DNA fingerprinting in botany: past, present, future

Authentication of important medicinal herbal species through DNA-based molecular characterization

DNA-based molecular markers have great importance among other methods used for the authentication, detection, and identification of medicinal herbal species. Currently, it is more common to identify the medicinal herbal species (monoherbal or polyherbal forms) morphologically by using sensory, macroscopic, and microscopic methods. DNA-based markers made an easy for accurate detection of herbal species by using the polymerase chain reaction (PCR) which involves in vitro amplification of a particular region of DNA sequence. In the current study, we used heterogenic parts for isolation of DNA from twelve important medicinal herbal species followed by purity determination, and yield calculation. We optimized a PCR reaction using universal primer sets to amplify the target DNA followed by DNA sequencing, and species identification. We also performed phylogenetic analysis for determining the evolutionary relationship between the herbal species, by using MEGAX32 software. Further, we prepared adulterated herbal species samples to validate the method. The method was able to amplify the target gene through PCR in 11 out of 12 herbal species samples (sensitivity 91.66%).The DNA from cinnamon could not yield a truly amplified product. On DNA sequencing, all the amplified products were identified as true herbal species (specificity 100%). In the adulterated samples, non-specific DNA bands were observed after performing the PCR reaction, indicating the mixing of more than one herbal species. To conclude, DNA sequencing-based molecular analysis is advantageous for the correct identification, and detection of adulterated herbal species.

Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China

Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12-5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47-4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11-2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae.

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.

Assessment of intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on omega, gamma and alpha-gliadin profiles

Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega (ω), gamma (γ) and alpha (α)-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)-polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω, γ, and α-gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω, γ, and α-gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω, γ, and α-gliadins. The alignment of ω-gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α-gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α-gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω, γ, and α-gliadins profiles.

Development of species-specific ISSR-derived SCAR marker for early discrimination between Cinnamomum verum and Cinnamomum cassia

BACKGROUND

Cinnamomum verum (true cinnamon) and Cinnamomum cassia (cassia cinnamon) are two important species belonging to family Lauraceae. These species are recognized by morphological, chemical composition and essential oil contents. The appropriate identification of species would be considerably improved by a genetic method. The main objective of the present study was to develop molecular markers distinguishing between C. verum and C. cassia.

METHODS AND RESULTS

A total 71 ISSR (Inter simple sequence repeat) and four universal barcoding (ITS, rbcL, matK, and psbA-trnH) genes were used to distinguish both the species. No sequence variation was observed between the two species for any DNA barcode gene. However, one ISSR i.e. ISSR-37 showed a clear distinction between the species and produced 570 bp and 746 bp amplicons in C. verum and C. cassia, respectively. The polymorphic bands were converted into species-specific SCAR markers. The SCAR-CV was specific to C. verum and amplified 190 bp band, however there was no amplification seen in the C. cassia samples.

CONCLUSION

The SCAR marker generated in this study can be employed as efficient, economical, and reliable molecular tool for the identification of C. verum.

Genotyping of Jujube (Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas

Since the early 19th century, a substantial amount of jujube (Ziziphus spp.) germplasm has been introduced from China and Europe into the United States. However, due to a lack of passport data, cultivar mislabeling is common and the genetic background of the introduced germplasm remains unknown. In the present study, a low-density SNP array was employed to genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. Multilocus matching of SNP profiles revealed a significant rate of genetic redundancy among these jujube samples. A total of 14 synonymous groups were detected, comprising 48 accessions. Bayesian clustering analysis and neighbor-joining tree partitioned the US jujube germplasm into two major clusters. The first cluster included cultivated genotypes (Ziziphus jujuba Mill.), whereas the other major cluster comprised the wild/sour jujube (Ziziphus spinosa Hu.). The results also revealed a unique jujube population at Fabens/Tornillo, Texas, and a semi-naturalized population at Tucumcari, NM. These findings will provide valuable guidance to jujube growers and researchers on the effective utilization of jujube germplasm in the horticultural industry.

