathway, for instance, triterpene biosynthesis was also identified and its metabolite analysis revealed localization of oleanane-type triterpenes exclusively to the cuticular wax layer. The results illuminated biochemical specialization of Catheranthus leaf epidermis for the production of multiple classes of metabolites (Murata et al. 2008). Also, jasmonate-induced changes on the transcripts and alkaloid profiles of tobacco BY-2 and C. roseus cell cultures have been monitored through similar approach (Rischer et al. 2006; Goossens et al. 2003). ESTs analogous to 40 enzymes involved in the conversion of sucrose to sanguinarine were identified from elicitor-induced cell culture of Papaver somniferum. Significant enhancement in the level of RNA was observed in case of elicitate cell culture as compared to control and the identified metabolites were sanguinarin, dihydrosanguinarine, methoxylated derivatives, dihydrochelirubine and chelibine and the identified alkaloid pathway intermediates were N-methylcoclaurine, N-methylestylopine, and protopine (Zulak et al. 2005). Likewise, cDNA library of Artimisia annua glandular trichome revealed the occurrence of scores of ESTs implicated in isoprenoid biosynthesis for instance enzymes from the methylerythritol phosphate pathway and the mevalonate pathway, amorpha-4, 11-diene synthase and other sesquiterpene synthase, monoterpene synthases and 2-cDNAs revealing prominent resemblance to germacrene-A-synthases (Berteaa et al. 2006). Siju et al. (2010) used ESTs from turmeric (Curcuma longa L.) for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). Recently, to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, Koo et al. (2013) evaluated an assembled collection of ESTs from eight different ginger and turmeric tissues. In Panax ginseng, Kim et al. (2006) found that 2,896 cDNA clones represent 1,576 unique sequences, consisting of 1,167 singletons and 409 contig sequences. The ESTs referenced in their report were the first transcriptomes in a leaf from a half-shade ginseng plant. The majority of the identified transcripts were found to be genes related with energy, metabolism, subcellular localization, protein synthesis and transport. Xie et al. (2008) built an EST database from four basil (Ocimum basilicum L.) lines with distinct product profiles providing the sequence foundation required for comparative proteomic studies. Cloutier et al. (2009) exploited EST to develop SSRs for genomic assessment of flax (Linum usitatissimum L.). Sathiyamoorthy et al. (2010) obtained a total of 6,757 ESTs from cDNA libraries in Panax ginseng C. A. Meyer. This EST dataset provides a wide outlook of the genes expressed in hairy roots, 14-year root and 4-year root. The dataset contains more than 1,365 EST sequences related to plant secondary metabolism and 745 sequences related to stresses. Li et al. (2010) used the 454 GS FLX platform and Titanium regents to produce a substantial EST dataset from the vegetative organs of Glycyrrhiza uralensis. Based on the EST analysis, novel candidate genes related to the secondary metabolite pathway of glycyrrhizin, including novel genes encoding cytochrome P450 s and glycosyltransferases, were found. However, there are a few and limited genomic resources available for Picrorhiza (Bantawa et al. 2012) in spite of its immense medicinal importance. A total of 728 ESTs of P. kurroa and 27 of P. scrophulariflora have been deposited at NCBI (www.ncbi.nlm.nih.gov). Kawoosa et al. (2010) have identified two regulatory genes of terpenoid metabolism, namely- 3-hydroxy-3-methylglutaryl coenzyme A reductase (pkhmgr) and 1-deoxy-d-xylulose-5-25 phosphate synthase (pkdxs) from P. kurroa. An account of hundreds of genes implicated not only in alkaloid biosynthesis but also in plant secondary metabolism. Subsequently, large-scale functional analysis of genes from this inventory, potentially involved in plant secondary metabolism, was carried out. This comprises isolation, introduction, and functional assay of full-length open reading frames in transgenic plant cells. Tools to enhance and accelerate functional analysis of candidate genes in transgenic plant cells with reporter gene constructs, transient protoplast expression assays, and microarray facilities, have been designed and their uses validated.
Microchip based genomic profiling
High-throughput and automated genomic techniques have been proven to speed up modern day research for generating large number of data. DNA microarray is a arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles (10–12 mol) of a specific DNA sequence, known as probes (or reporters). It can be used to measure changes in expression levels, detection of SNPs, to genotype or resequence mutant genomes (Hao et al. 2010). This techniques was successfully applied to identify toxic traditional Chinese medicinal plants, where species- specific oligonucleotide probes were obtained from the 5S rRNAgene of Aconitum carmichaeli Debx., A. kusnezoffi Reichb., Alocasia macrorrhiza (Linn.) Schott, Croton tiglium L., Datura inoxia Mill., D. metel L., D. tatula L., Dysosma pleiantha (Hance) Woodson, D. versipellis (Hance) M. Cheng ex Ying, Euphorbia kansui L., Hyoscyamus niger L., Pinellia cordata N.e. Brown, P. pedatisecta Schott, P. ternata (Thunb.) Breit., Rhododendron molle (Blum) G. Don, Strychnos nux-vomica L., Typhonium divaricatum (Linn.) Decne., and T. giganteum Engl., and the leucine transfer RNA gene of A. pendulum Busch and Stellera chamaejasme L. (Carles et al. 2005). This is a rapid tool for quality control and safety monitoring of herbal pharmaceuticals and neutraceuticals. There are other reports on the use of microarray for high throughput identification of the plant resource of commercial FDSH [Fengdu Shihu (Dendrobium officinale Kimura et Migo)] (Sze et al. 2008), identification of various Panax plants and drugs (Zhu et al. 2008), genotyping, and identification of the origin of various species of Fritillaria L. at molecular level (Tsoi et al. 2003).
