PCR assay for the identification of animal species in cooked sausages

A species-specific PCR assay was developed for the detection of low levels of pork, horse and donkey meat in cooked sausages. Oligonucleotid primers were designed for amplification of species-specific mitochondrial DNA sequences of each species and detected the presence of 0.01 ng of template DNA in water. When applying the assay to DNA extracts from sausages samples that were prepared from binary meat mixtures, it was possible to detect each species when spiked in any other species at the 0.1% level. In conclusion, it can be suggested that this assay can be used to determine mislabelled and/or fraudulent species substitution in comminuted meat products.     

Detection of chicken and turkey meat in meat mixtures by using real-time PCR assays

In this study, TaqMan-based real-time Polymerase Chain Reaction (PCR) techniques were developed for the detection of chicken and turkey meat in raw and heat-treated meat mixtures. Primers and TaqMan probe sets were designed to amplify 86 bp and 136 bp fragments for the chicken and turkey species, respectively, on the mitochondrial NADH dehydrogenase subunit 2 gene. In the results, it was possible to detect each species at the level of 0.1 pg template DNA with the TaqMan probe technique without any cross-reactivity with nontarget species (bovine, ovine, donkey, pork, and horse) while the detection level was 1 pg template DNA using conventional PCR. The TaqMan probe assays used in this study allowed the detection of as little as 0.001% level of both species in the experimental meat mixtures, prepared by mixing chicken and turkey meat with beef at different levels (0.001% to 10%). In conclusion, TaqMan probe assays developed in this research are promising tools in the specific identification and sensitive quantification of meat species even in the case of heat-treated meat products, and suitable for a rapid, automated, and routine analysis.     

Identification of meat species by TaqMan-based real-time PCR assay

In this study, a convenient, sensitive and specific real-time PCR assay was described for the species identification and their quantification in raw and cooked meat products. Specific primers and TaqMan probes were designed on the mitochondrial ND2, ND5 and ATP 6-8 genes for donkey, pork and horse, respectively, and the performance of the method was tested. In the results, no cross-reaction was observed between the donkey and pork species specific primer-probe systems and non-target species (bovine, ovine, chicken and turkey). Only one cross reaction was observed between the horse species specific primer-probe set and 100 ng pork DNA at the ct 33.01 level (corresponding to 0.01 ng horse DNA). The real-time quantitative assay used in this study allowed the detection of as little as 0.0001 ng template DNA from pure meat for each species investigated and experimental meat mixtures. In conclusion, it can be suggested that the TaqMan probe assay used in this research might be a rapid and sensitive method for the routine meat species identifications studies in raw or cooked meat products.     

Duplex PCR approach for the detection and quantification of donkey,horse and mule in raw and heat‐processed meat products

Donkey‐related products have been paid more attention for their high nutritional value to human beings. Due to donkey resource scarcity, coupled with gradually increasing market demand, adulterated donkey meat products with other low‐cost animal meat, especially with the similar species horse and mule, are often found in market. Therefore, detection of species fraud in donkey meat products is important for consumer protection and food industries. In this study, a simple and highly specific duplex PCR method, based on the simultaneous amplification of fragments of the mitochondrial ATP synthase subunit 8/6 and ND2, was developed and optimised for the identification of horse, donkey and mule species in raw and heat‐processed meat products. To the best of our knowledge, it was the first time for this strategy applied to these three genetically related animal meat products differentiation to date. The duplex PCR generated a 153‐bp and 83‐bp amplification products for horse and donkey, respectively. While for mule, both of the two length amplification products are appeared on the agarose gel. Target meat species could be detected at a level of 1%, and the results indicated that the duplex PCR assay could be used in the authentification of donkey‐related products with high specificity, cost‐effectiveness and simplicity.     