Botanical Ingredient Forensics: Detection of Attempts to Deceive Commonly Used Analytical Methods for Authenticating Herbal Dietary and Food Ingredients and Supplements

Botanical ingredients are used widely in phytomedicines, dietary/food supplements, functional foods, and cosmetics. Products containing botanical ingredients are popular among many consumers and, in the case of herbal medicines, health professionals worldwide. Government regulatory agencies have set standards (collectively referred to as current Good Manufacturing Practices, cGMPs) with which suppliers and manufacturers must comply. One of the basic requirements is the need to establish the proper identity of crude botanicals in whole, cut, or powdered form, as well as botanical extracts and essential oils. Despite the legal obligation to ensure their authenticity, published reports show that a portion of these botanical ingredients and products are adulterated. Most often, such adulteration is carried out for financial gain, where ingredients are intentionally substituted, diluted, or "fortified" with undisclosed lower-cost ingredients. While some of the adulteration is easily detected with simple laboratory assays, the adulterators frequently use sophisticated schemes to mimic the visual aspects and chemical composition of the labeled botanical ingredient in order to deceive the analytical methods that are used for authentication. This review surveys the commonly used approaches for botanical ingredient adulteration and discusses appropriate test methods for the detection of fraud based on publications by the ABC-AHP-NCNPR Botanical Adulterants Prevention Program, a large-scale international program to inform various stakeholders about ingredient and product adulteration. Botanical ingredients at risk of adulteration include, but are not limited to, the essential oils of lavender (Lavandula angustifolia, Lamiaceae), rose (Rosa damascena, Rosaceae), sandalwood (Santalum album, Santalaceae), and tea tree (Melaleuca alternifolia, Myrtaceae), plus the extracts of bilberry (Vaccinium myrtillus, Ericaceae) fruit, cranberry (Vaccinium macrocarpon, Ericaceae) fruit, elder (Sambucus nigra, Viburnaceae) berry, eleuthero (Eleutherococcus senticosus, Araliaceae) root, ginkgo (Ginkgo biloba, Ginkgoaceae) leaf, grape (Vitis vinifera, Vitaceae) seed, saw palmetto (Serenoa repens, Arecaceae) fruit, St. John's wort (Hypericum perforatum, Hypericaceae) herb, and turmeric (Curcuma longa, Zingiberaceae) root/rhizome, among numerous others.

Micropropagation Protocol and Genetic Stability of the Salix myrtilloides Plants Cultivated In Vitro

Salix myrtilloides L. is a relict species, threatened with extinction in many European countries. To prevent the loss of the species, tissue culture was established to produce plant material for reintroduction in natural habitats. Micropropagation was chosen as a method to obtain new plants. S. myrtilloides shoots were disinfected with NaOCl, AgNO₃, or with a two-step disinfection with NaOCl, and then placed on MS medium supplemented with BA at 1 mg·dm^-3 and IBA at 0.1 mg·dm^-3. Regenerated shoots were cultivated in presence of BA, KIN, and 2iP to select the treatment with the highest multiplication rate. The obtained plants were acclimatized to ex vitro conditions. Inter-simple sequence repeat (ISSR) and flow cytometric analyses were conducted on in vitro regenerated plants to check their genetic stability. The best disinfection results were obtained when explants were treated with 1.5% NaOCl for 20 min. The highest multiplication rate and good quality plants were noted in the control media, without growth regualtors and in presence of kinetin at 0.5 mg·dm^-3. Flow cytometry and ISSR analyses confirmed genetic stability in plantlets, which indicated the possibility to use the in vitro obtained plants for reintroduction.

A Novel Perilla frutescens (L.) Britton Cell-Derived Phytocomplex Regulates Keratinocytes Inflammatory Cascade and Barrier Function and Preserves Vaginal Mucosal Integrity In Vivo