DNA barcoding
DNA barcoding is the application of molecular phylogeny where, the species of an individual organism is signatured using small sections of chloroplast/nuclear/mitochondrial DNA. A DNA barcode is a potential tool for taxonomic identification that employs short, standardized DNA sequences (mostly 400–800 bp) present universally in target lineages and has ample sequence variation to differentiate among species of a specific organism. This offers a quick and precise system for definite species identification through/via adequate sequence variation amongst species and little intraspecific variation. The universally accepted genes for plant DNA barcoding are of plastid origin. Twenty-five years following the publication of the first complete sequence of a chloroplast genome by Shinozaki et al. (1986); several scientists have used next-generation sequencing technology to sequence the complete chloroplast genomes from quite a few number of plants (Parks et al. 2009) (Doorduin et al. 2011). Polymorphism of chloroplast DNA particularly trnK, matK, and intergenic trnL–trnF regions have been exploited to learn the phylogeny of several plants (Kress et al. 2005; Selvaraj et al. 2008). However, Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae) have comparatively strong chloroplast genome information that can be tapped (Hansen et al. 2007). Hao et al. (2009) showed the evolutionary patterns of gene sequence divergence from the medicinal genus Taxus L., encoding paclitaxel biosynthetic enzymes taxadiene synthase (TS) and 10-deacetyl- baccatin III-10 beta-O-acetyltransferase (DBAT). According to Yao et al. (2009), the psbA-trnH spacer regions were effective barcodes for species of Dendrobium Sw. This technique was used for the first time to discriminate the Polygonaceae in Chinese Pharmacopoeia and their adulterants (Song et al. 2009). Chen et al. (2010) compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Gao et al. (2010) showed ITS2 sequences to show considerable variation at the genus and species level within the family Fabaceae.
Conclusion: future of medicinal plant genomics
Molecular techniques have been well proven for authentication of medicinal plants based on phylogenic variation signatured on chloroplast and nuclear DNA regions. DNA markers are the powerful tool for the characterization of sample homogeneity and detection of adulterants and thus assure quality control in medicinal plant research as well as in the production, clinical use, and forensic examination of herbal medicines for their safest use. So, there is always an immediate need to scrutinize the genomic tools in detail so as to harvest the advantages of genomics in total for the broad use of medicinal plant genome. A comprehensive study and research is a demand for all-round use of genomics for authentic and safe use of botanical products and medicinal plants. With the advent of new DNA sequencing platforms that achieve an ever-increasing degree of speed, coverage, and sharply decreasing costs for obtaining the data, we can expect to see many genome libraries, SNP chips and, ultimately, a complete genome sequencing (of plastid) effort. More recently, marker systems of various types have been developed and these have increased our knowledge of the population structure of various medicinal plant populations. The more recent sequencing of the nuclear and chloroplast genomes will allow the development of additional tools for studying not only the population structure but also the genetic basis of various traits and their inheritance. Genome sequencing projects may be initiated vividly for all the plants having medicinal use. In this regard, sequence databases with all the bioinformatics tools should be made available for public use by different nations; as such platforms are only available for rice and some other crop plants.
Abbreviations
- ESTs:
-
Expressed sequence tags
- RFLP:
-
Restriction fragment length polymorphism
- RAPD:
-
Randomly amplified polymorphic DNA
- AFLP:
-
Amplified fragment length polymorphism
- SSR:
-
Simple sequence repeat
- ISSR:
-
Inter simple sequence repeat
- SNP:
-
Single-nucleotide polymorphism
- UPGMA:
-
Unweighted pair group method arithmetic average
References
Agarwal M, Shrivastava N, Padh H (2011) Development of sex-linked AFLP markers in Simmondsia chinensis. Plant Breed 130:114–116
Agostini G, Echeverrigaray S, Souza-Chies TT (2008) Genetic relationships among South American species of Cunila D. Royen ex L. based on ISSR. Plant Syst Evol 274:135–141
Agrawal V, Sharma K, Sarika G, Kumar R, Prasad M (2007) ISSR marker-assisted selection of male and female plants in a promising dioecious crop: jojoba (Simmondsia chinensis). Plant Biotech Rep 2:239–243
Ahmad N, Anis M (2011) An efficient in vitro process for recurrent production of cloned plants of Vitex negundo L. Euro J For Res 130:135–144
Ahmad N, Javed SB, Khan MI, Anis M (2013) Rapid plant regeneration and analysis of genetic fidelity in micropropagated plants of Vitex trifolia: an important medicinal plant. Acta Physiol Plant 35:2493–2500
