Application of plant DNA markers in forensic botany: Genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites

Using plants in forensics: State-of-the-art and prospects

The increasing use of plant evidence in forensic investigations gave rise to a powerful new discipline - Forensic Botany - that analyses micro- or macroscopic plant materials, such as the totality or fragments of an organ (i.e., leaves, stems, seeds, fruits, roots) and tissue (i.e., pollen grains, spores, fibers, cork) or its chemical composition (i. e., secondary metabolites, isotopes, DNA, starch grains). Forensic botanists frequently use microscopy, chemical analysis, and botanical expertise to identify and interpret evidence crucial to solving civil and criminal issues, collaborating in enforcing laws or regulations, and ensuring public health safeguards. The present work comprehensively examines the current state and future potential of Forensic Botany. The first section conveys the critical steps of plant evidence collection, documentation, and preservation, emphasizing the importance of these initial steps in maintaining the integrity of the items. It explores the different molecular analyses, covering the identification of plant species and varieties or cultivars, and discusses the limitations and challenges of these techniques in forensics. The subsequent section covers the diversity of Forensic Botany approaches, examining how plant evidence exposes food and pharmaceutical frauds, uncovers insufficient or erroneous labeling, traces illegal drug trafficking routes, and combats the illegal collection or trade of protected species and derivatives. National and global security issues, including the implications of biological warfare, bioterrorism, and biocrime are addressed, and a review of the contributions of plant evidence in crime scene investigations is provided, synthesizing a comprehensive overview of the diverse facets of Forensic Botany.

Discrimination of Camellia cultivars using iD-NA analysis

Recently, many new cultivars have been taken abroad illegally, which is now considered an international issue. Botanical evidence found at a crime scene provides valuable information about the origin of the sample. However, botanical resources for forensic evidence remain underutilized because molecular markers, such as microsatellites, are not available without a limited set of species. Multiplexed intersimple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and its analysis method, identification of not applicable (iD-NA), have been used to determine several genome-wide genetic markers, making them applicable to all plant species, including those with limited available genetic information. Camellia cultivars are popular worldwide and are often planted in many gardens and bred to make new cultivars. In this study, we aimed to analyze Camellia cultivars/species through MIG-seq. MIG-seq could discriminate similar samples, such as bud mutants and closely related samples that could not be distinguished based on morphological features. This discrimination was consistent with that of a previous study that classified cultivars based on short tandem repeat (STR) markers, indicating that MIG-seq has the same or higher discrimination ability as STR markers. Furthermore, we observed unknown phylogenetic relationships. Because MIG-seq can be applied to unlimited species and low-quality DNA, it may be useful in various scientific fields.

Investigating DNA barcodes of plants growing in some areas of Iran with high crime rate: Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana

According to criminal botany, the offender unknowingly carries plant samples from the crime scene. Therefore, studying the genetic data of plants native to the crime scene can solve many ambiguities in the criminal files. In this regard, the aim of this study was to investigate the genome of 5 endemic plants in some areas of Iran with high crime rate. Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana were assessed using 1 genetic fragment on plastid regions (trnH-psbA) as well as 1 gene on nuclear chromosome called ITS. The alignment of DNA sequences of trnH-psbA and ITS genes was done using BioEdit, Clustal X, and Muscle v4.0 software programs. The phylogenetic analysis was performed on aligned data using Maximum Parsimony (MP) and the Bayesian methods. The Splits Tree v.4.14.4 software program was used for phylogenetic network analysis. Finally, the data combinability test was conducted using the Incongruence Length Difference (ILD) test by PAUP* software program. All data from nrDNA ITS and trnH-psbA sequences were consistent with Information Compatibility Test (ICT) results. Moreover, the nrDNA ITS indicated more resolved relationship than trnH-psbA. The results from MP and Bayesian analyses did not differ significantly between singular and combined forms, except for a slight variance in confidence interval of branches. As the phylogenetic trees provide more thorough and deeper conception of species relations, it is hoped that they would be useful to illuminate some forensic gaps in regions with high crime rates enriched by these plants, not only in Iran, but also in all areas over the world with this vegetation.

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

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.

Pollen molecular biology: Applications in the forensic palynology and future prospects: A review

Palynology, which is the study of pollen and spores in an archaeological or geological context, has become a well-established research tool leading to many significant scientific developments. The term palynomorph includes pollen of spermatophytes, spores of fungi, ferns, and bryophytes, as well as other organic-walled microfossils, such as dinoflagellates and acritarches. Advances in plant genomics have had a high impact on the field of forensic botany. Forensic palynology has also been used and applied more recently to criminal investigation in a meaningful way. However, the use of pollen DNA profiling in forensic investigations has yet to be applied. There were earlier uses of dust traces in some forensic analyses that considered pollen as a type of botanical dust debris. Pollen grains can be studied for comparative morphological data, clues to unexpected aspects relating to breeding systems, pollination biology and hybridization. This can provide a better understanding of the entire biology of the group under investigation. Forensic palynology refers to the use of pollen and other spores when it is used as evidence in legal cases to resolve criminal issues by proving or disproving relationships between people and crime scenes. This overview describes the various contributions and the significance of palynology, its applications, different recent approaches and how it could be further employed in solving criminal investigations.

