Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers

Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore

Background

The Neotropics harbors the largest species richness of the planet; however, even in well-studied groups, there are potentially hundreds of species that lack a formal description, and likewise, many already described taxa are difficult to identify using morphology. Specifically in small mammals, complex morphological diagnoses have been facilitated by the use of molecular data, particularly from mitochondrial sequences, to obtain accurate species identifications. Obtaining mitochondrial markers implies the use of PCR and specific primers, which are largely absent for non-model organisms. Oxford Nanopore Technologies (ONT) is a new alternative for sequencing the entire mitochondrial genome without the need for specific primers. Only a limited number of studies have employed exclusively ONT long-reads to assemble mitochondrial genomes, and few studies have yet evaluated the usefulness of such reads in multiple non-model organisms.

Methods

We implemented fieldwork to collect small mammals, including rodents, bats, and marsupials, in five localities in the northern extreme of the Cordillera Central of Colombia. DNA samples were sequenced using the MinION device and Flongle flow cells. Shotgun-sequenced data was used to reconstruct the mitochondrial genome of all the samples. In parallel, using a customized computational pipeline, species-level identifications were obtained based on sequencing raw reads (Whole Genome Sequencing). ONT-based identifications were corroborated using traditional morphological characters and phylogenetic analyses.

Results

A total of 24 individuals from 18 species were collected, morphologically identified, and deposited in the biological collection of Universidad EAFIT. Our different computational pipelines were able to reconstruct mitochondrial genomes from exclusively ONT reads. We obtained three new mitochondrial genomes and eight new molecular mitochondrial sequences for six species. Our species identification pipeline was able to obtain accurate species identifications for up to 75% of the individuals in as little as 5 s. Finally, our phylogenetic analyses corroborated the identifications from our automated species identification pipeline and revealed important contributions to the knowledge of the diversity of Neotropical small mammals.

Discussion

This study was able to evaluate different pipelines to reconstruct mitochondrial genomes from non-model organisms, using exclusively ONT reads, benchmarking these protocols on a multi-species dataset. The proposed methodology can be applied by non-expert taxonomists and has the potential to be implemented in real-time, without the need to euthanize the organisms and under field conditions. Therefore, it stands as a relevant tool to help increase the available data for non-model organisms, and the rate at which researchers can characterize life specially in highly biodiverse places as the Neotropics.

Advances and challenges in conventional and modern techniques for halal food authentication: A review

Food is one of the most necessary needs since human civilization. For Muslims, it is mandatory to consume halal food. From a halal authentication perspective, adulteration of food products is an emerging challenge worldwide. The demand for halal food consumption has resulted in an ever-increasing need for halal product validity. In the market, there are several food products in which actual ingredients and their source are not mentioned on the label and cannot be observed by the naked eye. Commonly nonhalal items include pig derivatives like lard, pork, and gelatin derivatives, dead meats, alcohol, blood, and prohibited animals. Purposely, various conventional and modern methods offer precise approaches to ensure the halalness and wholesomeness of food products. Conventional methods are physiochemical (dielectric) and electrophoresis. At the same time, modern techniques include high-pressure liquid chromatography (HPLC), gas chromatography (GC), electronic nose (E-Nose), polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), near-infrared (NIR) spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. This review intends to give an extensive and updated overview of conventional and modern analytical methods for ensuring food halal authenticity.

Development of loop-mediated isothermal method and comparison with conventional PCR assay for rapid on spot identification of tissue of cattle origin

Loop-mediated isothermal amplification (LAMP) is a diagnostic method for meat speciation with rapid and minimal equipment requirements. In this study, we developed cattle-specific tube-based LAMP assays targeting mitochondrial Cyt b gene sequence, compared with conventional PCR assay for specificity, sensitivity, and validation of the assay was made. The LAMP reaction was carried at 64 °C for 45 min, and results were confirmed by SYBR Green I dye and agarose gel-electrophoresis. The specificity of the assays was cross-tested with DNA of buffalo, goat, sheep, and pork. The amplification was observed with samples from cattle only without cross-reactivity with other meat species. The analytical sensitivity of LAMP and PCR method for cattle DNA detection was 0.0001 ng and 1 ng, respectively. Repeatability of the assay was achieved on samples from known/blind and admixture meat with other than cattle at the relative percentage of 20%, 10%, 5%, and 1%. The study concluded that the developed assay can be easily employed for the rapid identification of tissue of cattle origin in meat and meat products in low resource areas.