Ahuja S, Mandal BB, Dixit S, Srivastava PS (2002) Molecular, phenotypic and biosynthetic stability in Dioscorea floribunda plants derived from cryopreserved shoot tips. Plant Sci 163:971–977
Alan AR, Zeng H, Assani A, Shi WL, McRae HE, Murch SJ, Saxena PK (2007) Assessment of genetic stability of the germplasm lines of medicinal plant Scutellaria baicalensis Georgi (Huang-qin) in long-term, in vitro maintained cultures. Plant Cell Rep 26:1345–1355
Althoff DM, Gitzendanner MA, Segraves KA (2007) The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst Biol 56:477–484
Amarger V, Mercier L (1995) Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L. Schneider). Biochimie 77:931–936
Appleby N, Edwards D, Batley J (2009) New technologies for ultra-high throughput genotyping in plants. Plant Genomics 513:19–39
Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K (2011) Discovery of genome-wide DNA polymorphisms in a Landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol 52:274–282
Aziz AN, Sauve RJ (2008) Genetic mapping of Echinacea purpurea via individual pollen DNA fingerprinting. Mol Breed 21:227–232
Badr A, El-Shazly HH, Helail NS, El Ghanim W (2012) Genetic diversity of Artemisia populations in central and north Saudi Arabia based on morphological variation and RAPD polymorphism. Plant Syst Evol 298:871–886
Balaraju K, Saravanan S, Agastian P, Ignacimuthu S (2011) A rapid system for micropropagation of Swertia chirata Buch- Ham. ex Wall.: an endangered medicinal herb via direct somatic embryogenesis. Acta Physiol Plant 33:1123–1133
Balasubramani SP, Goraya GS, Venkatasubramanian P (2011) Development of ITS sequence-based markers to distinguish Berberis aristata DC. from B. lycium Royle and B. asiatica Roxb. 3. Biotech 1:11–19
Bantawa P, Das A, Mondal TK (2012) Genetic variation of extremely threatened medicinal plant Nepalese Kutki (Picrorhiza scrophulariiflora). Ind J Genet Plant Bred 72:103–106
Barbazuk WB, Schnable PS (2011) SNP discovery by transcriptome pyrosequencing. cDNA Libr 729:225–246
Bardakci F (2001) Random amplified polymorphic DNA (RAPD) markers. Turk J Biol 25:185–196
Berteaa CM, Vostera A, Francel WA, Maffeib VM, Beekwildera J et al (2006) Isoprenoid biosynthesis in Artemisia annua: cloning and heterologous expression of a germacrene A synthase from a glandular trichome cDNA library. Arch Biochem Biophy 448:3–12
Bhardwaj M, Uppal S, Jain S, Kharb P, Dhillon R, Jain RK (2010) Comparative assessment of ISSR and RAPD marker assays for genetic diversity analysis in jojoba [Simmondsia chinensis (Link) Schneider]. J Plant Biochem Biotechnol 19:255–258
Bua-in S, Paisooksantivatana Y (2010) Study of clonally propagated cassumunar ginger (Zingiber montanum (Koenig) Link ex Dietr.) and its relation of wild Zingiber species from Thailand revealed by RAPD markers. Genet Resour Crop Evol 57:405–414
Buehler D, Graf R, Holderegger R, Gugerli F (2011) Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpine (Brassicaceae). Am J Bot 98:103–105
Buetow KH, Edmonson MN, Cassidy AB (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21:323–332
Carles M, Cheung MK, Moganti S, Dong TT, Tsim KW, Ip NY, Sucher NJ (2005) A DNA microarray for the authentication of toxic traditional Chinese medicinal plants. Planta Med 71:580–584
Carolan JC, Hook ILI, Walsh JJ, Hodkinson TR (2002) Using AFLP markers for species differentiation and assessment of genetic variability of in vitro-cultured Papaver bracteatum (section Oxytona). In Vitro Cell Dev Biol-Plant 38:300–307
Ceasar SA, Maxwell SL, Prasad KB, Karthigan M, Ignacimuthu S (2010) Highly efficient shoot regeneration of Bacopa monnieri (L.) using a two-stage culture procedure and assessment of genetic integrity of micropropagated plants by RAPD. Acta Physiol Plant 32:443–452
Chandrasekar AR, Sithara K, Anoop S, Eapen SJ (2009) Identification of single nucleotide polymorphism in ginger using expressed sequence tags. Bioinformation 4:119
Chandrika M, Thoyajaksha, Rai VR, Kini KR (2008) Assessment of genetic stability of in vitro grown Dictyospermum ovalifolium. Biol Plant 52:735–739
Chaudhary S, Pandey R, Sharma V, Tripathi BN, Kumar S (2013) Detection and mapping of QTLs affecting contents of pharmaceutical alkaloids in leaf and root of Catharanthus roseus. Agric Res 2:9–23
Chavan JJ, Gaikwad NB, Umdale SD, Kshirsagar PR, Bhat KV, Yadav SR (2014) Efficiency of direct and indirect shoot organogenesis, molecular profiling, secondary metabolite production and antioxidant activity of micropropagated Ceropegia santapaui. Plant Growth Regul 72:1–15
Chen SL, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5:e8613
Ching ADA, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19
Cloutier S, Niu Z, Datla R, Duguid S (2009) Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119:53–63
Csencsics D, Brodbeck S, Holderegger R (2010) Cost-effective, species-specific microsatellite development for the endangered dwarf Bulrush (Typha minima) using next-generation sequencing technology. J Hered 101:789–793
Das A, Gantait S, Mandal N (2011) Micropropagation of an elite medicinal plant: Stevia rebaudiana Bert. Int J Agricultural Res 6:40–48