Determination of Porcine Contamination in Laboratory Prepared dendeng Using Mitochondrial D-Loop686 and cyt b Gene Primers by Real Time Polymerase Chain Reaction

The identifications of species in meat products have created interests since these foods became the target of forgery and fraud in the market. The presence of pork in food products is not allowed for the Muslim community. Hence, an analysis is necessary to detect the presence of pork in processed meat products, such as in dendeng (dried meat) product. Real time polymerase chain reaction using mitochondrial displacement loop686 and cytochrome b (cytb) gene primers was used to identify specific pork DNA among other four types of DNA species; namely beef, chicken, goat, and horse. This method was also used to identify pork DNA in the laboratory processed pork-beef dendeng as well as commercial dendeng from market. The results showed that real time polymerase chain reaction using displacement loop686 and cytb gene primers were able specifically to distinguish between pork DNA and the other species. The lowest concentration of 0.5% of pork DNA in a mixture of pork-beef processed products of dendeng was able to be detected by both primers with the product amplification of 114 and 134 bp (base pair) for the displacement loop686 and 149 bp for cytb gene, respectively. High sensitivity was also obtained when both primers were applied with the lowest detection limit of 5 pg/µL pork DNA. The results of the six commercial dendeng amplification using both primers showed no amplified products present, meaning that these products do not contain porcine DNA.     

TaqMan probe real‐time polymerase chain reaction targeting the ATPase 6 gene for the detection of pork adulteration in meat and meatballs

We developed an assay for detecting pork adulteration in meat and meatballs using real‐time polymerase chain reaction involving specific primers and a TaqMan probe targeting the porcine mitochondrial (mt) ATPase 6 gene. We proved the specificity of the probe by showing no amplification from DNA isolated from six different meat‐providing species: cattle, dog, mouse, chicken, goat, and horse. On the contrary, DNA isolated from pork was positive for amplification, with a Ct (threshold cycle) of 18.69 using a standard amount of DNA template (50 ng). The presence of matrix and food processing steps in meatball sample had no influence on the specificity of the probe. The developed technique also has a good repeatability (CV, coefficient of variation = 3.86% for meat and 5.07% for meatballs), showing good linearity and sensitivity, with a limit of detection up to 5 pg of pork total DNA, which equivalent to approximately 6.8 copies of pork mtDNA. In addition, the analysis of spiked pork in beef meatballs showed that the method could determine up to 1% pork contamination. Moreover, the system was successfully applied to detect pork adulteration in commercial meatballs by detecting the presence of pork DNA in two samples.     

基于TaqMan实时荧光PCR检测鲜肉及加工肉制品中的驴源性成分

根据出入境检验检疫行业标准SN/T 3730.4—2013《食品及饲料中常见畜类品种的鉴定方法 第4部分：驴 成分检测 实时荧光PCR法》合成引物和探针,利用TaqMan实时荧光聚合酶链式反应（polymerase chain reaction, PCR）技术检测鲜肉及加工肉制品中的驴源性成分。首先对13 种不同动物鲜肉组织的DNA进行驴源性成分特异 性检测,然后对驴源性DNA模板原液进行梯度稀释,检测方法灵敏度,最后在加工肉制品中检测方法的适用性。 结果表明：本研究建立的方法特异性强,除驴肉外,牛、羊、猪、马、骆驼、鹿、狗、兔、鸡、鸭、鸽子、鹌鹑 12 种动物鲜肉组织均无特异性扩增;方法的灵敏度较高,驴组分DNA的检出限可达100 fg/μL,灵敏度可达0.01%; 方法的适用性较广,可以用于加工肉制品中驴源性成分的检测。     

Development of real-time PCR assays for the detection of Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar) and European plaice (Pleuronectes platessa) in complex food samples

We have developed species-specific real-time PCR assays for the identification of Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar) and European plaice (Pleuronectes platessa) in food products. The species-specific assays, comprising a set of primers and probe for each species, were designed using genomic genes (pantophysin for Atlantic cod, growth hormone for Atlantic salmon and parvalbumin for European plaice) which were then optimised for specificity and selectivity. The sensitivity and the effect of heat and pressure on amplification efficiency were then determined for each assay. These assays were then used to analyse DNA extracted from commercial fish products and model food samples spiked with each of the fish species. The target species was successfully identified in all samples analysed, demonstrating the applicability of these assays to the analysis of food products.     