PCR based method for authentication of pork in raw and processed products as well as in binary meat mixtures

In this study, amplification of species-specific marker of mitochondrial DNA origin was carried out to detect pork in raw, processed and meat mixtures containing varying concentrations of pork, viz. 1, 10, 50, 75 and 100%. The species-specific marker for pork was tested in raw pork from different breeds/varieties of pig such as Hampshire, Yorkshire, Ghungroo, Duroc, Rani, and Asha. The size of the amplified product was 290 bp in all the breeds/ varieties. The results were consistent in processed pork products, viz. frankfurter sausage, salami, cocktail sausage, pork slice, ham, and pork curry which were subjected to different cooking temperatures ranging from 75 to 121°C. In case of all the mixtures with different concentrations of pork, similar results were observed. Subsequently, this marker was tested for cross-amplification by checking them with beef, carabeef, mutton, chevon, chicken, and duck meat and no amplification was observed. The results suggested that the DNA marker used in this study is highly species-specific and reliable to detect pork adulteration, unambiguously, in raw, processed as well as in meat mixtures containing pork. This technique is rapid, simple and economical as compared to other methods of pork adulteration detection.

Paper-based loop-mediated isothermal amplification and lateral flow (LAMP-LF) assay for identification of tissues of cattle origin

The present study was made with the objectives of development and standardization of cattle specific paper-based loop-mediated isothermal amplification cum lateral flow assay (LAMP-LFA), as a Point-of-care test (POCT) for identification of tissue of cattle origin. The components of standardized LAMP reaction utilizing cattle specific primer sets were lyophilized over paper buttons, identified best as the carrier of LAMP reagents. Based on probable LAMP amplicon, a pair of probes was designed, tagged and its hybridization with the amplified product of paper LAMP reaction was optimized. The components of lateral flow assay for detection of probe hybridized LAMP products were standardized. Analysis of successful amplification was made by using HNB dye, LAMP-LFA strip, and also by the typical ladder-like pattern on gel electrophoresis. The assay was found highly specific for cattle with an analytical sensitivity of 0.1 pg of absolute DNA. Laboratory validation carried out on samples from different individuals of cattle, coded samples, binary meat admixture, and heat-processed cattle tissues substantiated the accuracy of the assay. Comparison with pre-standardized species-specific PCR assay taken as gold standards revealed 100% conformity. The field utility of the developed assay was further established by its compatibility with the commercial kit eliminating the lengthy DNA extraction step and storage stability of LAMP reagent carrier buttons for 4 months under refrigeration. Thus, the developed assay capable of the result within 3 h in resource-limited settings can be used as POCT for identification of tissue of cattle origin.

Development of RAPD-PCR assay for identifying Holstein, Angus, and Taiwan Yellow Cattle for meat adulteration detection

Incidents of food fraud have occurred worldwide, particularly in the form of meat adulteration. In this study, molecular probes were developed using the Random amplification of polymorphic DNA (RAPD) polymerase chain reaction (PCR) technique in order to identify three beef subspecies-Holstein, Angus, and Taiwan Yellow Cattle. Four RAPD-PCR 10-nucleotide primers were chosen out of a total of 60 primers. The selection was based on the reproducibility of species-specific amplicons able to detect various origins of cattle breeds. The results demonstrated that primer OPK12 produced three unique amplicons (1100 bp, 1000 bp and 480 bp) in Holstein; primer OPK14 generated one amplicon that only appeared in Holstein and Angus (200 bp); primer OPK19 amplified two species-specific amplicons in Holstein measuring 550 bp and 650 bp, respectively. However, due to the relatively lower repeatability of RAPD-PCR, higher and more specific testing repeats were required to increase the accuracy of the conclusion.