Delmas CEL, Lhuillier E, Pornon A, Escaravage N (2011) Isolation and characterization of microsatellite loci in Rhododendron ferrugineum (Ericaceae) using pyrosequencing technology. Am J Bot 98:120–122
Deschamps S, Campbell M (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Mol Breeding 25:553–570
Deshwal RS, Singh R, Malik K, Randhawa GJ (2005) Assessment of genetic diversity and genetic relationships among 29 populations of Azadirachta indica A. Juss. using RAPD markers. Gen Resour Crop Evol 52:285–292
Diao Y, Lin XM, Liao CL, Tang CZ, Chen ZJ, Hu ZL (2009) Authentication of Panax ginseng from its adulterants by PCR-RFLP and ARMS. Planta Med 75:557–560
Ding G, Zhang D, Feng Z, Fan W, Ding X, Li X (2008) SNP, ARMS and SSH authentication of medicinal Dendrobium officinale Kimura et Migo and application for identification of Fengdou drugs. Biol Pharma Bulletin 31:553–557
Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin AWT, Vrieling K (2011) The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res 18:93–105
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:19379
Faisal M, Alatar AA, Ahmad N, Anis M, Hegazy AK (2012) An efficient and reproducible method for in vitro clonal multiplication of Rauvolfia tetraphylla L. and evaluation of genetic stability using DNA-based markers. Appl Biochem Biotechnol 168:1739–1752
Gantait S, Mandal N, Bhattacharyya S, Das PK, Mandal N, Bhattacharyya S, Das PK (2009) In vitro mass multiplication with genetic clonality in elephant garlic (Allium ampeloprasum L.). J Crop Weed 5:100–104
Gantait S, Mandal N, Bhattacharyya S, Das PK (2010a) A novel strategy for in vitro conservation of Aloe vera L. through long term shoot culture. Biotechnology 9:326–331
Gantait S, Mandal N, Bhattacharyya S, Das PK (2010b) Determination of genetic integrity in long-term micropropagated plantlets of Allium ampeloprasum L. using ISSR markers. Biotechnology 9:218–223
Gantait S, Mandal N, Das PK (2011) In vitro accelerated mass propagation and ex vitro evaluation of Aloe vera L. with aloin content and superoxide dismutase activity. Natural Product Res 25:1370–1378
Gao T, Yao H, Song J, Liu C, Zhu Y, Ma X, Pang X, Xu H, Chen S (2010) Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. J Ethnopharmacol 130:116–121
Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ (2011) Rise of the machines—recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 11:1093–1101
Goossens A, Hakkinen ST, Laakso I et al (2003) A functional genomic approach toward the understanding of secondary metabolism in plant cells. Proc Nat Acad Sci USA 100:8595–8600
Griffin PC, Robin C, Hoffmann AA (2011) A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 9:19
Guenaoui C, Mang S, Figliuolo G, Neffati M (2013) Diversity in Allium ampeloprasum: from small and wild to large and cultivated. Genet Resour Crop Evol 60:97–114
Gul Y, Wang W, Wang H (2010) The isolation and characterization of 10 dinucleotide microsatellite markers from enriched Channa argus genomic library. Conservation Genet Resour 2:59–61
Gupta S, Pandey-Rai S, Srivastava S, Naithani SC, Prasad M, Kumar S (2007) Construction of genetic linkage map of the medicinal and ornamental plant Catharanthus roseus. J Genet 86:259–268
Hansen DR, Dastidar S, Zhengqiu CG, Penaflor C, Kuehl J, Jeffrey V, Boore L, Jansen RK (2007) Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol 45:547–563
Hao DC, Chen SL, Xiao PG (2009) Authentication of medicinal plants based on molecular biology and genomics. Chinese J Pharm Biotech 16:490–494
Hao DC, Chen SL, Xiao PG, Peng Y (2010) Authentication of medicinal plants by DNA-based markers and genomics. Chinese Herbal Med 2:250–261
He J, Chen L, Si Y, Huang B, Ban X, Wang Y (2009) Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae). Genetica 135:233–243
Heider B, Fischer E, Berndl T, Schultze-Kraft R (2007) Analysis of genetic variation among accessions of Pueraria montana (Lour.) Merr. var. lobata and Pueraria phaseoloides (Roxb.) Benth. based on RAPD markers. Gen Resour Crop Evol 54:529–542
Hon CC, Chow YC, Zeng FY, Leung FC (2003) Genetic authentication of ginseng and other traditional Chinese medicine. Acta Pharmacol Sin 24:841–846
Hosseini FS, Hassani HS, Arvin MJ, Baghizadeh A, Nejad GM (2011) Sex determination of jojoba (Simmondsia chinensis cv. Arizona) by random amplified polymorphic DNA (RAPD) molecular markers. Afr J Biotechnol 10:470–474
Huang HR, Zhou G, Ge XJ, Wei X, Jiang YS, Tang H (2009) Eight polymorphic microsatellite loci for the Chinese medicinal plant Artemisia annua L. (Asteraceae). Conserv Genet 10:593–595
Hyten D, Song Q, Fickus E, Quigley C, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan P (2010) High-throughput SNP discovery and assay development in common bean. BMC Genom 11:475
Jacoby A, Labuschagne MT, Viljoen CD (2003) Genetic relationships between Southern African Solanum retroflexum Dun. and other related species measured by morphological and DNA markers. Euphytica 132:109–113
Jayasinghe R, Hai Niu L, Coram TE, Kong S, Kaganovitch J, Xue CC, Li CG, Pang EC (2009) Effectiveness of an innovative prototype subtracted diversity array (SDA) for fingerprinting plant species of medicinal importance. Planta Med 75:1180–1185
