Practical application of DNA fingerprinting to trace beef

A review of conventional and rapid analytical techniques coupled with multivariate analysis for origin traceability of soybean

Soybean has developed a reputation as a superfood due to its nutrient profile, health benefits, and versatility. Since 1960, its demand has increased dramatically, going from a mere 17 MMT to almost 358 MMT in the production year 2021/22. These extremely high production rates have led to lower-than-expected product quality, adulteration, illegal trade, deforestation, and other concerns. This necessitates the development of an effective technology to confirm soybean's provenance. This is the first review that investigates current analytical techniques coupled with multivariate analysis for origin traceability of soybeans. The fundamentals of several analytical techniques are presented, assessed, compared, and discussed in terms of their operating specifics, advantages, and shortcomings. Additionally, significance of multivariate analysis in analyzing complex data has also been discussed.

Rapid discrimination of intact beef, venison and lamb meat using Raman spectroscopy

With increasing demand for fast and reliable techniques for intact meat discrimination, we explore the potential of Raman spectroscopy in combination with three chemometric techniques to discriminate beef, lamb and venison meat samples. Ninety (90) intact red meat samples were measured using Raman spectroscopy, with the acquired spectral data preprocessed using a combination of rubber-band baseline correction, Savitzky-Golay smoothing and standard normal variate transformation. PLSDA and SVM classification were utilized in building classification models for the meat discrimination, whereas PCA was used for exploratory studies. Results obtained using linear and non-linear kernel SVM models yielded sensitivities of over 87 and 90 % respectively, with the corresponding specificities above 88 % on validation against a test set. The PLSDA model yielded over 80 % accuracy in classifying each of the meat specie. PLSDA and SVM classification models in combination with Raman spectroscopy posit an effective technique for red meat discrimination.

Genetic traceability practices in a large-size beef company in China

An effective and trustworthy traceability system is important for food safety and quality; however, traditional traceability systems that only rely on the recording method do not completely prevent food fraud. DNA-based traceability techniques facilitate seamless connectivity within the entire food supply chain. A convenient and low-cost ear tag device was invented for collecting animal blood samples as an identity control, and a panel including 12 single nucleotide polymorphic (SNP) loci was selected to distinguish individuals with a matching probability of 1.70 × 10^-5. The exact animal individual was identified by comparing the SNP genotype barcodes between the meat and blood samples derived from the recording system to further validate authenticity of the recording system. These results illustrate that a combination of the genetic traceability method and a traditional recording system can provide trustworthy traceability for consumers.

Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market

Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

Recent development of allele frequencies and exclusion probabilities of microsatellites used for parentage control in the German Holstein Friesian cattle population

Background

Methods for parentage control in cattle have changed since their initial implementation in the late 1950’s from blood group typing to more current single nucleotide polymorphism determination. In the early 1990’s, 12 microsatellites were selected by the International Society for Animal Genetics based on their informativeness and robustness in a variety of different cattle breeds. Since then this panel is used as standard in cattle herd book breeding and its application is accompanied by recurrent international comparison tests ensuring permanent validity for the most common commercial dairy and beef cattle breeds for example Holstein Friesian, Simmental, Angus, and Hereford. Although, nearly every parentage can be resolved using these microsatellites, cases with very close relatives became an emerging resolution problem during recent years. This is mainly due to an increase of monomorphism and a trend to the fixation of alleles, although no direct selection against their variability was applied. Thus other effects must be presumed resulting in a loss of polymorphism information content, heterozygosity, and exclusion probabilities.

