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Microsatellite markers for animal identification and meat traceability of six beef cattle breeds in the Chinese market
... Dalvit et al. [55] tested a set of 12 SSR markers for assessment of a genetic traceability system of six cattle breeds of Italy when genotyping five most polymorphic loci and found out that the probability of finding two identical animals was five in one million. Zhao et al. [56] used 16 SSRs to conduct individual identification and meat traceability for six common breeds of beef cattle in China. The results showed that when a combination of six highly polymorphic loci are used, the match probability value is about seven in one million. ...
... In the process of individual identification, different SSR markers usually exhibit different polymorphisms in the same population, while the identical markers may also show different polymorphisms in the different genetic background population. Under this circumstance, the selection of polymorphic markers is very important in the genetic traceability practices [56]. Thus, the SNP marker shows great potential in individual identification and meat traceability practice. ...
... Meanwhile, some factors may also affect the accuracy and reproducibility of DNA fingerprint authentication like DNA degradation and PCR inhibitors [51]. Furthermore, due to genetic differences between populations, the same DNA marker has varied polymorphism, raising the need to screen more specific genetic markers [56]. Finally, the cost of the DNA fingerprinting technique is higher, which is one of the reasons for limiting its application in a wide range. ...
An effective and trustworthy traceability system contributes to improving food quality and safety and responds to consumers’ demand for food provenance information. Safe meat and its products are crucial to consumers and society. Livestock feeding regime and geographical origin are closely related to the properties and the safety of animal origin food, but the information is often invisible to consumers, which makes is easier to use fraudulent practices throughout the whole supply chain. Technologies and their proper use in traceability systems are important for the safety of animal origin foods. An essential component in an integrated traceability chain includes individual animal identification and trace back of related meat products. In this review, we examine the technologies for individual animal identification, including the radio frequency identification system and DNA fingerprinting. For meat products, traceability technologies focus on the chemical components fingerprinting, including measurement of stable isotope ratios, mineral element tracing and organic component fingerprinting. Also, future trends in food traceability systems need to be improved to promote the establishment of more efficient and trustworthy traceability systems to ensure food safety and quality up to standard.
... Concern about the traceability of food products has arisen in the past two decades after outbreaks of spongiform encephalopathy in bovines -BSE [19], [4] and birds contaminated with dioxin in Europe [4], E. coli O157: H7 [19]. ...
... Concern about the traceability of food products has arisen in the past two decades after outbreaks of spongiform encephalopathy in bovines -BSE [19], [4] and birds contaminated with dioxin in Europe [4], E. coli O157: H7 [19]. ...
... To guarantee food safety, there was a need to improve the systems for monitoring production processes. In parallel, there was a process of expanding the food supply chain and the available traceability systems were unable to guarantee the consumer all the necessary information about the product he was purchasing [4], [5]. ...
Brazil is the 3rd largest egg producer in the Americas and for production to be achieved, it must be organized to produce with quality and productivity. For all quality requirements to be met, guidance documents such as EMBRAPA and the Brazilian Poultry Union cover all stages of the production process, from the origin of the inputs to the later stages of production. In addition to these instructions, other legislation dealing with traceability is used to regulate production processes in food chains. In this context, the objective of this work is to confront the main national and international standards related to traceability to verify common requirements and that can compose a system of data collection. The work was divided into three stages and presented as a result the common requirements: sanitary management in the breeding and rearing phases, lineage, input control, poultry vaccination, poultry feeding, sanitary monitoring, egg collection information, eggs, and biosafety, product description, batch identification, date of shipment and data of the sending company and data of the company of destination, in addition to the information retrieval system.
... Integrating all links in the production chain through the registration link is one of the major difficulties in implementing the traceability system (Zhao et al. 2017;Badia-Meliset al., 2015, GoglianoSobrinhoet al. 2010. These updated and linked records are essential to Research, Society andDevelopment, v. 9, n. 9, e349997370, 2020 (CC BY 4.0) | ISSN 2525-3409 | DOI: http://dx.doi.org/10.33448/rsd-v9i9.7270 4 obtaining the necessary data to feed the system. ...
... At this moment, there is a break in the information link Research, Society and Development, v. 9, n. 9, e349997370, 2020 (CC BY 4.0) | ISSN 2525-3409 | DOI: http://dx.doi.org/10.33448/rsd-v9i9.7270 12 (Zhao et al. 2017;Badia-Meliset al., 2015, Gogliano Sobrinho et al. 2010, and a nonfulfillment of the important systematic requirements to organize the data collecting system pointed out by Machado (2000), which are :i) the batches produced must not be mixed; ii) any movement must be registered in the traceability control records; iii) the production documents must follow the production steps with records of all the carried out processes. In farms where the collecting system is only automatic, there is no possibility of egg segregation. ...
