Development of Species-Specific SCAR Markers, Based on a SCoT Analysis, to Authenticate Physalis (Solanaceae) Species

Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review

The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.

Screening of Comprehensive Panel of Cultivated and Wild Vigna Species for Resistance to Pulse Beetle, Callosobruchus chinensis L

Pulses are a key source of dietary proteins in human nutrition. Despite several efforts to increase the production, various constraints, such as biotic and abiotic factors, threaten pulse production by various means. Bruchids (Callosobruchus spp.) are the serious issue of concern, particularly in storage conditions. Understanding host-plant resistance at morphological, biochemical and molecular levels is the best way to minimize yield losses. The 117 mungbean (Vigna radiata L. Wilczek) genotypes, including endemic wild relatives, were screened for resistance against Callosobruchus chinensis; among them, two genotypes, PRR 2008-2 and PRR 2008-2-sel, which belong to V. umbellata (Thumb.), were identified as highly resistant. The expression of antioxidants in susceptible and resistant genotypes revealed that the activity of phenylalanine ammonia lyase (PAL) was upregulated in the highly resistant wild Vigna species and lower in the cultivated susceptible genotypes, along with other biomarkers. Further, the SCoT-based genotyping revealed SCoT-30 (200 bp), SCoT-31 (1200 bp) and SCoT-32 (300 bp) as unique amplicons, which might be useful for developing the novel ricebean-based SCAR markers to accelerate the molecular breeding programme.

Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China

Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei's gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources.

Analysis of Genetic Diversity and Population Structure in Yam (Dioscorea Species) Germplasm Using Start Codon Targeted (SCoT) Molecular Markers

Yam (Dioscorea spp.) is an important food security crop with economic, nutritional, and medicinal value. It is a source of carbohydrates for millions of people in tropical and sub-tropical regions of Africa, Asia, South America, the Caribbean, and the South Pacific Islands. Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize genetic variability and produce excellent recombinant varieties. However, adequate genetic diversity and the population structure of yam accessions in Kenya are not available to guide accurate selection of parents for breeding. In the present study, 25 start-codon-targeted (SCoT) molecular markers were used to determine the genetic diversity and population structure among 20 yam accessions grown in Kenya. A total of 294 fragments were amplified, of which 95% were polymorphic with an average of 11.16 polymorphic fragments per primer. The polymorphic information content (PIC) value and primer resolving power (Rp) of 0.58 and 5.91, respectively, revealed high genetic diversity among the accessions. A dendrogram based on the unweighted pair group method of arithmetic means (UPGMA) grouped the 20 yam accessions into two clusters at 0.61 genetic similarity coefficients. Bayesian structure analysis revealed the existence of three subpopulations and some admixed accessions. Analysis of molecular variance (AMOVA) revealed a variance of 60% within the subpopulations and 40% among the subpopulations. The high degree of genetic diversity in the yam accessions successfully exhibited by SCoT molecular markers may serve as a valuable aid to widen the genetic base in yam breeding programs. The selection and hybridization of parental lines from the different clusters and sub-clusters identified could provide a foundation and could be exploited for yam breeding and variety development.

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.

An overview of remote monitoring methods in biodiversity conservation

Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.

Development and Application of a Cultivar-Specific Sequence-Characterized Amplified Region (SCAR) Marker for the Detection of Chrysanthemum morifolium Ramat. 'Daboju'

Chrysanthemummorifolium Ramat. 'Daboju' is a C. morifolium cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of C. morifolium 'Daboju' are very similar to those of other C. morifolium cultivars, they are often confused in practice. However, the medicinal value and practical use of C. morifolium depends on using the correct rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, similar C. morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in C. morifolium 'Daboju' (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 C. morifolium cultivars, ten C. morifolium 'Daboju' populations, and different simulated adulterations of 'Daboju' with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested C. morifolium 'Daboju' samples but failed in the absence of 'Daboju'. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from C. morifolium 'Daboju'. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of C. morifolium 'Daboju'. It can play an important role in ensuring the quality of medicinal preparations and protecting C. morifolium 'Daboju' germplasm resources in breeding programs and in identifying lines generated from this cultivar.

Do we have infraspecific taxa of Salvia macrosiphon Boiss. (Lamiaceae) in Iran?

BACKGROUND

Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species.

METHODS AND RESULTS

We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno-Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes.

CONCLUSIONS

The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.

Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo

The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.

