A brief review of molecular techniques to assess plant diversity

Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals

BACKGROUND

Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in populations of Pinus sylvestris in the Urals and adjacent territories.

OBJECTIVES

The objects of the study were 13 populations of Scots Pine located in the Perm Territory, Chelyabinsk Region, and the Republic of Bashkortostan.

RESULTS

Sixteen pairs of primers to loci of potentially adaptively significant genes were developed, from which three pairs of primers were selected to detect the nucleotide diversity of the studied populations. The indicator of total haplotype diversity determined in the three studied loci varied from 0.620 (Pinus-12 locus) to 0.737 (Pinus-11 locus) and, on average, amounted to 0.662. The nucleotide diversity indicators in P. sylvestris in the study region were, on average, low (π = 0.004, θW = 0.013). Their highest values were found at the Pinus-12 locus (π = 0.005; θW = 0.032), and the lowest were found at the Pinus-15 locus (π = 0.003; θW = 0.002). This indicates that Pinus-15 is the most conserved of the three studied loci. In the three studied P. sylvestris loci associated with adaptation to environmental factors, 97 polymorphic positions were identified. The 13 populations of P. sylvestris are characterized by an average level of genetic diversity (Hd = 0.662; π = 0.004; θ = 0.013).

CONCLUSIONS

The polymorphic loci of adaptively significant genes of P. sylvestris can help identify the adaptive potential of pine forests in conditions of increasing ambient temperatures.

DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.

Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance

Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.

DBALM: A novel method for identifying ornamental flowering plants based on DNA barcodes-leaf morphology

Whereas the presence of flowers on ornamental flowering plants is essential for their identification via traditional methods, ornamental flowering plants cannot be reliably identified in non-flowering stages likewise. Here, DBALM (DNA Barcodes-Leaf Morphology), a new approach that combines DNA barcoding data with micromorphological features of the leaf epidermis and that is not limited by the flowering stage, was used to identify 16 evergreen rhododendron cultivars. First, the sequences of DNA barcodes, ITS, matK, psbA-trnH, and rbcL, were obtained from the DNA of leaves. Phylogenetic analysis was conducted to clarify the groupings among all the samples based on the four markers. Then, microscopic features of the leaf epidermis were used to further distinguish individuals from the same clade. DNA barcoding permitted the 16 cultivars to be divided into eight groups. The microscopic features of the leaf epidermis permitted cultivars within the same clade to be distinguished. The matK + psbA-trnH combination was the most effective barcode combination in this study. In addition, the new primer matK-Rh_R was designed, and it increased the amplification rate of evergreen rhododendron cultivars to 100%. In sum, DBALM was capable of accurately identifying the 16 evergreen rhododendron cultivars using data collected from a single leaf in the vegetative growth stage. This method can greatly facilitate the identification and breeding of ornamental flowering plants.

Identifying phytopathogenic fungi in Al-Baha province, Saudi Arabia through their molecular and morphological features: An overview

Fungi are major pathogens of plants. They are responsible for most of the spoilage that occurs to plants in fields or in storage conditions. In addition to the direct impacts of fungi upon the plant's fruiting body, such as leaf spot, wilt, rust, dieback and rot, fungi can contaminate plants with mycotoxins. Twenty isolates were molecularly identified in this study representing eight genera and twelve species. The most common species identified in this work belongs to Aspergillus (33.3%), Penicillium (16.6%) and Fusarium (16.6%) genera, which are well known to have mycotoxigenic species. Environmental factors have a significant influence on the biological activity of fungi, including growth, sporulation and mycotoxin production. Temperature and water activity affect fungal virulence factors, such as growth, colonisation, spread and mycotoxin production. This work found the optimal temperature for the growth of isolates, was 30 °C for 75 % of isolates and at 25 °C for 25 % of isolates. This information is useful, as it helps to identify the phytopathogenic and mycotoxigenic species, and determining optimal growth temperatures is important to control them and reduce their threats.