Species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin by targeting mitochondrial gene sequences

The present study was carried out with the objective of development of species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin. The cattle-specific LAMP primer set was designed by targeting mitochondrial D-loop gene. The conditions for LAMP reaction for amplification of template DNA from cattle using designed cattle-specific primer set were optimized for the components of mixture and temperature of reaction. Amplified products were analysed using SYBR Green I dye and by agarose gel electrophoresis. The developed species-specific LAMP assay was evaluated for its specificity, sensitivity and validated in laboratory on samples from known, coded, binary meat admixture with other than cattle at relative percentage of 20%, 10%, 5% and 1%, Phire tissue direct PCR master mix treated tissues of cattle and on species-specific polymerase chain reaction assay positive samples. The developed LAMP assay using self-designed primer set was highly specific, amplifying the DNA template exclusively from cattle tissue under the optimized LAMP reaction conditions. The sensitivity assay using serially diluted DNA templates revealed lowest level of detection as 0.01 ng of absolute DNA from target species. Laboratory validation substantiated the accuracy of assay in known/unknown (coded) samples and up to the 1% level of admixture in binary meat sample. DNA present in supernatant of Phire Animal tissue kit treated samples were also amplified successfully eliminating the extra step of extraction of genomic DNA. The developed assays exhibited comparable results with previously established species-specific PCR assay taken as gold standards. Thus, it was concluded that developed species-specific loop-mediated isothermal amplification assay was effective in identification of tissue of cattle origin.

A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification

There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.

A new method for the rapid detection of Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Gadus chalcogrammus) and ling (Molva molva) using a lateral flow dipstick assay

Species-specific lateral flow dipstick (LFD) assays for the identification of Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Gadus chalcogrammus) and ling (Molva molva) in food products were developed. The method comprises a PCR system with four sets of specific primers, for each target species. This step was also devised to dual-labeling of PCR products with biotin and 6-FAM, which are then easily read on a lateral flow dipstick, upon which these products are immobilized by a fixed biotin-ligand and visualized with anti-FAM antibody-coated gold nanoparticles. Sensitivity and selectivity were determined for each of the developed assays. Validation of the assays was performed with DNA extracted from commercial fish products, the identification of all samples by PCR-LFD was coherent with the results found with DNA sequencing. Target species were successfully detected in analyzed commercial samples, demonstrating the applicability of this method to the rapid analysis of food products.

Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences

Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.

Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.

Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.

Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.

Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.

An Updated Review of Meat Authenticity Methods and Applications

Adulteration of foods is a serious economic problem concerning most foodstuffs, and in particular meat products. Since high-priced meat demand premium prices, producers of meat-based products might be tempted to blend these products with lower cost meat. Moreover, the labeled meat contents may not be met. Both types of adulteration are difficult to detect and lead to deterioration of product quality. For the consumer, it is of outmost importance to guarantee both authenticity and compliance with product labeling. The purpose of this article is to review the state of the art of meat authenticity with analytical and immunochemical methods with the focus on the issue of geographic origin and sensory characteristics. This review is also intended to provide an overview of the various currently applied statistical analyses (multivariate analysis (MAV), such as principal component analysis, discriminant analysis, cluster analysis, etc.) and their effectiveness for meat authenticity.

Development and validation of a universal primer pair for the simultaneous detection of eight animal species

In the present study, we developed a novel simplex PCR assay for the simultaneous detection of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig and camel. A unique pair of universal primers was designed to target mitochondrial DNA variable regions in the eight animal species, generating, 787, 763, 563, 512, 507, 491, 455 and 385bp long fragments for goat, sheep, deer, buffalo, cattle, yak, pig and camel, respectively. The assay showed no cross-reactivity with other common domestic animals, and was validated by sequencing and enzyme digestion. Detection limit for DNA samples from the eight animal species varied between 6 and 20pg in a 20μl PCR mixture. Interestingly, the newly developed method successfully identified 170 commercial meat products, and is simple, fast, sensitive, specific, and cost-effective. Therefore, it could be used for the detection of goat, sheep, deer, buffalo, cattle, yak, pig, and camel species in foodstuffs.