Multiplex real-time PCR detection of fumonisin-producing and trichothecene-producing groups of Fusarium species

Some species of Fusarium can produce mycotoxins during food processing procedures that facilitate fungal growth, such as the malting of barley. The objectives of this study were to develop a 5' fluorogenic (Taqman) real-time PCR assay for group-specific detection of trichothecene- and fumonisin-producing Fusarium spp. and to identify Fusarium graminearum and Fusarium verticillioides in field-collected barley and corn samples. Primers and probes were designed from genes involved in mycotoxin biosynthesis (TRI6 and FUM1), and for a genus-specific internal positive control, primers and a probe were designed from Fusarium rDNA sequences. Real-time PCR conditions were optimized for amplification of the three products in a single reaction format. The specificity of the assay was confirmed by testing 9 Fusarium spp. and 33 non-Fusarium fungal species. With serial dilutions of purified genomic DNA from F. verticillioides, F. graminearum, or both as the template, the detection limit of the assay was 5 pg of genomic DNA per reaction. The three products were detectable over four orders of magnitude of template concentration (5 pg to 5 ng of genomic DNA per reaction); at 50 ng template per reaction, only the TRI6 and FUM1 PCR products were detected. Barley and corn samples were evaluated for the presence of Fusarium spp. with traditional microbiological methods and with the real-time PCR assay. The 20 barley samples and 1 corn sample that contained F. graminearum by traditional methods of analysis tested positive for the TRI6 and internal transcribed spacer (ITS) PCR products. The five corn samples that tested positive for F. verticillioides by traditional methods also were positive for the FUMI and ITS PCR products. These results indicate that the described multiplex real-time PCR assay provides sensitive and accurate differential detection of fumonisin- and trichothecene-producing groups of Fusarium spp. in complex matrices.     

Application of the novel Droplet digital PCR technology for identification of meat species

The authenticity and traceability of meat products are issues of primary importance to ensure food safety. Unfortunately, food adulteration (e.g. the addition of inexpensive cuts to minced meat products) and mislabelling (e.g. the inclusion of meat from species other than those declared) happens frequently worldwide. The aim of this study was to apply a droplet digital PCR assay for the detection and quantification (copies μL⁻¹) of the beef, pork, horse, sheep, chicken and turkey in meat products. The analysis conducted on commercial meat showed the presence of traces of DNA from other animal species than those declared. We show that the method is highly sensitive, specific and accurate (accuracy = 100%). This method could be adopted by competent food safety authorities to verify compliance with the labelling of meat products and to ensure quality and safety throughout the meat supply chain, from primary production to consumption.     

基于双拖尾重组聚合酶恒温扩增技术的核酸杂交试纸条快速检测驴肉中的马源性成分

目的：建立快速、操作简单、价格相对低廉的驴肉中马源性成分快速可视化检测技术。方法：采用双拖尾重组聚合酶恒温扩增技术(RPA)与核酸杂交试纸条相结合。针对马线粒体细胞色素b(cytb)基因设计RPA引物,引物包含3个功能区域,特异性绑定区域用于RPA扩增反应,spacer 9用于终止聚合酶的扩增,单链拖尾区域用于与试纸条上的探针杂交。这对特殊引物使RPA扩增子带有两个单链拖尾序列,这两个单链拖尾序列可以特异性地被金纳米探针和试纸条上的检测探针识别并捕获,形成一条肉眼可见的红色条带。整个扩增(15 min)和检测(5 min)过程在20 min即可完成,无需复杂的设备,仅需要一台数字化水浴锅。为进一步验证该方法的实际应用性能,对市面上的20份驴肉产品进行测定,并采用PCR(Polymerase Chain Reaction,PCR)结合琼脂糖凝胶电泳的方法进行验证。结果：该方法对马肉的检测限达到0.01%,且仅对马肉核酸有特异性扩增,与其他8个物种的核酸均无交叉反应,20份驴肉样品中有2份存在马源性成分。结论：该方法特异性强、灵敏度高,可实现驴肉中马源性成分的可视化快速检测。     