Genetic variation of Cerastium alpinum L. from Babia Góra, a critically endangered species in Poland

Babia Góra massif is the only site of occurrence of the Cerastium alpinum L. in Poland, an arctic-alpine perennial plant with a wide distribution in North America, northwestern Asia, and Europe. To determine whether the isolated Polish populations are genetically distinct, we have performed an evaluation of C. alpinum from Babia Góra with the use of iPBS markers. A total number of 133 individuals of C. alpinum from seven populations representing four localizations of the species were analyzed, i.e., from Babia Góra (Poland), Alps (Switzerland), Nuolja massif (Sweden), and Kaffiøyra (Svalbard, Norway). Genetic analysis of all C. alpinum samples using eight PBS primers identified 262 bands, 79.4% of which were polymorphic. iPBS markers revealed low genetic diversity (average H_e = 0.085) and high population differentiation (F_ST = 0.617). AMOVA results confirmed that the majority of the genetic variation (62%) was recorded among populations. The grouping revealed by PCoA showed that C. alpinum from Svalbard is the most diverged population, C. alpinum from Switzerland and Sweden form a pair of similar populations, whereas C. alpinum from the Babia Góra form a heterogeneous group of four populations. Results of isolation by distance analysis suggested that the spatial distance is the most probable cause of the observed differentiation among populations. Although significant traces of a bottleneck effect were noted for all populations of C. alpinum from Babia Góra, the populations still maintain a low but significant level of genetic polymorphism. These results are of great importance for developing conservation strategies for this species in Poland.

Selection of Sweetpotato Parental Genotypes Using Simple Sequence Repeat Markers

Knowledge of the genetic diversity and genetic relationship is important in crop improvement. The objective of this study was to determine the genetic diversity of 31 sweetpotato genotypes and furthermore to select distantly related individuals for breeding of superior parental clones. The genotypes (sourced from the Agricultural Research Council, South Africa) originating from Africa and American continent were genotyped using eight highly polymorphic SSR markers. The SSR markers generated a total of 83 putative alleles. The polymorphic information content (PIC) of the tested simple sequence markers varied from 0.73 to 0.91, with a mean of 0.85. At least 11 different alleles were found in 8 loci within the population, with 7 effective alleles per locus. Although high diversity was found among the genotypes, genetic distances among the genotypes were relatively low. Cluster analysis revealed the existence of three distinct genetic groups, and the clustering patterns follow to some extent the geographic origin and pedigree of the genotypes. High gene flow was observed among different sweetpotato accessions. The selected SSR markers were found to be highly polymorphic with high discriminatory power for genetic characterization studies and are useful genomic tool to complement phenotyping of sweetpotato genotypes. Two heterotic groups were found in the study. The heterotic group A was composed of 14 genotypes mainly of South African origin, while the heterotic group B consisted of 17 genotypes of American origin. The two distinct groups were important for the selection of breeding clones that were distantly related to be used as parental clones in the advancement of traits of interest.

Inheritance of seedlessness and the molecular characterization of the INO gene in Annonaceae

The inheritance of the seedless fruit characteristic of Annona squamosa has not yet been explained. Molecular techniques may aid breeding programs, mainly in the assisted selection of the target gene. The INO gene may be related to seed development in these fruits. The objective of the present paper was to investigate the inheritance of seedlessness in the 'Brazilian seedless' sugar apple and INO gene conservation in Annona squamosa and Annona cherimola x Annona squamosa genotypes by assessing their homology with the INO database genes. The F1 generation was obtained by crossing the mutant 'Brazilian seedless' (male genitor) (P1) with the wild-type A. squamosa with seeds (M1 and M2, female genitors). The INO gene was studied in mutant and wild-type A. squamosa (P1, M1, M2 and M3) and in the Gefner atemoya (A. cherimola x A. squamosa) (M4) cultivar. The DNA was extracted from young leaves, and four sets of specific primers flanking the INO gene were amplified. The seedless characteristic was identified as stenospermatic in the fruits of parental P1, suggesting monogenic inheritance with complete dominance. High sequence similarity of the INO gene amplifications in the sugar apple accessions (M1, M2, M3) and the atemoya cultivar Gefner (M4) reinforces the hypothesis of their conservation.