A Three-Locus, PCR-based Method for Forensic Identification of Plant Material

Plant residue is currently an underutilized resource in forensic investigations despite the fact that many crime scenes, as well as suspects and victims, harbor plant-derived residue that could be recovered and analyzed. Notwithstanding the considerable skill of forensic botanists, current methods of species determination could benefit from tools for DNA-based species identification. However, DNA barcoding in plants has been hampered by sequence complications in the plant genome. Following a database search for usable barcodes, broad-spectrum primers were designed and utilized to amplify and sequence the rbcL, trnL-F, and rrn18 genetic loci from a variety of household plants. Once obtained, these DNA sequences were used to design species-targeted primers that could successfully discriminate the source of plant residue from among the 21 species tested.

Forensic genetics and genomics: Much more than just a human affair

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

Use of non-human DNA analysis in forensic science: a mini review

Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.

Identification of DNA-microsatellite markers for the characterization of somatic embryos in Quercus suber

Nuclear DNA-microsatellite markers led the possibility to characterize individually both Quercus suber trees and somatic embryos. The genotype inferred by SSR markers opens the possibility to obtain a fingerprint for clonal lines identification. Furthermore, allow to infer the origin of somatic embryos from haploid cells (microspores) or from diploid tissues. Using few SSR markers from other Quercus species and an automatic system based in fluorescence, it is possible to obtain a high discrimination power between genotypes. This method is sufficient to assign tissues to an individual tree with high statistical certainty. Nevertheless, it is necessary to take care to select the adequate DNA extraction method to avoid PCR inhibitors present in diverse Q. suber tissues.

Plant genetics for forensic applications

An emerging application for plant DNA fingerprinting and barcoding involves forensic investigations. Examples of DNA analysis of botanical evidence include crime scene analysis, identifying the source of commercial plant products, and investigation of trade in illicit drugs. Here, we review real and potential applications of DNA-based forensic botany and provide a protocol for microsatellite genotyping of leaf material, a protocol that could be used to link a suspect to a victim or to a crime scene.

Field testing of collection cards for Cannabis sativa samples with a single hexanucleotide DNA marker

The validity and feasibility of using DNA collection cards in the field for preservation and analysis of Cannabis sativa genotypes were investigated using a highly specific hexanucleotide marker. Collection cards were submitted to the National Marijuana Initiative, which selectively trained and managed the collection of specific types of samples from a variety of participating agencies. Samples collected at seizure sites included fresh marijuana leaf samples, dried "dispensary" samples, U.S. border seizures, and hashish. Using a standardized PCR kit with custom-labeled oligonucleotide primers specific to marijuana, collection cards produced eight genotypes and 13 different alleles, extremely low baselines, and no cross-reactivity with control plant species. Results were produced from all sample types with the exception of hashish. Plant DNA collection cards represent an easily implementable method for the genetic identification and relatedness of C. sativa street and grow site-seized samples with applications for databasing and market disruption.

Potential utility of DNA sequence analysis of long-term-stored plant leaf fragments for forensic discrimination and identification

This study examined the potential utility of DNA sequence analysis to discriminate and identify plant material in forensic investigations. DNA was extracted from plant leaf fragments of 11 species stored for 5 to 22 years after collection. The trnH-psbA intergenic spacer and 316 bp of the rbcL gene were successfully amplified and sequenced for all fragments except for the trnH-psbA spacer of one sample. All of the plant samples were discriminated in pairwise comparisons of the sequences. Using a combination of local and global genetic databases is likely to provide greater reliability in search results to identify forensic samples from sequence data.

The identification of ingested dandelion juice in gastric contents of a deceased person by direct sequencing and GC-MS methods

DNA and chemical analysis of gastric contents of a deceased person were handled in this work. The body of the victim was discovered in his car, submerged in a lake. We were asked to determine whether or not the gastric contents of the victim harbored drugs and dandelion material. It was suspected that the victim had been murdered by poisoning with an excess amount of sleeping medication (doxylamine), which had been homogenized with dandelion. The concentrations of 11.4 and 27.5 mg/kg of doxylamine detected from spleen and liver of the victim were far higher than the assumed therapeutic concentration. Via gas chromatography-mass spectrometry (GC-MS) analysis and direct sequencing analysis of plant genetic markers such as intergenic transcribed spacer, 18S ribosomal RNA (rRNA), rbcL and trnLF, it was confirmed that the gastric contents of the victim contained taraxasterol, which is one of the marker compounds for dandelion and contained dandelion species-specific rbcL and trnL-trnF IGS (trnLF) sequences. The initial PCR of the genomic DNA isolated from the gastric contents showed insufficient quantity, and the second PCR, of which the template was a portion of the initial PCR products, exhibited a sufficient quantity for direct sequencing. rbcL and trnLF located in the cpDNA resulted in the successful determination of dandelion DNA in a decedent's stomach contents. GC-MS identifies the actual presence of a taraxasterol at 28.4 min. Raw dandelion was assumed to be used as a masking vehicle for excess sleeping drug (doxylamine).

Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach

Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.