可视化LAMP检测常见肉制品中猪肉成分

根据GenBank中公布的猪线粒体色素细胞b基因序列设计6 条特异性环介导等温扩增（loop-mediated isothermal amplification,LAMP）引物,通过简化线粒体DNA提取步骤,优化反应体系,以常见的牛、羊、鸡、鸭、马、驴肉为阴性对照验证该方法的特异性,掺假率梯度稀释以验证该LAMP法的最低检测限,建立常见肉制品中猪肉成分的可视化LAMP检测方法。结果表明：该方法提取目的基因操作简单、稳定,该可视化LAMP检测法以4-(2-吡啶偶氮)-间苯二酚钠盐为指示剂,能准确检测出常见肉类中猪肉是否掺杂,检测结果肉眼可见,灵敏度为10 pg/μL。     

阿胶中马和驴成分的实时荧光PCR检测

建立阿胶中马和驴成分高特异、高灵敏的实时荧光聚合酶链式反应（polymerase chain reaction,PCR）检 测方法。选择马和驴线粒体基因tRNA-Thr及D-loop区为靶序列,设计合成特异引物,通过普通PCR和实时荧光PCR 检测,结果表明,这两对引物能够准确检测阿胶或动物胶中马和驴成分。     

Determination of mitochondrial cytochrome B gene sequence for red deer (Cervus elaphus) and the differentiation of closely related deer meats

The cytochrome b gene sequence for red deer was determined using the Dye Terminator Cycle Sequencing method and used for identification of deer meat in meat and meat products. Red deer showed a similarity of 94.1, 84.0, 81.1, 85.5 and 85.6% to sika deer (Cervus nippon), bovine, pigs, sheep and goats, respectively. To differentiate the deer meat, oligonucleotide primers RD-1(5′-TCATCGCAGCACTCGCTATAGTACACT-3′), RD-2(5′-ATCTCCAAGTAGGTCTGGTGCGAATAA-3′) were designed for the region of the cytochrome b gene of red deer. The PCR amplified 194 bp fragments from red and sika deer, but no fragments from bovine, pig, chicken, sheep, goat, horse and rabbit DNA. Although cooking the meats reduced the PCR products, red deer could still be detected in meat heated at 120 °C. To discriminate between red and sika deer, these PCR products were digested by a restriction enzyme (EcoRI,BamHI,ScaI) and analyzed by 4% agorose gel electrophoresis. As a result, the red deer fragment was digested by EcoRI to 67/127 bp fragments but not by BamHI and ScaI. The sika deer fragment was digested to 48/146 bp and 49/145 bp fragments with the two other enzymes, and thus it is possible to differentiate between the two kinds of deer from the digestion pattern of restriction enzymes.     

Species-specific multiplex real-time PCR assay for identification of deer and common domestic animals

A multiplex real-time PCR method for discriminating deer and common domestic species, including cattle, goat, horse, donkey, pig, and chicken was developed. Species-specific primer pairs were designed and used to produce different size DNA fragments with diverse melting temperature (T _m ) values. The specificity and sensitivity of these primer pairs were separately confirmed using simplex real-time PCR analysis. Multiplex real-time PCR analysis was performed using combined primers, yielding distinct melting curve profiles for each species. The sensitivity limit of the multiplex PCR method was evaluated. Trace DNA of other species in deer DNA could be identified. Common deer products, including blood, meat, and antler were tested using this multiplex PCR method and different species of deer and domestic animals were identified. The rapid multiplex real-time PCR assay described herein is a specific, sensitive, and reliable method for high-throughput authentication of deer and domestic animal products.     

The Development of Species-specific Real-time PCR Assays for the Detection of Pheasant and Quail in Food

The development of species-specific real-time PCR assays for the detection of pheasant and quail in commercial food products are reported. Real-time PCR primer and probe sets were designed to detect the mitochondrial cytochrome b gene of pheasant (Phasianus colchicus) and quail (Coturnix coturnix) and were optimized to achieve species specificity. The efficiency and sensitivity of the assays were determined and their applicability to the analysis of commercial samples assessed. The assays successfully detected pheasant and quail in complex food matrices of raw, oven-cooked, and autoclaved meat, demonstrating their suitability for use in enforcement and food control laboratories.     