The efficiency of technologies used for epidemiological characterization of Listeria monocytogenes isolates: an update

The characterization of pathogenic bacteria by providing information regarding the identification and source-tracking of the causes of outbreaks is vital for the epidemiological investigations of foodborne diseases. The knowledge of transmission of Listeria monocytogenes (L. monocytogenes) strains from the environment, directly or indirectly (through food processing facilities) to the final food products, due to the complexity of evaluating numerous, affecting parameters is quite limited. The food trade globalization also adds difficulties in tracking the association between the infection occurrence and causative pathogens, aiming to prevent their spread. The occurrence of listeriosis, a notifiable disease throughout the world, can either be sporadic or outbreak-related. Due to the importance of foodborne outbreaks from a public health aspect and its correspondence enormous economic losses, cross-linked surveillance studies regarding the contamination of foods by L. monocytogenes, besides identifying clusters and tracing the sources of infections on an international-scale to prevent and control L. monocytogenes outbreaks sounds very crucial. Contrary to the conventional typing methods, molecular-based techniques, such as whole-genome sequencing, owing to the capacity to discriminate L. monocytogenes strains down to single nucleotide differences, provide an accurate characterization of strains and tracking the causes of outbreaks. However, routinely using molecular-based methods depends on the required improvements in the affordability, proper timing, and preparing reliable, standardized bioinformatics facilities. This work was conducted to critically review the practical potential of diverse typing methods have been used for the characterization of L. monocytogenes and discuss how they might change the future of efforts for control of listeriosis.

Study on Galanthus species in the Bulgarian flora

Genus Galanthus (Amaryllidaceae) includes 19 species in Europe and the Middle East. The Flora of Bulgaria recognizes two species: G. nivalis L. and G. elwesii Hook. Galanthus elwesii is characterized by relatively high morphological variability, leading some authors to identify some populations as G. gracilis Celak. However, the occurrence of G. gracilis in the Bulgarian flora is disputed. The hypothesis was that populations previously identified as G. gracilis belong indeed to a separate species. Therefore, the objective of this study was to compare G. nivalis and G. elwesii with plants from populations previously identified as G. gracilis. Morphological, DNA, embryological and anatomical analyzes were conducted to meet the objective. The morphological characteristics and DNA dendrogram revealed that G. gracilis and G. elwesii were situated in the same cluster and had significant morphological similarity, whereas plants from populations identified as G. nivalis were dissimilar in morphology and situated in a separate cluster. The revealed features of the generative sphere showed similarities across the species. Scanning electron microscopy (SEM) analyses of the surface revealed that the anticillinal walls of G. elwesii and G. gracilis were straight, while those of G. nivalis were wavy. This research demonstrated that the plants of G. elwesii and those from populations identified as G. gracilis are morphologically, embryologically and genetically similar, thus refuting the hypothesis. This study did not provide sufficient evidence to support the claim of the existence of G. gracilis in the Bulgarian flora; the populations identified as G. gracilis in Bulgaria may be forms of G. elwesii.

Genetic diversity and nonparametric statistics to identify possible ISSR marker association with fiber quality of pineapple

Due to the increasing search for renewable resources, plant fibers have become an alternative when creating new products. Studies demonstrate the potential use of pineapple fibers in composites. The objective of this work was to evaluate the genetic diversity and verify any association between ISSR (Inter Simple Sequence Repeats) bands and quality of pineapple fibers for use in cements in the civil construction. The study analyzed the genetic variability of 11 pineapple genotypes, as well as the possible association of 131 bands from 16 ISSR markers with fiber quality characteristics. Eleven bands were selected based on their high correlations (0.64578* to 0.72457*) with three fiber quality variables. Of these, two bands were purified, sequenced, and blasted against sequences in GenBank at NCBI. These markers can be used in marker assisted selection to genetically improve the quality of pineapple fiber. Bands that returned no hits in the NCBI BLAST search can be deposited as new sequences in the GenBank. Therefore, the SCAR markers, once validated, can be useful in pineapple genetic breeding programs worldwide by using molecular marker assisted selection for fiber resistance, which could subsidize the development of more promising genotypes for industrial use and contribute to the sustainability of this new production sector.

The Development of Plant Conservation in Botanic Gardens and the Current and Future Role of Conservation Genetics for Enhancing Those Conservation Efforts

Botanic gardens play major roles in plant conservation globally. Since the 1980s, the number of botanic gardens worldwide and their involvement in integrating ex situ and in situ plant conservation has increased significantly, with a growing focus on understanding, documenting, and capturing genetic diversity in their living collections. This article outlines why genetic diversity is important for conservation, and explores how botanic gardens can establish and expand the use of molecular techniques to support their plant conservation efforts.