Results

To determine changes of allele frequencies and exclusion probabilities, we analyzed the development of these parameters for the 12 microsatellites from 2004 to 2014. One hundred sixty eight thousand recorded Holstein Friesian cattle genotypes were evaluated. During this period certain alleles of nine microsatellites increased significantly (t-values >5). When calculating the exclusion probabilities for 11 microsatellites, reduction was determined for the three situations, i.e. one parent is wrongly identified (p = 0.01), both parents are wrongly identified (p = 0.005), and the genotype of one parent is missing (p = 0.048). With the addition of BM1818 to the marker set in 2009, this development was corrected leading to significant increases in exclusion probabilities. Although, the exclusion probabilities for the three family situations using the 12 microsatellites are >99 %, the clarification of 142 relationships in 40,000 situations where one parent is missing will still be impossible.

Twenty-five sires were identified that are responsible for the most significant microsatellite allele increases in the population. The corresponding alleles are mainly associated with milk protein and fat yield, body weight at birth and weaning, as well as somatic cell score, milk fat percentage, and longissimus muscle area.

Conclusions

Our data show that most of the microsatellites used for parentage control in cattle show directional changes in allele frequencies consistent with the history of artificial selection in the German Holstein population.

A false single nucleotide polymorphism generated by gene duplication compromises meat traceability

Controlling meat traceability using SNPs is an effective method of ensuring food safety. We have analyzed several SNPs to create a panel for bovine genetic identification and traceability studies. One of these was the transversion g.329C>T (Genbank accession no. AJ496781) on the cytochrome P450 17A1 gene, which has been included in previously published panels. Using minisequencing reactions, we have tested 701 samples belonging to eight Spanish cattle breeds. Surprisingly, an excess of heterozygotes was detected, implying an extreme departure from Hardy-Weinberg equilibrium (P<0.001). By alignment analysis and sequencing, we detected that the g.329C>T SNP is a false positive polymorphism, which allows us to explain the inflated heterozygotic value. We recommend that this ambiguous SNP, as well as other polymorphisms located in this region, should not be used in identification, traceability or disease association studies. Annotation of these false SNPs should improve association studies and avoid misinterpretations.

Molecular traceability of beef from synthetic Mexican bovine breeds

Traceability ensures a link between carcass, quarters or cuts of beef and the individual animal or the group of animals from which they are derived. Meat traceability is an essential tool for successful identification and recall of contaminated products from the market during a food crisis. Meat traceability is also extremely important for protection and value enhancement of good-quality brands. Molecular meat traceability would allow verification of conventional methods used for beef tracing in synthetic Mexican bovine breeds. We evaluated a set of 11 microsatellites for their ability to identify animals belonging to these synthetic breeds, Brangus and Charolais/Brahman (78 animals). Seven microsatellite markers allowed sample discrimination with a match probability, defined as the probability of finding two individuals sharing by chance the same genotypic profile, of 10(-8). The practical application of the marker set was evaluated by testing eight samples from carcasses and pieces of meat at the slaughterhouse and at the point of sale. The DNA profiles of the two samples obtained at these two different points in the production-commercialization chain always proved that they came from the same animal.

Effect of consanguinity on Argentinean Angus beef DNA traceability

Since the 1990s several authors have envisaged the use of DNA to certify meat origin. Two major parameters must be assessed before a DNA based traceability protocol can be implemented in the food chain: (i) the information content of a DNA marker set in a specific livestock breed or group of breeds; (ii) the minimum number of DNA markers needed to obtain a statistically acceptable match probability. The objective of the present work was to establish the effect of different levels of inbreeding in the matching efficiency, and the minimum number of microsatellite markers needed, in a DNA based meat traceability program, starting from an 11-microsatellite marker panel. Samples were obtained from beef production farms in South America, where animals are typically bred under pasture-based extensive conditions. Three groups of animals with different consanguinity rates were sampled. Exclusion power (Q) was higher than 0.999998 and match probability lower than 3.01E-08, for the whole set of markers within each group. Both values were affected by consanguinity. To reach a two mismatch criteria exclusion power (Q(2)) of 99.99, six markers were needed in unrelated animals whereas seven markers were needed in related animals. To reach Q(2)=99.9999, 8 and 10 microsatellite markers, respectively, were needed. In general, one or two more microsatellite markers were needed to identify consanguineous animals. This study proved the DNA marker set used to be suitable for the identification of the meat from all slaughtered animals in Argentina, per week, month, and year.