Multiplex polymerase chain reaction assay for the differential detection of trichothecene- and fumonisin-producing species of Fusarium in cornmeal

The genus Fusarium comprises a diverse group of fungi including several species that produce mycotoxins in food commodities. In this study, a multiplex polymerase chain reaction (PCR) assay was developed for the group-specific detection of fumonisin-producing and trichothecene-producing species of Fusarium. Primers for genus-level recognition of Fusarium spp. were designed from the internal transcribed spacer regions (ITS1 and ITS2) of rDNA. Primers for group-specific detection were designed from the TRI6 gene involved in trichothecene biosynthesis and the FUM5 gene involved in fumonisin biosynthesis. Primer specificity was determined by testing for cross-reactivity against purified genomic DNA from 43 fungal species representing 14 genera, including 9 Aspergillus spp., 9 Fusarium spp., and 10 Penicillium spp. With purified genomic DNA as a template, genus-specific recognition was observed at 10 pg per reaction; group-specific recognition occurred at 100 pg of template per reaction for the trichothecene producer Fusarium graminearum and at 1 ng of template per reaction for the fumonisin producer Fusarium verticillioides. For the application of the PCR assay, a protocol was developed to isolate fungal DNA from cornmeal. The detection of F. graminearum and its differentiation from F. verticillioides were accomplished prior to visible fungal growth at <10(5) CFU/g of cornmeal. This level of detection is comparable to those of other methods such as enzyme-linked immunosorbent assay, and the assay described here can be used in the food industry's effort to monitor quality and safety.     

Polymerase chain reaction coupled with peptide nucleic acid high-performance liquid chromatography for the sensitive detection of traces of potentially allergenic hazelnut in foodstuffs

A new DNA extraction method suitable for a wide variety of complex food matrices has been devised and applied in combination with a new polymerase chain reaction (PCR) method for the sensitive detection of a specific DNA sequence univocally identifying the presence of potentially allergenic hazelnut (Corylus avellana). A 156 base pair amplicon corresponding to an internal region of the complementary DNA of the major hazelnut allergen (Cor a 1) was designed, and was found to be highly specific; the method was tested on both pure and complex food matrices and was found to be able to confirm the presence of hazelnut down to 5 pg of its DNA. The sequence of the amplicon was further confirmed by high-performance liquid chromatography (HPLC) analysis with a specific peptide nucleic acid (PNA) probe. A 15-mer PNA probe was expressly designed and synthesized to hybridize an internal sequence of the previously described amplicon. Given its reported sequence specificity and high hybridization efficiency, the PNA probe was used to develop an anion-exchange HPLC method allowing for a fast and reliable confirmation of the identity of the amplified products. The PCR–HPLC method was successfully tested on commercial samples, allowing for the detection of the presence of potentially hidden allergens even in products where the presence of hazelnut as an ingredient or possible contaminant was not reported.     

DNA extraction and fingerprinting of commercial rice cereal products

DNA was extracted from commercial rice cereal products using modified conventional methods (CTAB, SDS and a commercial kit) in large fragments (>3 kb) and with relatively high yields (1.4–10.7 μg DNA per g of sample) and was used as template for the amplification of a single copy rice gene (i.e. MIPS) fragment (ca. 850 bp) and microsatellite DNAs (ca. 120–400 bp). The cereal products were further discriminated by using six microsatellite markers. The usefulness of DNA analysis was discussed for quality control and authenticity testing of raw rice materials in rice-based food production, and to monitor genetically modified (GM) rice ingredients in commercial food products.     

Turkey breast meat functionality differences among turkeys selected for body weight and/or breast yield

Functional meat characteristics were studied in three turkey lines, (1) RBC2: representing 1960s commercial turkeys, (2) F-line: a line selected for body weight (BW) and (3) C-line: a fast growing commercial line with enhanced breast muscle yield. The RBC2s Warner-Bratzler shear force values for the Pectoralis major (PM) were lower than the F- and C-lines’ values (P < 0.05). The WHC of the breast muscle from the C-line was lower compared with the RBC2 line (P < 0.05), with the F-line being intermediate between, though not different from either the RBC2 or C-lines. A trend was observed, as the thermally induced meat gels from the RBC2 line PM had the highest storage modulus (G′), the F-line was intermediate and the C-line had the lowest storage modulus (P = 0.09). These results suggest that selection for increased growth and breast muscle yield may be associated with decreased meat functionality in modern commercial turkeys.