Genetic diversity and population structure of watermelon (Citrullus sp.) genotypes

Genetic polymorphism amid plant species is a crucial factor for plant improvement and maintaining their biodiversity. Evaluation of genetic diversity amongst plant species is significant to deal with the environmental stress conditions and their effective involvement in the breeding programs. Hence, in present study, an attempt has been made towards the genetic assessment of individual and bulked populations of 25 watermelon genotypes, belonging to Citroides (citron watermelon) and Lanatus (dessert watermelon) group from Konya, Thrace, Turkmenistan, Saudi Arabia and Turkey. The employed Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Polymorphism (ISSR) marker systems provided 69.4 and 95.4% polymorphisms, respectively. Different clustering methods showed clear grouping of the genotypes based on the geographical origin and species. Citron genotypes from Turkmenistan stood apart from all the Turkish Lanatus genotypes. However, Saudi Arab Lanatus genotype grouped with native Turkish varieties indicating the genetic linkage. Among all the Turkmenistan Citron genotypes, Turkmenistan-11 was the most distinct form. Moreover, sufficient genetic variation was found between the commercial and native Lanatus genotypes of Turkey as well as Citron genotypes of Turkmenistan. Hence, it will be beneficial to include these genotypes in the future breeding programs to transfer disease-resistant alleles from Citron to Lanatus genotypes.

New microsatellites for the Atacama Desert endemic Balsamocarpon brevifolium (Fabaceae)

PREMISE

Algarrobilla (Balsamocarpon brevifolium, Fabaceae) is an endemic xerophytic shrub restricted to the Atacama Desert in northern Chile. Extensive utilization of the region for coal production has endangered this species. Conservation efforts are underway, with genetic diversity analyses being key to the restoration of these populations.

METHODS AND RESULTS

Fifteen new microsatellite markers were developed for B. brevifolium and used to analyze three populations from the Atacama and Coquimbo regions in Chile. Microsatellites were highly polymorphic, with an average of 5.77 alleles per marker and an average level of expected heterozygosity of 0.72. These markers were evaluated and cross-amplified on two related species (Senna cumingii and Caesalpinia angulata) with partial success.

CONCLUSIONS

The development of this set of markers permits an extensive study of B. brevifolium populations for conservation purposes.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Phylogenetic implications and secondary structure analyses of Vigna mungo (L.) Hepper genotypes based on nrDNA ITS2 sequences

The internal transcribed spacers are highly preferred nuclear markers for the phylogenetic assessment of most eukaryotes, including plants. More recently, ITS2 has shown to possess equivalent phylogenetic significance as the entire ITS region. Vigna mungo L. Hepper is comparatively less explored from the molecular aspects as compared to the other species of the Vigna genus. The study presents the intra-individual characterization of 24 distinct genotypes Vigna mungo L. Hepper, using morphological as well as nrDNA ITS2 sequences and secondary structural data. The morphological characterization has been carried out using nine important agro-morphological traits. The molecular phylogeny of the sequence data, using the maximum parsimony and neighbor joining methods, shows the significant distinction based on the haplotypic variations amongst blackgram genotypes. The ITS2 secondary structures predicted using the homology modeling approach were compatible with the eukaryote-universal ITS2 secondary structure. The sequence-structure phylogeny reconstructed using the profile neighbour joining approach, also showed the presence of haplotypic variations in form of clusters on the phylogenetic tree. Further, the high GC content in the sequence data and highly negative ΔG values of the folded secondary structures ruled out the possibilities of the presence of any pseudogenes in the data set. Our analysis recommends the use of ITS2 sequence and secondary structure data at the intraspecific levels of plant taxonomical classification. Moreover, this study for the very first time reports the combined use morphological, and molecular data (using ITS2 sequence and secondary structural information) for the characterization of plants at the varietal level of taxonomical classification.

Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.

Life Cycle and Genetic Diversity of Symplocarpus nipponicus (Araceae), an Endangered Species in Japan

Symplocarpus nipponicus, a member of the Araceae family, is an endangered plant in several prefectures in Japan. For the conservation of this wild species, we investigated the morphology, life cycle, and genetic diversity of three wild populations. By fixed-point observation over several years, we found that it takes at least four years for the plant to set the inflorescences consisting of spadices and spathes, and another two years for it to set mature seeds. To examine the genetic diversity in the wild population, we developed 11 novel microsatellite markers and investigated the genetic variation in three populations in Kyoto Prefecture: Ayabe, Hanase, and Momoi. The Ayabe population carried less genetic variation than the other two areas, suggesting the isolation of the habitat and thus a higher risk of extinction. Our results provide basic knowledge of the ecological aspects of S. nipponicus, as well as molecular techniques for the assessment of its genetic diversity, and thus are useful for the conservation of this endangered species.

Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging

DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a ribulose diphosphate carboxylase (rbcL) SNP barcoding (RSB) strategy using a decision tree algorithm. After alignment and trimming, 31 SNPs were discovered in the rbcL sequences from 38 Brassicaceae plant species. In the decision tree construction, these SNPs were computed to set up the decision rule to assign the sequences into 2 groups level by level. After algorithm processing, 37 nodes and 31 loci were required for discriminating 38 species. Finally, the sequence tags consisting of 31 rbcL SNP barcodes were identified for discriminating 38 Brassicaceae species based on the decision tree-selected SNP pattern using RSB method. Taken together, this study provides the rational that the SNP aspect of DNA barcode for rbcL gene is a useful and effective sequence for tagging 38 Brassicaceae species.

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence

The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of finger millet is expected to help to understand this and other important molecular mechanisms in finger millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of finger millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the finger millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the finger millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa.

Inspecting the True Identity of Herbal Materials from Cynanchum Using ITS2 Barcode

Cynanchum is a large genus with some important medicinal species in China. The medicinal species in Cynanchum are easily confused, leading to potential safety risks. In this study, the internal transcribed spacer 2 (ITS2) barcode was used to discriminate the medicinal plants in Cynanchum. The identifying capability of ITS2 was assessed using the specific genetic divergence, BLAST1, neighbor-joining (NJ) tree, maximum-likelihood (ML) tree, and single-nucleotide polymorphism (SNP) methods. Results indicated that the intra-specific genetic divergences of Cynanchum species were lower than their inter-specific genetic divergences. Of the 87 samples from 17 species, ITS2 showed a high identification efficiency of 90.8 and 87.4% at the species level through BLAST1 and the nearest distance methods. NJ tree and ML tree also demonstrated the suitability of ITS2 to differentiate Cynanchum species. Meanwhile, a stable SNP was found, and it could accurately authenticate Cynanchum paniculatum and Cynanchum atratum. Furthermore, we collected 64 commercial samples from three commonly used herbal medicines and evaluated the capability of ITS2 to survey their authentication. Of these samples, Cynanchi Atrati Radix et Rhizoma (Baiwei) showed a potential safety problem, and all the 11 test samples were adulterants. In conclusion, ITS2 can distinguish medicinal species in Cynanchum effectively, and its application could greatly improve the identification efficiency and accuracy of commercial herbal medicines in this genus.

Saudi medicinal plants for the treatment of scorpion sting envenomation

Scorpion sting envenoming poses major public health problems. The treatment modalities include antivenoms, chemical antidotes and phytotherapy, with varying degrees of effectiveness and side effects. In this investigation, we reviewed the use of Saudi medicinal plants for the treatment of scorpion sting patients. The relevant literature was collected using the online search engines including Science Direct, Google and PubMed with the help of specific keywords. We also used the printed and online resources at our institutional library to gather the relevant information on the use of medicinal plants for the treatment of scorpion sting patients. A descriptive statistics was used for data compilation and presentation. The results of this survey showed the use of at least 92 medicinal plants with beneficial effects for treating victims of stings of different scorpion species. These commonly used herbs spanned to 37 families whilst different parts of these plants were employed therapeutically for alleviation of envenomation symptoms. The application of leaves (41%) was preferred followed by roots (19%), whole plant (14%) and seeds (9%). The use of latex (4%), stem (3%), flowers (3%) and bark (3%) was also reported. In some cases, tannin (2%), rhizome (1%) and shoot (1%) were also used. In conclusion, herbal medicines are effectively used for the treatment of patients with scorpion envenomation. This type of medication is free from side effects as observed with chemical antidotes or antivenom therapy. It is important to identify the active ingredients of herbal drugs for improving their therapeutic potential in traditional medicine.