A statistical approach to identifying the batch of origin of mixed-meat products using DNA profiles

Comparison of DNA samples at different points of a supply chain offers a powerful means of verifying tracing systems for primal cuts of meat. However, this approach is problematic for products made from ground (or mixed) meat because such products are typically made from an unknown (and random) number of unidentified animals. We present a statistical method that uses DNA profiles to verify or refute the contention that a particular mixed-meat product came from a particular manufacturing batch. This method involves randomly isolating a number of individual DNA samples (comprising an unknown number of individual genotypes) from the end product and comparing them with a set of DNA samples (also comprising an unknown number of individuals) that had been collected randomly before preparation of a manufacturing batch. Confidence levels are given for refuting spurious claims, and the development of optimum sampling strategies is discussed. The results are discussed in relation to batch verification of mixed-meat products in the food industry, with an emphasis on traceability issues.

Genetic traceability of livestock products: A review

Traceability is the ability to maintain the identification of animal, or animal products, all along the production chain. It represents an essential tool to safeguard public and animal health and to valorize typical production systems. European food legislation is particularly strict and traceability systems, based on product labeling, have become mandatory in all European countries. However, the implementation of this system does not ensure consumers against fraud. Paper documents can be counterfeit so researchers have focused on the study of genetic traceability systems based on products identification through DNA analysis. In fact DNA is inalterable, detectable in every cell, resistant to heat treatments, and allows for individual, breed or species identification. Even if results are promising, these techniques are too expensive to be converted in routine tests but they could be a trusted tool for verification of suspected fraud. The present review proposes a synthesis of the major advances made in individual, breed, and species genetic identification in the last years, focusing on advantages and disadvantages and on their real future applications for animal productions.

Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing

OBJECTIVE

To determine whether a selected set of 20 single nucleotide polymorphism (SNP) markers derived from beef cattle populations can be used to verify sample tracking in a commercial slaughter facility that processes primarily market (ie, culled) dairy cows.

DESIGN

Prospective, blinded validation study.

ANIMALS

165 cows and 3 bulls from 18 states (82% Holstein, 8% other dairy breeds, and 10% beef breeds).

PROCEDURE

Blood was collected by venipuncture from randomly chosen animals just prior to slaughter. The purported corresponding liver samples were collected during beef processing, and genotype profiles were obtained for each sample.

RESULTS

On the basis of SNP allele frequencies in these cattle, the mean probability that 2 randomly selected individuals would possess identical genotypes at all 20 loci was 4.3 x 10(-8). Thus, the chance of a coincidental genotype match between 2 animals was 1 in 23 million. Genotype profiles confirmed appropriate matching for 152 of the 168 (90.5%) purported blood-liver sample pairs and revealed mismatching for 16 (9.5%) pairs. For the 16 mismatched sample pairs, 33% to 76% of the 20 SNP genotypes did not match (mean, 52%). Discordance that could be attributed to genotyping error was estimated to be < 1% on the basis of results for split samples.

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggest that this selected set of 20 bovine SNP markers is sufficiently informative to verify accuracy of sample tracking in slaughter plants that process beef or dairy cattle. These or similar SNP markers may facilitate high-throughput, DNA-based, traceback programs designed to detect drug residues in tissues, control of animal diseases, and enhance food safety.

Methods to improve the yield and quality of DNA from dried and processed figs

We describe here a molecular method that can be used to detect genome traits of a given horticultural item at each stage from the farm to the market. We developed a procedure to extract and amplify by PCR DNA obtained from complex matrixes, such as dried figs and fig jam. Few fragmented DNA molecules can be recovered from food products. However, we were able to increase the yield of PCR reactions by successfully applying an enzymatic repair protocol to retrieved DNA.