Jones N, Ougham H, Thomas H, Pašakinskieṅe I (2009) Markers and mapping revisited: finding your gene. New Phytol 183:935–966
Joshi P, Dhawan V (2007) Analysis of genetic diversity among Swertia chirayita genotypes. Biol Plant 51:764–768
Kakani RK, Singh SK, Pancholy A, Meena RS, Pathak R, Raturi A (2011) Assessment of genetic diversity in Trigonella foenum-graecum based on nuclear ribosomal DNA, internal transcribed spacer and RAPD analysis. Plant Mol Biol Rep 29:315–323
Karthikeyan A, Madhanraj A, Pandian SK, Ramesh M (2011) Genetic variation among highly endangered Bacopa monnieri (L.) Pennell from Southern India as detected using RAPD analysis. Genet Resour Crop Evol 58:769–782
Katoch M, Hussain MA, Ahuja A (2013) Comparison of SSR and cytochrome P-450 markers for estimating genetic diversity in Picrorhiza kurrooa L. Plant Syst Evol 299:1637–1643
Kawiak A, Łojkowska E (2004) Application of RAPD in the determination of genetic fidelity in micropropagated Drosera plantlets. In Vitro Cell Dev Biol-Plant 40:592–595
Kawoosa T, Singh H, Kumar A, Sharma SK, Devi K, Dutt S, Vats SK, Sharma M, Ahuja PS, Kumar S (2010) Light and temperature regulated terpene biosynthesis: hepatoprotective monoterpene picroside accumulation in Picrorhiza kurroa. Funct Integr Genomics 10:393–404
Khanuja SPS, Shasany AK, Srivastava A, Kumar S (2000) Assessment of genetic relationships in Mentha species. Euphytica 111:121–125
Kiers AM, Mes TMH, Van der MR, Bachmann K (2000) A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups. Genome 43:470–476
Kim MK, Lee BS, In JG, Sun H, Yoon JH, Yang DC (2006) Comparative analysis of expressed sequence tags (ESTs) of ginseng leaf. Plant Cell Rep 25:599–606
Koo HJ, McDowell ET, Ma X, Greer KA, Kapteyn J, Xie Z, Descour A, Kim HR, Yu Y, Kudrna D, Wing RA, Soderlund CA, Gang DR (2013) Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biol 13:27
Kress WJ, Kenneth JW, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374
Kumar J, Verma V, Shahi AK, Qazi GN, Balyan HS (2007) Development of simple sequence repeat markers in Cymbopogon species. Planta Med 73:262–266
Kumar A, Aggarwal D, Gupta P, Reddy MS (2010) Factors affecting in vitro propagation and field establishment of Chlorophytum borivilianum. Biol Plant 54:601–606
Kumar S, Mangal M, Dhawan AK, Singh N (2011) Assessment of genetic fidelity of micropropagated plants of Simmondsia chinensis (Link) Schneider using RAPD and ISSR markers. Acta Physiol Plant 33:2541–2545
Kundu Chaudhuri R, Pal A, Jha TB (2008) Conservation of Swertia chirata through direct shoot multiplication from leaf explants. Plant Biotechnol Rep 2:213–218
Lahiri K, Mukhopadhyay MJ, Desjardins Y, Mukhopadhyay S (2012) Rapid and stable in vitro regeneration of plants through callus morphogenesis in two varieties of Mucuna pruriens L.: an anti Parkinson’s drug yielding plant. Nucleus 55:37–43
Lata H, Chandra S, Techen N, Khan IA, ElSohly MA (2010) Assessment of the genetic stability of micropropagated plants of Cannabis sativa by ISSR markers. Planta Med 76:97–100
Lattoo SK, Bamotra S, Sapru Dhar R, Khan S, Dhar AK (2006) Rapid plant regeneration and analysis of genetic fidelity of in vitro derived plants of Chlorophytum arundinaceum Baker: an endangered medicinal herb. Plant Cell Rep 25:499–506
Lee OR, Kim MK, Yang DC (2012) Authentication of medicinal plants by SNP-based multiplex PCR. In: Plant DNA Fingerprinting and Barcoding. Humana Press, pp 135–147
Li Y, Ding WL (2010) Genetic diversity assessment of Trollius accessions in China by RAPD Markers. Biochem Genet 48:34–43
Li L, Yao X, Chen X, Huang H (2009) Development and characterization of microsatellite loci in Chinese medicinal plant Akebia trifoliate ssp. australis and cross-species amplification in closely related taxa. Conserv Genet 10:959–962
Li Y, Luo HM, Sun C, Song JY, Sun YZ, Wu Q, Wang N, Yao H, Steinmetz A, Chen SL (2010) EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genom 11:268
Liao L, Liu J, Dai Y, Li Q, Xie M, Chen Q, Yin H, Qiu G, Liu X (2009) Development and application of SCAR markers for sex identification in the dioecious species Ginkgo biloba L. Euphytica 169:49–55
Liu J, Wang L, Geng Y, Wang Q, Luo L, Zhong Y (2006) Genetic diversity and population structure of Lamiophlomis rotate (Lamiaceae), an endemic species of Qinghai-Tibet Plateau. Genetica 128:385–394
Mace ES, Lester RN, Gebhradt CG (1999) AFLP analysis of genetic relationship in the tribe Datureae (Solanaceae). Theor Appl Genet 99:642–648
Mahar KS, Rana TS, Ranade SA, Pande V, Palni LMS (2013) Estimation of genetic variability and population structure in Sapindus trifoliatus L., using DNA fingerprinting methods. Trees 27:85–96
Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, Cattonaro F, Morgante M (2011) Large scale detection of rare variants via pooled multiplexed next generation sequencing: towards next generation Ecotilling. Plant J 67:736–745
Martin KP, Pradeep AK, Madassery J (2011) High frequency in vitro propagation of Trichopus zeylanicus subsp. travancoricus using branch–petiole explants. Acta Physiol Plant 33:1141–1148