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

The genus Fritillaria belongs to the widely distributed Liliaceae. The bulbs of Fritillaria, F. ussuriensis and F. cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species are therefore required. Here, we report the complete chloroplast (CP) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria CP genomes were 151,524 and 151,083 bp in length, respectively, and each included a pair of inverted repeated regions (52,678 and 52,156 bp) that was separated by a large single copy region (81,732 and 81,390 bp), and a small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding regions in F. ussuriensis and 78 in F. cirrhosa, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The gene order, content, and orientation of the two Fritillaria CP genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ CP genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of the two Fritillaria species and a comparison study are useful genomic information for identifying and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) gene pool was analyzed with 117 microsatellite markers scattered throughout A, B, and D genomes. Ninety microsatellite markers were giving 1620 polymorphic alleles in 55 different bread wheat genotypes. These genotypes were found to be divided into three subgroups based on Bayesian model and Principal component analysis. The highest polymorphism information content value for the markers resides on A genome was estimated for wmc262 marker located on 4A chromosome with the polymorphism information content value of 0.960. The highest polymorphism information content value (0.954) among the markers known to be located on B genome was realized for wmc44 marker located on 1B chromosome. The highest polymorphism information content value for the markers specific to D genome was found in gwm174 marker located on 5D chromosome with the polymorphism information content value of 0.948. The presence of linkage disequilibrium between 81 pairwise SSR markers reside on the same chromosome was tested and very limited linkage disequilibrium was observed. The results confirmed that the most distant genotype pairs were as follows Ceyhan-99-Behoth 6, Gerek 79-Douma 40989, and Karahan-99-Douma 48114.

DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market

The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.

Internal transcribed spacer 2 barcode: a good tool for identifying Acanthopanacis cortex

Acanthopanacis cortex has been used in clinical applications for a long time. Considering some historical and geographical factors, Acanthopanacis cortex is easily confused with other herbs in medicine markets, thereby causing potential safety issues. In this study, we used the internal transcribed spacer 2 (ITS2) barcode to identify 69 samples belonging to six species, including Acanthopanacis cortex and its adulterants. The nearest distance, single-nucleotide polymorphisms (SNPs), and neighbor-joining (NJ) tree methods were used to evaluate the identification ability of the ITS2 barcode. According to the kimura-2-parameter model, the intraspecific distance of Eleutherococcus nodiflorus ITS2 sequences ranged from 0 to 0.0132. The minimum interspecific distance between E. nodiflorus and E. giraldii was 0.0221, which was larger than the maximum intraspecific distance of E. nodiflorus. Three stable SNPs in ITS2 can be used to distinguish Acanthopanacis cortex and its closely related species. The NJ tree indicated that the Acanthopanacis cortex samples clustered into one clade, which can be distinguished clearly from the adulterants of this herb. A secondary structure of ITS2 provided another dimensionality to identify species. In conclusion, the ITS2 barcode effectively identifies Acanthopanacis cortex, and DNA barcoding is a convenient tool for medicine market supervision.

Diagnosis of toxoplasmosis and typing of Toxoplasma gondii

Toxoplasmosis, caused by the obligate intracellular protozoan Toxoplasma gondii, is an important zoonosis with medical and veterinary importance worldwide. The disease is mainly contracted by ingesting undercooked or raw meat containing viable tissue cysts, or by ingesting food or water contaminated with oocysts. The diagnosis and genetic characterization of T. gondii infection is crucial for the surveillance, prevention and control of toxoplasmosis. Traditional approaches for the diagnosis of toxoplasmosis include etiological, immunological and imaging techniques. Diagnosis of toxoplasmosis has been improved by the emergence of molecular technologies to amplify parasite nucleic acids. Among these, polymerase chain reaction (PCR)-based molecular techniques have been useful for the genetic characterization of T. gondii. Serotyping methods based on polymorphic polypeptides have the potential to become the choice for typing T. gondii in humans and animals. In this review, we summarize conventional non-DNA-based diagnostic methods, and the DNA-based molecular techniques for the diagnosis and genetic characterization of T. gondii. These techniques have provided foundations for further development of more effective and accurate detection of T. gondii infection. These advances will contribute to an improved understanding of the epidemiology, prevention and control of toxoplasmosis.