In the last years, the medicinal plant Perilla frutescens (L.) Britton has gained scientific interest because leaf extracts, due to the presence of rosmarinic acid and other polyphenols, have shown anti-allergic and skin protective potential in pre-clinical studies. Nevertheless, the lack of standardized extracts has limited clinical applications to date. In this work, for the first time, a standardized phytocomplex of P. frutescens, enriched in rosmarinic acid and total polyphenols, was produced through innovative in vitro cell culture biotechnology and tested. The activity of perilla was evaluated in an in vitro inflammatory model of human keratinocytes (HaCaT) by monitoring tight junctions, filaggrin, and loricrin protein levels, the release of pro-inflammatory cytokines and JNK MAPK signaling. In a practical health care application, the perilla biotechnological phytocomplex was tested in a multilayer model of vaginal mucosa, and then, in a preliminary clinical observation to explore its capacity to preserve vaginal mucosal integrity in women in peri-menopause. In keratinocytes cells, perilla phytocomplex demonstrated to exert a marked activity in epidermis barrier maintenance and anti-inflammatory effects, preserving tight junction expression and downregulating cytokines release through targeting JNK activation. Furthermore, perilla showed positive effects in retaining vaginal mucosal integrity in the reconstructed vaginal mucosa model and in vivo tests. Overall, our data suggest that the biotechnological P. frutescens phytocomplex could represent an innovative ingredient for dermatological applications.

A Phytocomplex Obtained from Salvia officinalis by Cell Culture Technology Effectively Controls the Grapevine Downy Mildew Pathogen Plasmopara viticola

The negative impact of using conventional fungicides in plant disease protection has increased the interest in safer alternatives such as plant secondary metabolites, generally having a better toxicological profile. However, cultivation conditions and plant material strongly affect the quality and quantity of secondary metabolites obtained from field grown plants, limiting the standardization needed for industrial production. Plant cell culture technology can provide highly homogeneous biomasses with specific chemical characteristics. A phytocomplex with high rosmarinic acid content (10.12% w/w) was obtained from a selected cell line of Salvia officinalis and was tested against the grapevine downy mildew pathogen, Plasmopara viticola. Grapevine leaf discs were sprayed with the phytocomplex at 5 g/L and then inoculated with P. viticola sporangia. Sporulation level on each disc was assessed after 7 days with an image processing software. The phytocomplex reduced by 95% the sporulation level compared to the control and was also more effective than rosmarinic acid alone, used at the same concentration found in the phytocomplex. Persistence of the phytocomplex was also assessed: when applied 5 days before inoculation, it reduced by 90% the sporulation level compared to the control. These results highlight the possibility to take advantage of cell culture techniques to produce safer pesticides with high quality standards.

Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence

BACKGROUND

Illegal logging is a global crisis with significant environmental, economic, and social consequences. Efforts to combat it call for forensic methods to determine species identity, provenance, and individual identification of wood specimens throughout the forest products supply chain. DNA-based methodologies are the only tools with the potential to answer all three questions and the only ones that can be calibrated "non-destructively" by using leaves or other plant tissue and take advantage of publicly available DNA sequence databases. Despite the potential that DNA-based methods represent for wood forensics, low DNA yield from wood remains a limiting factor because, when compared to other plant tissues, wood has few living DNA-containing cells at functional maturity, it often has PCR-inhibiting extractives, and industrial processing of wood degrades DNA. To overcome these limitations, we developed a technique-organellar microcapture-to mechanically isolate intact nuclei and plastids from wood for subsequent DNA extraction, amplification, and sequencing.

RESULTS

Here we demonstrate organellar microcapture wherein we remove individual nuclei from parenchyma cells in wood (fresh and aged) and leaves of Carya ovata and Tilia americana, amyloplasts from Carya wood, and chloroplasts from kale (Brassica sp.) leaf midribs. ITS (773 bp), ITS1 (350 bp), ITS2 (450 bp), and rbcL (620 bp) were amplified via polymerase chain reaction, sequenced, and heuristic searches against the NCBI database were used to confirm that recovered DNA corresponded to each taxon.

CONCLUSION

Organellar microcapture, while too labor-intensive for routine extraction of many specimens, successfully recovered intact nuclei from wood samples collected more than sixty-five years ago, plastids from fresh sapwood and leaves, and presents great potential for DNA extraction from recalcitrant plant samples such as tissues rich in secondary metabolites, old specimens (archaeological, herbarium, and xylarium specimens), or trace evidence previously considered too small for analysis.