Mathur A, Mathur AK, Sangwan RS, Gangwar A, Uniyal GC (2003) Differential morphogenetic responses, ginsenoside metabolism and RAPD patterns of three Panax species. Gen Resour Crop Evol 50:245–252
McGregor CE, Lambert CA, Greyling MM, Louw JH, Warnich L (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144
Mehrotra S, Khwaja O, Kukreja AK, Rahman L (2012) ISSR and RAPD based evaluation of genetic stability of encapsulated micro shoots of Glycyrrhiza glabra following 6 months of storage. Mol Biotechnol 52:262–268
Michalczyk IM, Schumacher C, Mengel C, Leyer I, Liepelt S (2011) Identification and characterization of 12 microsatellite loci in Cnidium dubium (Apiaceae) using next-generation sequencing. Am J Bot 98:127–129
Mignouna HD, Asiedu R, Ng NQ, Knox M, Ellis NTH (1997) Analysis of genetic diversity in Guinea yams (Dioscorea spp.) using AFLP fingerprinting. In: 11th Symp Soc Trop Root Crops. Trinidad and Tobago, pp 70
Mohanty S, Parida R, Singh S, Joshi RK, Subudhi E, Nayak S (2011) Biochemical and molecular profiling of micropropagated and conventionally grown Kaempferia galanga. Plant Cell Tiss Organ Cult 106:39–46
Mohapatra KP, Sehgal RN, Sharma RK, Mohapatra T (2009) Genetic analysis and conservation of endangered medicinal tree species Taxus wallichiana in the Himalayan region. New For 37:109–121
Moraes RM, Lata H, Sumyanto J, Pereira AM, Bertoni BW, Joshi VC, Pugh ND, Khan IA, Pasco DS (2011) Characterization and pharmacological properties of in vitro propagated clones of Echinacea tennesseensis (Beadle) Small. Plant Cell Tiss Organ Cult 106:309–315
Mukherjee PK, Wahile A (2006) Integrated approaches towards drug development from Ayurveda and other Indian system of medicines. J Ethnopharmacol 103:25–35
Muluvi GM, Sprent JI, Soranzo N, Provan J, Odee D, Folkard G, McNicol JW, Powell W (1999) Amplified Fragment Length Polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam. Mol Ecol 8:463–470
Murata J, Roepke J, Gordon H, Luca VD (2008) The leaf epidermome of Catharanthus roseus reveals its biochemical specialization. Plant Cell 20:524–542
Myles S, Chia J-M, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D (2010) Rapid genomic characterization of the genus Vitis. PLoS ONE 5:8219
Narula A, Kumar S, Srivastava PS (2007) Genetic fidelity of in vitro regenerants, encapsulation of shoot tips and high diosgenin content in Dioscorea bulbifera L., a potential alternative source of diosgenin. Biotechnol Lett 29:623–629
Negi MS, Singh A, Lakshmikumaran M (2000) Genetic variation and relationship among and within Withania species as revealed by AFLP markers. Genome 43:975–980
Niu L, Mantri N, Li CG, Xue C, Pang E (2011) Array-based techniques for fingerprinting medicinal herbs. Chin Med 6:18
Nongrum I, Kumar S, Kumaria S, Tandon P (2012) Genetic variation and gene flow estimation of Nepenthes khasiana Hook. F- A threatened insectivorous plant of India as revealed by RAPD markers. J Crop Sci Biotech 15:101–105
Padmesh P, Reji JV, Dhar MJ, Seeni S (2006) Estimation of genetic diversity in varieties of Mucuna pruriens using RAPD. Biol Plant 50:367–372
Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84
Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255
Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. Proc Natl Acad Sci USA 91:5222–5226
Plaschke J, Ganal MW, Roder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007
Prathepha P, Baimai V (1999) Genetic differentiation in Thai populations of the rare species Afgekia sericea Craib (Leguminosae) revealed by RAPD-PCR assays. Genetica 105:193–202
Qin J, Leung FC, Fung Y, Zhu D, Lin B (2005) Rapid authentication of ginseng species using microchip electrophoresis with laser-induced fluorescence detection. Anal Bioanal Chem 381:812–819
Qiu YX, Zong M, Yao Y, Chen BL, Zhou XL, Chen ZL, Fu CX (2009) Genetic variation in wild and cultivated rhizoma corydalis revealed by ISSRs markers. Planta Med 75:94–98
Rahimmalek M, Bahreininejad B, Khorrami M (2009) Tabatabaei BES (2009), Genetic variability and geographic differentiation in Thymus daenensis subsp. daenensis, an endangered medicinal plant, as revealed by inter simple sequence repeat (ISSR) markers. Biochem Genet 47:831–842
Rahimmalek M, Tabatabaei BES, Arzani A, Khorrami M (2011) Development and characterization of microsatellite markers for genomic analysis of yarrow (Achillea millefolium L.). Genes & Genomics 33:475–482
Rajkumar S, Singh SK, Nag A, Ahuja PS (2011) Genetic structure of Indian valerian (Valeriana jatamansi) populations in Western Himalaya revealed by AFLP. Biochem Genet 49:674–681
Ramesh M, Vijayakumar K, Karthikeyan A, Pandian S (2011) RAPD based genetic stability analysis among micropropagated, synthetic seed derived and hardened plants of Bacopa monnieri (L.): a threatened Indian medicinal herb. Acta Physiol Plant 33:163–171
Rana S, Dhar N, Bhat WW, Razdan S, Khan S, Dhar RS, Dutt P, Lattoo SK (2012) A 12-deoxywithastramonolide-rich somaclonal variant in Withania somnifera (L.) Dunal: molecular cytogenetic analysis and significance as a chemotypic resource. In Vitro Cell Dev Biol-Plant 48:546–554
Ranade SA, Nair KN, Srivastava AP, Pushpangadan P (2009) Analysis of diversity amongst widely distributed and endemic Atalantia (family Rutaceae) species from Western Ghats of India. Physiol Mol Biol Plants 15:211–224