Skim-based genotyping by sequencing

Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of individuals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the individual study design GBS protocols can take multiple forms, however most share a sequence of core steps that have to be undertaken. These include: sequencing of the DNA from the individuals of interest (usually two parents of a mapping population and their progeny), mapping of the sequencing reads to the reference sequence, SNP calling and filtering, SNP genotyping and imputation, followed by haplotype identification and downstream analysis. GBS has a range of applications from general marker discovery, haplotype identification, and recombination characterization to quantitative trait locus (QTL) analysis, genome-wide association studies (GWAS), and genomic selection (GS). It has already been applied to a range of plant species including: rice, maize, artichoke, and Arabidopsis thaliana. It is a promising approach which is likely to provide new and important insights into plant biology.

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.)

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

Randomly amplified polymorphic DNA (RAPD) and derived techniques

Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, developing molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest and cost-effective and can be performed in a moderate laboratory for most of its applications. In addition RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented.

A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding

Medicinal plants of the Panax genus belonging to Araliaceae family are well-known, rare plants used as tonics in traditional Chinese medicine and have been described in the Chinese Pharmacopoeia. Because of the high price and the huge human demand, these commercial products often contain adulterants. In this study, 377 sequences from four species were analyzed. Single nucleotide polymorphisms (SNPs) were detected and patterns of intragenomic variation in internal transcribed spacer 2 (ITS2) from the four Panax species were studied. Intraspecific variations were analyzed based on three typical DNA barcodings (ITS2, matK and psbA-trnH). Results from this study revealed that intraspecific genetic distances in Panax ginseng and Panax quinquefolius were quite low (0-0.002) and the multi-copy ITS2 could be considered a single locus in the genomes of these two species. Five stable SNPs were detected in ITS2 region to identify the Panax medicinal species. Considering the mixed powder of P. ginseng and P. quinquefolius, double peaks could be clearly examined at SNP positions and the height of the peaks could indicate the mixed ratio roughly. Our findings indicate that SNP-based molecular barcodes could be developed as a routine method for the identification of the Panax genus with closely related species and the mixed powder P. ginseng and P. quinquefolius.

DNA fingerprinting of Chinese melon provides evidentiary support of seed quality appraisal

Melon, Cucumis melo L. is an important vegetable crop worldwide. At present, there are phenomena of homonyms and synonyms present in the melon seed markets of China, which could cause variety authenticity issues influencing the process of melon breeding, production, marketing and other aspects. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for cultivar identification. The aim of this study was to construct a DNA fingerprinting database of major melon cultivars, which could provide a possibility for the establishment of a technical standard system for purity and authenticity identification of melon seeds. In this study, to develop the core set SSR markers, 470 polymorphic SSRs were selected as the candidate markers from 1219 SSRs using 20 representative melon varieties (lines). Eighteen SSR markers, evenly distributed across the genome and with the highest contents of polymorphism information (PIC) were identified as the core marker set for melon DNA fingerprinting analysis. Fingerprint codes for 471 melon varieties (lines) were established. There were 51 materials which were classified into17 groups based on sharing the same fingerprint code, while field traits survey results showed that these plants in the same group were synonyms because of the same or similar field characters. Furthermore, DNA fingerprinting quick response (QR) codes of 471 melon varieties (lines) were constructed. Due to its fast readability and large storage capacity, QR coding melon DNA fingerprinting is in favor of read convenience and commercial applications.

Development and multiplex PCR amplification of microsatellite markers in the commercial clam Venerupis rhomboides (Mollusca: Bivalvia)

Venerupis rhomboides is a commercial clam whose production could be enhanced through effective management of natural and hatchery stocks. This study provides the first panel of microsatellite markers for the exploitation of this species according to genetic criteria. A total of 22 polymorphic microsatellite loci were isolated and characterized from two genomic libraries enriched for different motifs. The number of alleles per locus ranged from 2 to 14 in a sample of 20 clams from Spain, and the observed and expected heterozygosity from 0 to 0.95 and 0.05-0.901, respectively. Sixteen loci were in agreement with Hardy-Weinberg equilibrium after sequential Bonferroni correction and linkage disequilibrium between loci pairs was not detected. To reduce the cost of the genotyping process, tri- and pentaplex PCRs, amplifying a total of 13 microsatellites loci were optimized. The microsatellites developed here represent the first nuclear markers described in V. rhomboides and will be useful tools for genetic studies involving assessment of genetic variation and population structure of natural and cultivated populations, assignment testing, construction of genetic linkage maps and dissection of production traits.