Relating Invasibility and Invasiveness: Case Study of Impatiens parviflora

Data on alien species show that plant invasions are caused by a complex combination of characteristics of invasive species (invasiveness) and characteristics of invaded environment (invasibility). Impatiens parviflora is one of Europe’s top invasive species. The present study aimed to evaluate molecular diversity of populations of highly invasive in Lithuania I. parviflora by applying several DNA markers and relating genetic parameters to abiotic and biotic environment. For sampling, urban forests, riparian forests, and agrarian shrublands were selected. Three different DNA-based techniques, Simple Sequence Repeats (SSR), Inter Simple Sequence Repeat (ISSR) markers, and Random Amplified Polymorphic DNA (RAPD), were used for detecting genetic variation between 21 populations. All population individuals were monomorphic and homozygotic for four loci and heterozygotic for one locus by SSR analysis. Hierarchical analyses of molecular variance at ISSR and RAPD loci revealed significant differentiation of populations depending on geographic zones of the country. Bayesian Structure analyses of molecular data demonstrated existence of many genetic clusters and this finding is in support to multiple introduction of the species. The polymorphism extent at ISSR loci was positively correlated with the total coverage of herbaceous plant species. The coverage by I. parviflora was negatively correlated with the total number of herbaceous species and light in the sites. Our results indicate that Lithuanian sites with I. parviflora might be distinguished by high soil nutrient levels. According to the principal component analysis, the coverage by I. parviflora was a more important variable of populations compared to molecular data or parameters of abiotic environment. In conclusion, complexity of invasibility and invasiveness factors determine the variability of I. parviflora sites, including genetic traits, coverage of invasive species and conditions of environment that were significant and interrelated.

In Vitro Cell Culture of Rhus coriaria L.: A Standardized Phytocomplex Rich of Gallic Acid Derivatives with Antioxidant and Skin Repair Activity

This study focused on the biological evaluation and chemical characterization of a new ingredient obtained by in vitro cell culture of Rhus coriaria L. An in vitro plant cell culture method permits to cultivate plant in a short period of time and to obtain extract with a high safety profile for the consumer, free from heavy metals, pesticides, aflatoxins, bacterial or fungal contamination. Through the selection of specific cell culture media, it was possible to obtain a Rhus coriaria cell line with a high content of gallic acid derivatives. The Rhus coriaria L. phytocomplex (RC-P), containing 7.6% w/w of acid gallic derivatives, was obtained by drying of plant cell biomass after 14 days of growth in the final selected culture medium. UPLC-ESI-MS and UPLC-DAD analysis allowed to identify numerous gallic acid derivatives, such as galloyl hexose, trigalloyl hexose and high molecular weight galloyl derivatives, and to quantify their overall content. The antioxidant activity of the RC-P was tested by DPPH assay and the wound healing activity was evaluated using a scratch wound healing test on human keratinocytes and fibroblasts. This work showed that RC-P could be a new effective cosmetic ingredient with antioxidant and skin repair activity.

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.

Silica and secondary metabolites as chemophenetic markers for characterization of bamboo species in relation to genetic and morphometric analysis

Bamboo is a non-timber forest product and one of the most important grass plants of industrial and domestic use. It is widely distributed in tropical countries including India, China and Southeast Asian countries with wide genetic diversity. The diversity in the available genotypes becomes an important resource for the selection and improvement of the plants for ecological and commercial use. This study investigates eight commercially and ecologically important bamboo species of six genera (Bambusa, Dendrocalamus, Thyrsostachys, Vietnamosasa, Cephalostachyum and Indocalamus) from India, Thailand and Laos. These were evaluated for genetic differences by molecular makers, chemo-morphological variation and ability of silicon accumulation. The genetic cluster analyses of eight RAPD primers revealed genetic similarities in the ranges of 24-55%. The total silica content varied from 18.34 to 40.08 ppm in leaves of different bamboo species. Chemical analysis of the silicon content by ICP-OES and secondary metabolite profiling on TLC depicted the prominent distinction among the species. The PCA analysis of quantitative morphological data grouped the species in two major clusters and found to correlate with chemical pattern and genetic similarity to some extent. This is the first report that summarizes species-specific variability of leaf silica content, secondary metabolites, and quantitative morphological data towards delineation of genetic phylogeny of bamboo species.