A comparative assessment of morphological and molecular characterization among three Ziziphus species

Genetic variability of 84 accessions of three Ziziphus species including Z. spina-christi, Z. nummularia and Z. mauritiana were analyzed using a combination of morphological traits and translation initiation codon (ATG) polymorphism. Both morphological and molecular data revealed a high level of inter and intra specific variations among the accessions. Accordingly, 90.49% of amplified fragments were polymorphic among the accessions with the mean values of 0.37 for polymorphic information content (PIC), 3.31 for resolving power (RP), and 1.95 for marker index (MI). The phylogenetic clustering clearly delineated the entire germplasm into three well supported distinct clusters according to the species sources. According to the Nei's genetic identity, Z. spina-christi and Z. nummularia were the most similar species and had high differentiation with Z. mauritiana. Moreover, the highest values for Shannon's information index (I = 0.505) and gene diversity (h = 0.347) were recorded in Z. spina-christi indicating there is higher genetic diversity compared with two other species. Four private alleles were identified in two species which could be beneficial for accessions authentication in argumentative situations. Moreover, results of the Mantel test showed there were moderate correlation between molecular and morphological matrices. In addition, estimation of bivariate correlations revealed there were significant positive and negative correlations between different variables, which offer a practical application of this information during phenotype based selection in ber improvement programs. The results of this investigation highlight the efficiency of translation initiation codon polymorphism for genetic characterization and accurate authentication of Ziziphus accessions as well as detecting and tagging morphologically important traits in this genus that would be helpful for implementation of effective conservation strategies and even broaden current genetic diversity.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01000-7.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships

BACKGROUND

Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana.

RESULTS

The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value.

CONCLUSION

Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.

Development of an In Vitro Propagation Protocol and a Sequence Characterized Amplified Region (SCAR) Marker of Viola serpens Wall. ex Ging

An efficient protocol of plant regeneration through indirect organogenesis in Viola serpens was developed in the present study. Culture of leaf explants on MS (Murashige and Skoog) medium supplemented with 2.0 mg/L 6-benzyladenine and 0.13 mg/L 2,4-dichloro phenoxy acetic acid. Adventitious shoot formation was observed when calli were transferred on to MS medium containing 0.5 mg/L α-naphthalene acetic acid and 2.25 mg/L kinetin, which showed the maximum 86% shoot regeneration frequency. The highest root frequency (80.92%) with the 5.6 roots per explant and 1.87 cm root length was observed on MS medium supplemented with 2 mg/L indole-3-butyric acid. The plantlets were transferred to the mixture of sand, coffee husk and soil in the ratio of 1:2:1 in a pot, and placed under 80% shade net for one month. It was then transferred to 30% shade net for another one month, prior to transplantation in the field. These plantlets successfully acclimatized under field conditions. A Sequence Characterized Amplified Region (SCAR) marker was also developed using a 1135 bp amplicon that was obtained from RAPD (Random Amplification of Polymorphic DNA) analysis of six accessions of V. serpens. Testing of several market samples of V. serpens using the SCAR marker revealed successful identification of the genuine samples of V. serpens. This study, therefore, provides a proficient in vitro propagation protocol of V. serpens using leaf explants and a SCAR marker for the authentic identification of V. serpens. This study will be helpful for conservation of authentic V. serpens.

Metabolomic Profiling of Carotenoid Constituents in Physalis peruviana During Different Growth Stages by LC-MS/MS Technology

With the current ongoing changes in global food demands, natural carotenoids are preferred by consumers and are gaining attention among food scientists and producers alike. Metabolomic profiling of carotenoid constituents in Physalis peruviana during distinct on-tree growth stages was performed with liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology. The results show that the β rings of β-carotene are hydroxylated with great efficiency, and there is a continual synthesis of zeaxanthin at half-ripe and full-ripe stages, which is confirmed by relating the zeaxanthin content to that of its precursor (β-carotene). Lutein was, in terms of mass intensity, the most abundant carotenoid constituent (64.61 µg/g at the half-ripe stage) observed in this study. In addition, γ-carotene, which is rare in dietary fruits and vegetables, was detected in the mature and breaker stages, albeit at a relatively low level. The results suggest that when we consider the variation in carotenoid content during different growth stages, Physalis peruviana can be considered a good source of natural carotenoids.

Genetic homogeneity revealed in micropropagated Bauhinia racemosa Lam. using gene targeted markers CBDP and SCoT

Two gene targeted markers i.e. CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism were applied to analyze the genetic stability of in vitro propagated plants of Bauhinia racemosa Lam. multiplied by enhanced axillary shoot proliferation of mature tree derived nodal explant. Nine randomly selected micropropagated plants of 1 year age were subjected to molecular analysis. The isolated genomic DNA samples were subjected to PCR amplification with a total of 61 primers (25 CBDP and 36 SCoT) out of which 39 primers (21 CBDP and 18 SCoT) produced scorable amplicons. A total of 97 and 88 clear, distinct and reproducible amplicons were produced by CBDP and SCoT primers, respectively. The monomorphic banding pattern obtained through all the tested primers corroborated the true to type nature of in vitro propagated plants of B. racemosa.