Genotyping-by-Sequencing in Plants

The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.

DNA barcoding as an effective tool in improving a digital plant identification system: a case study for the area of Mt. Valerio, Trieste (NE Italy)

BACKGROUND

Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting). DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences.

METHODOLOGY/PRINCIPAL FINDINGS

In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy). The core barcode markers (plastidial rbcL and matK), plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios.

CONCLUSIONS/SIGNIFICANCE

Our results show that the core barcode markers univocally identify most species of our local flora (96%). The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant biodiversity surveys.

SCAR markers for discriminating species of two genera of medicinal plants, Liriope and Ophiopogon

The development of DNA markers that can closely discriminate between Liriope and Ophiopogon species is vital for efficient and accurate identification of these species, and to ensure the quality, safety, and efficacy of medicines made from these plants. We developed species-specific molecular markers for these two genera. Forty RAPD primers were tested to detect polymorphism; species-specific RAPD bands were gel-purified, cloned, and sequenced. Primers for sequence-characterized amplified regions (SCARs) were then designed, based on nucleotide sequences of specific RAPD primers. SCAR markers SA06 and SB05, specific to Ophiopogon japonicus, amplified 460- and 553-bp DNA fragments, respectively. The marker SA12 amplified a 485-bp fragment specific to Liriope platyphylla. This is the first report of a species-specific SCAR marker for this group. These markers will be useful for rapid identification of closely related Liriope and Ophiopogon species.

Comparison of primers for RAPD-PCR from environmental isolates of Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus laurentii complex

Various organisms have been characterized by molecular methods, including fungi of the genus Cryptococcus. The purposes of this study were: to determine the discriminatory potential of the RAPD (Random Amplified Polymorphic DNA) primers, the pattern of similarity of the Cryptococcus species, and discuss their useful application in epidemiological studies. We analyzed 10 isolates of each specie/group: C. albidus, C. laurentii complex, C. neoformans var. grubii, all from environmental source, and two ATCC strains, C. neoformans var. grubii ATCC 90112, and C. neoformans var. neoformans ATCC 28957 by RAPD-PCR using the primers CAV1, CAV2, ZAP19, ZAP20, OPB11 and SEQ6. The primers showed a good discriminatory power, revealing important differences between them and between species; the SEQ6 primer discriminated a larger number of isolates of three species. Isolates of C. laurentii showed greater genetic diversity than other species revealed by all six primers. Isolates of C. neoformans were more homogeneous. Only the primer CAV2 showed no amplification of DNA bands for C. albidus. It was concluded that the use of limited number of carefully selected primers allowed the discrimination of different isolates, and some primers (e.g., CAV2 for C. albidus) may not to be applied to some species.

ISSR: a reliable and cost-effective technique for detection of DNA polymorphism

With the emergence of more and more molecular markers as useful tools in plethora of population genetic and phylogenetic studies, choice of marker system for a particular study has become mind boggling. These marker systems differ in their advantages and disadvantages, so it is imperative to keep in mind all the pros and cons of the technique while selecting one for the problem to be addressed.Here, we have shed light on the ISSR (intersimple sequence repeat) technique, as a marker of choice if one wants to go for properties such as reliability, simplicity, cost effectiveness, and speed, in addition to assessing genetic diversity between closely related individuals. We have outlined here the whole methodology of this technique with an example of Tribulus terrestris as case study.

Molecular systematics of Polygonum minus Huds. based on ITS sequences

Plastid trnL-trnF and nuclear ribosomal ITS sequences were obtained from selected wild-type individuals of Polygonum minus Huds. in Peninsular Malaysia. The 380 bp trnL-trnF sequences of the Polygonum minus accessions were identical. Therefore, the trnL-trnF failed to distinguish between the Polygonum minus accessions. However, the divergence of ITS sequences (650 bp) among the Polygonum minus accessions was 1%, indicating that these accessions could be distinguished by the ITS sequences. A phylogenetic relationship based on the ITS sequences was inferred using neighbor-joining, maximum parsimony and Bayesian inference. All of the tree topologies indicated that Polygonum minus from Peninsular Malaysia is unique and different from the synonymous Persicaria minor (Huds.) Opiz and Polygonum kawagoeanum Makino.