Microbiomes in forensic botany: a review

Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.

Stevia rebaudiana germplasm characterization using microsatellite markers and steviol glycosides quantification by HPLC

Stevia rebaudiana Bertoni, Asteraceae, is an herbaceous perennial plant native to Paraguay. This species is considered since ancient times a medicinal plant with important bioactive compounds and pharmacologic and food properties, namely diterpenes glycosides. The high natural sweetener potential stevioside and rebaudioside A produced by S. rebaudiana plants are suitable sucrose substitutes, and their obtention is influenced by environmental, phytosociological, and genetic factors. The plants’ genetic profile and sweet potential depiction are needed for suitable plant selection for improvement and deployment. Thirty-one S. rebaudiana accessions grown in the same plot where leaves samples were collected in early 2019, were genotyped using six microsatellite markers, including two steviol glycosides biosynthesis functionally involved markers. Additionally, an aqueous extract of each sample was obtained in a water bath and purified by SPE for stevioside and rebaudioside A quantification by normal phase HPLC. Stevioside and rebaudioside A contents varied between 0.53–7.36% (w w⁻¹) and 0.37–3.60% (w w⁻¹), respectively. Two genotypes displayed interesting ratios of rebaudioside A/stevioside (number 3 and 33). The level of genetic similarity between genotypes was tested through a pairwise similarity coefficient, and two groups of individuals had the same fingerprinting. Strong relatedness was found within genotypes, possibly due to cloning, thus, influx of new germplasm ought to be made to prevent mating between relatives, and for further selection and genetic improvement.

In Vitro Cultured Melissa officinalis Cells as Effective Ingredient to Protect Skin against Oxidative Stress, Blue Light, and Infrared Irradiations Damages

Skin is being increasingly exposed to artificial blue light due to the extensive use of electronic devices, which can induce cell oxidative stress, causing signs of early photo aging. The Melissa officinalis phytocomplex is a new standardized cosmetic ingredient obtained by an in vitro plant cell culture with a high content of rosmarinic acid. In this study, we examine the activity of the Melissa officinalis phytocomplex to protect skin against blue light and infrared damages, evaluating the ROS (Radical Oxygen Species) level in keratinocyte cell line from human skin (HaCaT) and Nrf2 (Nuclear factor erythroid 2-related factor 2), elastin, and MMP1 (Matrix Metalloproteinase 1) immunostaining in living human skin explants ex vivo. This phytocomplex demonstrates antioxidant activity by reducing ROS production and thus the oxidant damage of the skin caused by UV and blue light exposure. In addition, it inhibits blue light-induced Nrf2 transcriptional activity, IR-induced elastin alteration, and IR-induced MMP-1 release. This Melissa officinalis phytocomplex is a new innovative active ingredient for cosmetic products that is able to protect skin against light and screen exposure damages and oxidative stress.

Biopiracy: Abolish Corporate Hijacking of Indigenous Medicinal Entities

Biopiracy as "a silent disease" is hardly detectable because it does not leave traces frequently. The corporate hijacking of food is the most important health hazard in this era; giant commercial enterprises are using intellectual property rights to patent indigenous medicinal plants, seeds, genetic resources, and traditional medicines. The new era of biotechnology relies on the genes of living organisms as raw materials. The "Gene Rush" has thus become similar to that of the old "Gold Rush." Sri Lanka has been spotted in the top 34 biodiversity hotspots globally. Moreover, localized in the tropics, human generations in Sri Lanka have utilized the array of plant species for herbal treatments and treatment of diseases. Sri Lanka after its 30-year civil war is moving towards a solid growth and conservation of the environment which is a major component in a sustainable development where the conservation of biodiversity plays a significant role. In this paper, we present an overview of typical cases of global biopiracy, bioprospecting via introduction of cost-effective deoxyribonucleic acid (DNA) fingerprinting and international protocol with Private-Public-People Partnership concept as excellent forms of utilization of natural resources. We propose certain perspectives as scientists towards abolishing biopiracy and also to foster the fair utilization of natural resources; since the economy of most developing countries is agriculture based, the gross domestic product of the developing countries could be increased by enhanced bioprospecting via introduction of cost-effective DNA fingerprinting technologies and thus not being a pray of corporate hijacking."Biopiracy is biological theft; illegal collection of indigenous plants by corporations who patent them for their own use" (Vandana Shiva).

Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China

Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.

Genetic Stability of the Endangered Species Salix lapponum L. Regenerated In Vitro during the Reintroduction Process

Simple Summary

Salix lapponum, a downy willow, is a boreal relict species, threatened with extinction in Poland. In order to save populations in their refugia on the southern limit of the specie’s range, some activities were undertaken to rebuild their resources. The in vitro propagation was chosen to produce new plants, as it allows obtaining many individuals in a relatively short time with no harm to natural populations. The collected shoot pieces were multiplicated on a special growing media, containing all the necessary macro- and micronutrients, with addition of plant growth regulators to make them form shoots and roots. The obtained plants were then planted into soil and acclimated to natural habitat conditions. On the basis of the conducted genetic analysis and flow cytometry, it was stated that the new plants were genetically unchanged in comparison to the mother plants. The research results confirmed that the tissue culture may be applied in the propagation of the endangered willow species and the obtained plants may be used to build new populations or to strengthen the present ones.

Abstract

Salix lapponum L. is a boreal relict species, threatened with extinction in Poland. An 80% decrease in the number of its stands was confirmed in the last half-century, so that to prevent the loss of downy willow, attempts were made to reintroduce this species in natural habitats. Micropropagation was chosen as a first stage of its active conservation. S. lapponum shoots were collected and disinfected with NaOCl, AgNO₃, or HgCl₂ or with a two-step disinfection with NaOCl and then placed on MS medium with BA 1 mg·dm⁻³ and IBA 0.1 mg·dm⁻³. Regenerated shoots were cultivated with addition of BA, KIN, or 2iP, alone or in combination with auxins, to find the highest multiplication rate. Inter-simple sequence repeat (ISSR) analysis and flow cytometric analyses were conducted on in vitro regenerated plants to check their genetic stability. Disinfection was quite difficult and the use of HgCl₂ was the most efficient. The highest multiplication rate was obtained in presence of KIN at 0.5 mg·dm⁻³ + IAA at 0.5 mg·dm⁻³. The analysis confirmed the genome size stability, which is in agreement with the results obtained by ISSR, revealing no somaclonal variation in plantlets and therefore allowing the use of the obtained plants for reintroduction.

Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview

India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.

Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses

BACKGROUND

Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species (Lolium) and diploid and hexaploid fescue species (Festuca). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species as well as one fescue and two ryegrass cultivars.

RESULTS

Partial genome sequences produced by Illumina sequencing technology were used for genome-wide comparative analyses with the RepeatExplorer pipeline. Retrotransposons were the most abundant repeat type in all seven grass species. The Athila element of the Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of the long terminal repeat (LTR) element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of fluorescence in situ hybridization (FISH) with a probe specific to the Fesreba element and immunostaining with centromeric histone H3 (CENH3) antibody showed their co-localization and indicated a possible role of Fesreba in centromere function.

CONCLUSIONS

Comparative repeatome analyses in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of the LTR element Fesreba. A new LTR element Fesreba was identified and found in abundance in centromeric regions of the fescues and ryegrasses. It may play a role in the function of their centromeres.

Paternity Assignment in White Guinea Yam (Dioscorea Rotundata) Half-Sib Progenies from Polycross Mating Design Using SNP Markers

White Guinea yam is mostly a dioecious outcrossing crop with male and female flowers produced on distinct plants. Fertile parents produce high fruit set in an open pollination polycross block, which is a cost-effective and convenient way of generating variability in yam breeding. However, the pollen parent of progeny from polycross mating is usually unknown. This study aimed to determine paternity in white Guinea yam half-sib progenies from polycross mating design. A total of 394 half-sib progenies from random open pollination involving nine female and three male parents was genotyped with 6602 SNP markers from DArTSeq platform to recover full pedigree. A higher proportion of expected heterozygosity, allelic richness, and evenness were observed in the half-sib progenies. A complete pedigree was established for all progenies from two families (TDr1685 and TDr1688) with 100% accuracy, while in the remaining families, paternity was assigned successfully only for 56 to 98% of the progenies. Our results indicated unequal paternal contribution under natural open pollination in yam, suggesting unequal pollen migrations or gene flow among the crossing parents. A total of 3.8% of progenies lacking paternal identity due to foreign pollen contamination outside the polycross block was observed. This study established the efficient determination of parental reconstruction and allelic contributions in the white Guinea yam half-sib progenies generated from open pollination polycross using SNP markers. Findings are useful for parental reconstruction, accurate dissection of the genetic effects, and selection in white Guinea yam breeding program utilizing polycross mating design.

Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.

A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

Screening of EMS-Induced Drought-Tolerant Sugarcane Mutants Employing Physiological, Molecular and Enzymatic Approaches

Drought stress is one of the major agronomic concerns that lead towards a sharp decline in sugarcane yield. An urgent demand to overcome drought is critical to ensure sugarcane production. Mutation breeding is one of the promising tools available to produce stress-resistant plants, with the induction of new alleles due to point mutation within existing sugarcane germplasm. The current study was directed to chemically mutagenize the calli of two sugarcane cultivars (ROC22 and FN39) via 0.1% EMS, with focus on inducing mutations in their genome. The 1644 regenerated plants of ROC22 and 1398 of FN39 were exposed to 28% PEG-6000 stimulated osmotic stress. Eighteen plants of ROC22 and 2 plants of FN39, that survived after in vitro osmotic stress treatment, were then subjected to preliminary greenhouse pot trials to confirm drought tolerance by analyzing them using various physiological parameters, including photosystem II (PSII) photochemical efficiency (Fv/Fm), leaf chlorophyll content, and photosynthetic rate. The genetic diversity among drought-resistant mutant lines was further assessed by 15 pairs of simple sequence repeat (SSR) markers amplification and CEL (Celery) I endonuclease digestion, to investigate the mutated sites. Mutant lines of ROC22 (i.e., MR22-15 and MR22-20) were found to be promising for future drought resistance breeding, due to better physiological adaptation under drought stress.

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

Development of genic-SSR markers and genetic diversity of Indian lettuce (Lactuca indica L.) in South Korea

Indian lettuce (Lactuca indica L.) is an undomesticated wild plant with high economic potential. We know little about the plant's genome, such as its DNA markers, making genetic research using this plant difficult. In this study, 100 genic simple sequence repeat (SSR) primers with a 99-250 bp target amplicon were synthesized from L. indica transcriptomic sequences. These primers were examined in 8 diverse L. indica accessions, and 90 polymorphic SSRs were obtained. Twenty-three of the 90 polymorphic SSRs were used to investigate transferability to another two Lactuca species, Lactuca serriola and Lactuca sativa. Genetic diversity was investigated in 77 Lactuca accessions, including 73 L. indica collected from across South Korea, 2 L. serriola, and 2 L. sativa. Our genic-SSR markers were highly polymorphic with a mean polymorphic information content of 0.61 and, on average, 10.83 alleles per locus. The average expected heterozygosity (0.76) was higher than the observed heterozygosity. An analysis of molecular variance revealed that most of the total variance in our population is attributable to genetic variation among accessions, rather than among provinces. STRUCTURE, unweighted neighbor-joining phylogenetic trees, and principal coordinate analyses resulted in three clusters, where northern and central-southern L. indica accessions were grouped into two clusters with some admixture. The L. serriola and L. sativa accessions did not produce a separate cluster due to a small sample size. These results show our SSR markers will be useful in germplasm assessment and genetic studies of L. indica and other Lactuca species.