Rathore MS, Chikara J, Mastan SG, Rahman H, Anand KGV, Shekhawat NS (2011) Assessment of genetic stability and instability of tissue culture-propagated plantlets of Aloe vera L. by RAPD and ISSR markers. Appl Biochem Biotechnol 165:1356–1365
Rawat JM, Rawat B, Mehrotra S, Chandra A, Nautiyal S (2013) ISSR and RAPD based evaluation of genetic fidelity and active ingredient analysis of regenerated plants of Picrorhiza kurroa. Acta Physiol Plant 35:1797–1805
Richard I, Beckman JS (1995) How neutral are synonymous codon mutations? Nat Genet 10:259
Rischer H, Oresi M, Seppanen-Laakso T, Katajamaa M, Lammertyn F et al (2006) Gene-to metabolic networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proc Nat Acad Sci USA 103:5614–5619
Rout GR (2006) Evaluation of genetic relationship in Typhonium species through random amplified polymorphic DNA markers. Biol Plant 50:127–130
Ruzicka J, Lukas B, Merza L, Gohler I, Abel G, Popp M, Novak J (2009) Identification of Verbena officinalis based on ITS sequence analysis and RAPD-derived molecular markers. Planta Med 75:1271–1276
Samantaray S, Maiti S (2010) An assessment of genetic fidelity of micropropagated plants of Chlorophytum borivilianum using RAPD markers. Biol Plant 54:334–338
Sangwan NS, Yadav U, Sangwan RS (2003) Genetic diversity among elite varieties of the aromatic grasses, Cymbopogon martini. Euphytica 130:117–130
Sarwat M, Das S, Srivastava PS (2008) Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb. Plant Cell Rep 27:519–528
Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DC (2010) Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C.A. Meyer roots. Mol Biol Rep 37:3465–3472
Satya P, Karan M, Sarkar D, Sinha MK (2012) Genome synteny and evolution of AABB allotetraploids in Hibiscus section Furcaria revealed by interspecific hybridization, ISSR and SSR markers. Plant Syst Evol 298:1257–1270
Schlag EM, McIntosh MS (2012) RAPD-based assessment of genetic relationships among and within American ginseng (Panax quinquefolius L.) populations and their implications for a future conservation strategy. Genet Resour Crop Evol 59:1553–1568
Schlotterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:2211–2215
Selvaraj D, Sarma RK, Ramalingam SK (2008) Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding. Bioinformation 3:24–27
Sharma K, Agrawal V, Sarika G, Kumar R, Prasad M (2008) ISSR marker-assisted selection of male and female plants in a promising dioecious crop: jojoba (Simmondsia chinensis). Plant Biotechnol Rep 2:239–243
Sharma R, Chowdhury V, Jain S, Jain RK (2009) A comparative study of genetic relationships among and within male and female genotypes of dioecious jojoba (Simmondsia chinensis L. Schneider) using RAPD and ISSR markers. Asian J Hortic 4:184–193
Shi W, Yang CF, Chen JM, Guo YH (2008) Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae). Plant Biol (Stuttg) 10:485–491
Shilpha J, Silambarasan T, Pandian SK, Ramesh M (2013) Assessment of genetic diversity in Solanum trilobatum L., an important medicinal plant from South India using RAPD and ISSR markers. Genet Resour Crop Evol 60:807–818
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049
Shukla N, Sangwan NS, Misra HO, Sangwan RS (2003) Genetic diversity analysis in Boerhavia diffusa L. of different geographic locations in India using RAPD markers. Gen Resour Crop Evol 50:587–601
Siju S, Dhanya K, Syamkumar S, Sasikumar B, Sheeja TE, Bhat AI, Parthasarathy VA (2010) Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.). Mol Biotechnol 44:140–147
Singh A, Negi MS, Rajagopal J, Bhatia S, Tomar UK, Srivastava PS, Lakshmikumaran M (1999) Assessment of genetic diversity in Azadirachta indica using AFLP markers. Theor Appl Genet 99:272–279
Singh A, Negi MS, Moses VK, Venkateswarlu B, Srivastava PS, Lakshmikumaran M (2002) Molecular analysis of micropropagated neem plants using AFLP markers for ascertaining clonal fidelity. In Vitro Cell Dev Biol-Plant 38:519–524
Sobrino B, Briona M, Carracedoa A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194
Soleimani VD, Baum BR, Johnson DA (2003) Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol Biol Rep 21:281–288
Song J, Yao H, Li Y, Li X, Lin Y, Liu C, Han J, Xie C, Chen S (2009) Authentication of the family Polygonaceae in Chinese Pharmacopoeiaby DNA barcoding technique. J Ethnopharmacol 124:434–439
Soni M, Kaur R (2014) Rapid in vitro propagation, conservation and analysis of genetic stability of Viola pilosa. Physiol Mol Biol Plants 20:95–101
Su H, Wang L, Ge Y, Feng E, Sun J, Liu L (2008) Development of strain-specific SCAR markers for authentication of Ganoderma lucidum. World J Microbiol Biotechnol 24:1223–1226
Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med 77:754–760
Sze SC, Zhang KY, Shaw PC, But PP, Ng TB, Tong Y (2008) A DNA microarray for differentiation of (Fengdou Shihu) by its 5S ribosomal DNA intergenic spacer region. Biotechnol Appl Biochem 49:149–154
Tamhankar S, Ghate V, Raut A, Rajput B (2009) Molecular profiling of “Chirayat” complex using inter simple sequence repeat (ISSR) markers. Planta Med 75:1266–1270