Identification of species origin of meat and meat products on the DNA basis: a review

The adulteration/substitution of meat has always been a concern for various reasons such as public health, religious factors, wholesomeness, and unhealthy competition in meat market. Consumer should be protected from these malicious practices of meat adulterations by quick, precise, and specific identification of meat animal species. Several analytical methodologies have been employed for meat speciation based on anatomical, histological, microscopic, organoleptic, chemical, electrophoretic, chromatographic, or immunological principles. However, by virtue of their inherent limitations, most of these techniques have been replaced by the recent DNA-based molecular techniques. In the last decades, several methods based on polymerase chain reaction have been proposed as useful means for identifying the species origin in meat and meat products, due to their high specificity and sensitivity, as well as rapid processing time and low cost. This review intends to provide an updated and extensive overview on the DNA-based methods for species identification in meat and meat products.

Development and use of a real-time polymerase chain reaction assay for the detection of Ophidiomyces ophiodiicola in snakes

Fungal pathogens threatening the conservation of wildlife are becoming increasingly common. Since 2008, free-ranging snakes across North America have been experiencing a marked increase in the prevalence of snake fungal disease associated with Ophidiomyces ophiodiicola. Diagnosis has historically relied on histology, microbiology, and conventional polymerase chain reaction (PCR). More sensitive methods are needed to adequately characterize the epidemiology. The current study describes the development of a real-time PCR (qPCR) assay for detecting a segment of the internal transcribed spacer 1 region between the 18S and 5.8S ribosomal RNA gene. The assay was able to detect as few as 1.05 × 10(1) gene copies per reaction. An additional 4 positive cases were detected when comparing a conventional PCR (n = 3) and the qPCR (n = 7) when used on swab samples from 47 eastern massasauga rattlesnakes. The newly developed assay is a sensitive and specific tool for surveillance and monitoring in the conservation of free-ranging snakes.

A Simultaneous Analytical Method for Duplex Identification of Porcine and Horse in the Meat Products by EvaGreen based Real-time PCR

A duplex real-time polymerase chain reaction (PCR) based assay for the detection of porcine and horse meat in sausages was designed by using EvaGreen fluorescent dye. Primers were selected from mitochondrial 12S rRNA and 16S rRNA genes which are powerful regions for identification of horse and porcine meat. DNA from reference samples and industrial products was successfully extracted using the GIDAGEN® Multi-Fast DNA Isolation Kit. Genomes were identified based on their specific melting peaks (Mp) which are 82.5℃ and 78℃ for horse and porcine, respectively. The assay used in this study allowed the detection of as little as 0.0001% level of horse meat and 0.001% level of porcine meat in the experimental admixtures. These findings indicate that EvaGreen based duplex real-time PCR is a potentially sensitive, reliable, rapid and accurate assay for the detection of meat species adulterated with porcine and horse meats.

Identification of Pork Contamination in Meatballs of Indonesia Local Market Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis

This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

Identification of Atlantic cod (Gadus morhua), ling (Molva molva), and Alaska pollock (Gadus chalcogrammus) by PCR-ELISA using duplex PCR

Species-specific PCR-ELISA assays for the identification of Atlantic cod (Gadus morhua), Alaska pollock (Gadus chalcogrammus), and ling (Molva molva) in food products have been developed. The method, comprising a set of primers common to the first two species, a set of primers for M. molva, and a probe for each species, was designed using ND4 and cytochrome b genes as molecular markers. The sensitivity and selectivity were then determined for each assay. These assays were afterward used to analyze DNA extracted from commercial fish products. The presence of the target species was successfully detected in all analyzed samples, demonstrating the applicability of this method to the analysis of food products.

Pet fur or fake fur? A forensic approach

BACKGROUND

In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, 'What species is this?' In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual.

RESULTS

Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples.

CONCLUSIONS

Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae.

Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

The development of DNA-based methods for the identification of fish species is important for fisheries research and control, as well as for the detection of unintentional or fraudulent species substitutions in the marketplace. The aim of this study was to generate a comprehensive reference database of DNA sequences from the mitochondrial 16S and 12S ribosomal RNA (rRNA) genes for 53 commercial fish species in South Africa and to evaluate the applicability of these genetic markers for the identification of fish at the species level. The DNA extracted from all target species was readily amplified using universal primers targeting both rRNA gene regions. Sequences from the 16S and 12S rRNA genes were submitted to GenBank for the first time for 34% and 53% of the fish species, respectively. Cumulative analysis of the 16S rRNA gene sequences revealed mean conspecific, congeneric and confamilial Kimura two parameter (K2P) distances of 0.03%, 0.70% and 5.10% and the corresponding values at the 12S level were 0.03%, 1.00% and 5.57%. K2P neighbour-joining trees based on both sequence datasets generally clustered species in accordance with their taxonomic classifications. The nucleotide variation in both the 16S and 12S sequences was suitable for identifying the large majority of the examined fish specimens to at least the level of genus, but was found to be less useful for the explicit differentiation of certain congeneric fish species. It is recommended that one or more faster-evolving DNA regions be analysed to confirm the identities of closely-related fish species in South Africa.

Authentication of meat and meat products

In recent years, interest in meat authenticity has increased. Many consumers are concerned about the meat they eat and accurate labelling is important to inform consumer choice. Authentication methods can be categorised into the areas where fraud is most likely to occur: meat origin, meat substitution, meat processing treatment and non-meat ingredient addition. Within each area the possibilities for fraud can be subcategorised as follows: meat origin-sex, meat cuts, breed, feed intake, slaughter age, wild versus farmed meat, organic versus conventional meat, and geographic origin; meat substitution-meat species, fat, and protein; meat processing treatment-irradiation, fresh versus thawed meat and meat preparation; non-meat ingredient addition-additives and water. Analytical methods used in authentication are as diverse as the authentication problems, and include a diverse range of equipment and techniques. This review is intended to provide an overview of the possible analytical methods available for meat and meat products authentication. In areas where no authentication methods have been published, possible strategies are suggested.

DNA typing in wildlife crime: recent developments in species identification

Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.

Using species-specific repeat and PCR-RFLP in typing of DNA derived from blood of human and animal species

Species determination of tissue specimens, including blood, is an important component of forensic analysis to distinguish human from animal remains. DNA markers based on a method of species-specific PCR and amplifying the 359-base pair (bp) fragment of the mitochondrially encoded cytochrome-b gene and then digestion with the TaqI restriction enzyme were developed for detection and discrimination of human, cattle, buffalo, horse, sheep, pig, dog, cat and chicken blood samples. The results reveal that PCR-amplification of the gene encoding the species-specific repeat (SSR) region generated 603 bp in cattle and buffalo, 221 bp in horse, 374 bp in sheep, <or=100 bp in pig, 808 bp in dog, 672 bp in cat and 50 bp in chicken. Restriction analysis of the amplified 359-bp portion of the cytochrome-b gene using the TaqI restriction enzyme results in species-specific restriction fragment length polymorphism (RFLP) between buffalo, cattle and human. Two different bands were generated in buffalo (191 and 168 bp) and human (209 and 150 bp), with no digestion in cattle (359 bp). Cytochrome-b is a highly conserved region and consequently a good molecular marker for diagnostic studies. Therefore, the two complementary techniques, SSR-PCR and PCR-RFLP, could be used successfully as routine methods in forensics for sensitive, rapid, simple and inexpensive identification of the species in bloodstains.

A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene

A novel species-specific multiplex to identify 18 common European mammalian species (badger, cat, cow, dog, donkey, fox, goat, guinea pig, harvest mouse, hedgehog, horse, house mouse, human, pig, rabbit, rat, red deer and sheep), many of which are often associated with forensic investigations, has been developed. The assay is based on the mitochondrial cytochrome b gene, which is commonly used in species identification and phylogeny studies. Areas of homology and variation were identified and were used to create universal and species-specific primers. The species-specific primers were designed such that they will only react with the species for which they were designed. Two primer sets were designed for each species making the test self-confirmatory. All primer sets produced the expected results. The multiplex was balanced at template concentration of 40 000 copies (approximately 1.36 pg). Validation was accomplished by analysing the same sample ten times to determine run variation and several samples for each species to determine between-sample variation. Twenty-eight additional mammalian species were reacted with the multiplex. The multiplex provides, for the first time, a definitive method for identification of species in a forensic context.