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

Genetic diversity in the candidate trees of Madhuca indica J. F. Gmel. (Mahua) revealed by inter-simple sequence repeats (ISSRs)

Madhuca indica provides livelihood to several tribal people in India, where the flowers are used for extraction of sweet juices having multiple applications. Certain trees have more value as judged by the tribal people mainly based on yield and quality performance of the trees, and these trees were selected for the genetic diversity analyses. Genetic diversity of 48 candidate Mahua trees from Etapalli, Dadagaon, and Jawhar, Maharashtra, India, was assessed using ISSR markers. Fourteen ISSR primers revealed a total of 132 polymorphic bands giving overall 92% polymorphism. Genetic diversity, in terms of expected number of alleles (Ne), the observed number of alleles (Na), Nei's genetic diversity (H), and Shannon's information index (I) was 1.921, 1.333, 0.211, and 0.337, respectively, and suggested lower genetic diversity. Region wise analysis revealed higher genetic diversity for site Etapalli (H = 0.206) and lowest at Dhadgaon (H = 0.140). Etapalli area possesses higher forest cover than Dhadgaon and Jawhar. Additionally, in Dhadgaon and Jawhar M. indica trees are restricted to field bunds; both reasons might contribute to lower genetic diversity in these regions. The dendrogram and the principal coordinate analyses showed no region-specific clustering. The clustering patterns were supported by AMOVA where higher genetic variance was observed within trees and lower variance among regions. Long-distance dispersal and/or higher human interference might be responsible for low diversity and higher genetic variance within the candidate trees.

Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans

Since tropical trees often have long generation times and relatively small reproductive populations, breeding systems and genetic variation are important for population viability and have consequences for conservation. Miconia albicans is an obligate, diplosporous, apomictic species widespread in the Brazilian Cerrado, the savanna areas in central Brazil and elsewhere in the Neotropics. The genetic variability would be, theoretically, low within these male-sterile and possibly clonal populations, although some variation would be expected due to recombination during restitutional meiosis. We used ISSR markers to assess genetic diversity of M. albicans and to compare with other tropical trees, including invasive species of Melastomataceae. A total of 120 individuals from six populations were analysed using ten ISSR primers, which produced 153 fully reproducible fragments. The populations of M. albicans presented mean Shannon's information index (I) of 0.244 and expected heterozygosity (H_e ) of 0.168. Only two pairs of apparently clonal trees were identified, and genetic diversity was relatively high. A hierarchical amova for all ISSR datasets showed that 74% of the variance was found among populations, while only 26% of the variance was found within populations of this species. Multivariate and Bayesian analyses indicated marked separation between the studied populations. The genetic diversity generated by restitutional meiosis, polyploidy and possibly other genome changes may explain the morpho-physiological plasticity and the ability of these plants to differentiate and occupy such a wide territory and different environmental conditions. Producing enormous amounts of bird-dispersed fruits, M. albicans possess weedy potential that may rival other Melastomataceae alien invaders.

Genotyping-by-Sequencing and Its Application to Oat Genomic Research

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.

Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, F_ST  = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.

Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.)

Salinity stress is a major abiotic factor that affects crop output, and as a pioneer crop in saline and alkaline land, salt tolerance study of cotton is particularly important. In our experiment, four salt-tolerance varieties with different salt tolerance indexes including CRI35 (65.04%), Kanghuanwei164 (56.19%), Zhong9807 (55.20%) and CRI44 (50.50%), as well as four salt-sensitive cotton varieties including Hengmian3 (48.21%), GK50 (40.20%), Xinyan96-48 (34.90%), ZhongS9612 (24.80%) were used as the materials. These materials were divided into salt-tolerant group (ST) and salt-sensitive group (SS). Illumina Cotton SNP 70K Chip was used to detect SNP in different cotton varieties. SNPv (SNP variation of the same seedling pre- and after- salt stress) in different varieties were screened; polymorphic SNP and SNPr (SNP related to salt tolerance) were obtained. Annotation and analysis of these SNPs showed that (1) the induction efficiency of salinity stress on SNPv of cotton materials with different salt tolerance index was different, in which the induction efficiency on salt-sensitive materials was significantly higher than that on salt-tolerant materials. The induction of salt stress on SNPv was obviously biased. (2) SNPv induced by salt stress may be related to the methylation changes under salt stress. (3) SNPr may influence salt tolerance of plants by affecting the expression of salt-tolerance related genes.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

BACKGROUND

The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.

RESULTS

A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.

CONCLUSIONS

The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

High-Resolution DNA Melting Analysis in Plant Research

Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.

Microsatellites in Pursuit of Microbial Genome Evolution

Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.