Tang SQ, Bin XY, Peng YT, Zhou JY, Wang L, Zhong Y (2007) Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (Siraitia grosvenorii [Swingle] AM Lu et ZY Zhang), a species with edible and medicinal sweet fruits endemic to southern China, using RAPD and AFLP markers. Gen Resour Crop Evol 54:1053–1061
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138
Techen N, Chandra S, Lata H, Elsohly MA, Khan IA (2010) Genetic identification of female Cannabis sativa plants at early developmental stage. Planta Med 76:1938–1939
Thul ST, Srivastava AK, Singh SC, Shanker K (2011) Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting. Mol Biotechnol 49:77–81
Tripathi N, Chouhan DS, Saini N, Tiwari S (2012) Assessment of genetic variations among highly endangered medicinal plant Bacopa monnieri (L.) from Central India using RAPD and ISSR analysis. 3. Biotech 2:327–336
Tsoi PY, Woo HS, Wong MS, Chen SL, Fong WF, Xiao PG, Yang MS (2003) Genotyping and species identification of Fritillariaby DNA chips. Acta Pharm Sin 38:185–190
Varshney A, Anis M (2013) Evaluation of clonal integrity in desert date tree (Balanites aegyptiaca Del.) by inter-simple sequence repeat marker assay. Acta Physiol Plant 35:2559–2565
Verma S, Rana TS (2013) Genetic relationships among wild and cultivated accessions of curry leaf plant (Murraya koenigii (L.) Spreng.), as revealed by DNA fingerprinting methods. Mol Biotechnol 53:139–149
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Wang QM, Wang YZ, Sun LL, Gao FZ, Sun W, He J, Gao X, Wang L (2012) Direct and indirect organogenesis of Clivia miniata and assessment of DNA methylation changes in various regenerated plantlets. Plant Cell Rep 31:1283–1296
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1991) DNA polymorphisms amplified by arbitrary primers are usefll as genetic markers. Nucleic Acids Res 18:6531–6535
Wiriyakarun S, Yodpetch W, Komatsu K, Zhu S, Ruangrungsi N, Sukrong S (2013) Discrimination of the Thai rejuvenating herbs Pueraria candollei (White Kwao Khruea), Butea superba (Red Kwao Khruea), and Mucuna collettii (Black Kwao Khruea) using PCR-RFLP. J Nat Med 67:562–570
Xie Z, Kapteyn J, Gang DR (2008) A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes. Plant J 54:349–361
Xue CY, Xue HG (2008) Application of real-time scorpion PCR for authentication and quantification of the traditional Chinese medicinal plant Drynaria fortunei. Planta Med 74:1416–1420
Yang W, Bai X, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breeding 14:21–34
Yang JY, Kim HK, Park SJ (2011) Development of genetic marker specific for Korean Hwanggi medicine (Radix Astragali). Food Sci Biotechnol 20:1561–1567
Yao H, Song JY, Ma XY, Liu C, Li Y, Xu HX, Han JP, Duan LS, Chen SL (2009) Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Med 75:667–669
Zerega NJC, Mori S, Lindqvist C, Zheng Q, Motley TJ (2002) Using amplified fragment length polymorphisms (AFLP) to identify black Corlosn (Actaea racemosa). Economic Bot 56:154–164
Zhang Z, Guo M, Zhang J (2009) Identification of AFLP fragments linked to hydroxysafflor yellow A in Flos Carthami and conversion to a SCAR marker for rapid selection. Mol Breeding 23:229–237
Zhang QS, Xu BL, Liu LD, Yuan QQ, Dong HX, Cheng XH, Lin DL (2012) Analysis of genetic diversity among Chinese Pleurotus citrinopileatus Singer cultivars using two molecular marker systems (ISSRs and SRAPs) and morphological traits. World J Microbiol Biotechnol 28:2237–2248
Zhou X, Li Q, Yin Y, Chen Y, Lin J (2008) Identification of medicinal Ganoderma species based on PCR with specific primers and PCR-RFLP. Planta Med 74:197–200
Zhou TH, Dong SS, Li S, Zhao GF (2012) Genetic structure within and among populations of Saruma henryi, an endangered plant endemic to China. Biochem Genet 50:146–158
Zhu S, Fushimi H, Komatsu K (2008) Development of a DNA microarray for authentication of ginseng drugs based on 18S rRNA gene sequence. J Agric Food Chem 56:3953–3959
Zong M, Liu HL, Qiu YX, Yang SZ, Zhao MS, Fu CX (2008) Genetic diversity and geographic differentiation in the threatened species Dysosma pleiantha in China as revealed by ISSR analysis. Biochem Genet 46:180–196
Zulak KG, Cornish A, Daskalchuk TE, Deyholos MK, Goodenowe DB et al (2005) Gene transcript and metabolite profiling of elicitor-induced opium poppy cell cultures reveal the coordinate regulation of primary and secondary metabolism. Planta 225:1085–1106
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The authors are appreciative of Department of Biotechnology, Instrumentation and Environmental Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India for providing research facilities.
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We, the authors of this article, declare that there is no conflict of interest and we do not have any financial gain from it.
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Gantait, S., Debnath, S. & Nasim Ali, M. Genomic profile of the plants with pharmaceutical value. 3 Biotech 4, 563–578 (2014). https://doi.org/10.1007/s13205-014-0218-9
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DOI: https://doi.org/10.1007/s13205-014-0218-9