... Food safety drove improvements in the systems for monitoring production processes, along with the process of expanding the food supply chain. Quality information is essential to achieve this expansion (Zhao et al. 2017, Gogliano Sobrinho et al. 2010. For information to reach consumers, it needs to have quality attributes that guarantee their future access (Pizzuti et al. 2014). ...
More demanding consumers pressure the food industry to attend the increasing demand for information. Traceability is a system that allows to gather information related to a product, from the beginning of its production chain to the moment of consumption. Data recording is the first stage of the Data Life Cycle, and supports the implementation of a system that is capable of tracking egg quality information. Egg is a widely consumed staple food and the Brazilian poultry production needs to be structured in order to attend quality and informational requirements. The aim of this paper is to identify the critical points of the traceability information gathering of eggs in commercial farms. The interviews carried for this paper allowed to validate the identified requirements, and to propose improvements in the process of collecting data of eggs. The steps of sanitary management in breeding and rearing, control of inputs, eggs collection, eggs classification and product identification were described as the critical steps for the implementation of traceability.
... Microsatellite marker analysis has been used to verify the parentage in breeding registries and identify individual animals that are linked to a particular database or owner. Microsatellite panels of cattle (Zhao et al., 2017), horse (Kang et al., 2016), sheep (Rosa et al., 2013), dog (Jeong et al., 2015), and parrot (Coetzer et al., 2017) have been well characterized. Parentage control in the beef cattle breeds, Charolais, Limousin, and Preta, in Portugal was assessed using 10 microsatellite markers, and the results revealed a combined exclusion probability (PE) above 0.9995, indicating their ability to exclude a random parent pair (Carolino et al., 2009). ...
... The application of 11 microsatellite loci in paternity testing in Yugoslav Pied cattle breed in Serbia revealed a combined PE of 0.999 (Stevanovic et al., 2010). A total of 16 specific microsatellite markers were used to develop a genetic system of meat traceability for several beef cattle breeds, including Japanese Black, Anduo yak, Limousin, Jiaxian Red, Nanyang Yellow, and Luxi Yellow (Zhao et al., 2017). Previous studies reported that microsatellite genotyping was used for population genetics analysis and parentage testing in yak. ...
... These practices that aim at genetic improvement of yak are essential for generating reliable breeding programs. Several reports have been published on the use of microsatellite markers for cattle identification (Sharma et al., 2015;Zhao et al., 2017), but the performance characteristics of yak identification panels have not yet been established. Parentage testing for yak breeding increases the profitability by improving the efficiency of selective breeding programs. ...
Background
Yak ( Bos grunniens ) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak.
Methods
A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy–Weinberg equilibrium without linkage disequilibrium.
Results
Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak.
Discussion
Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations.
... The CMP value was 3.4 × 10 −13 when the most polymorphic (highest PIC value) 12 markers were selected. The present study, using 12 STR core panel or using the most polymorphic 12 STRs, showed stronger discrimination power than previous studies [44,45]. Bovine Genotype Panel 2.2 (Thermo Scientific), which includes six additional STRs, could not be completely evaluated since ...
... The CMP value was 3.4 × 10 −13 when the most polymorphic (highest PIC value) 12 markers were selected. The present study, using 12 STR core panel or using the most polymorphic 12 STRs, showed stronger discrimination power than previous studies [44,45]. Bovine Genotype Panel 2.2 (Thermo Scientific), which includes six additional STRs, could not be completely evaluated since three of its STRs (MGTG4B, RM67 and SPS113) were not studied following the recommendations [10]. ...
Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest FST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest FST markers is proposed for a confident parentage analysis and high traceability.
... The International Society for Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO) of the United Nations have proposed to use microsatellites in population genetics studies of livestock breeds, in particular, to analyze their genetic diversity, genetic distances, population structure, breed purity, breed origin, effective population size, and other characteristics [14]. Different levels of multilocus heterozygosity and allelic diversity revealed in the early studies related to the microsatellite polymorphism analysis in the cattle have provided impetus for a whole series of studies in this field (see, for example, [5,8,[15][16][17][18][19][20][21][22][23][24]). Most studies have been performed on local and transboundary cattle breeds with a wide breeding range, helping address both applied (characterization and monitoring of animal genetic resources) and fundamental (genome mapping, phylogeny, molecular genetics classification, gene geography, genetic variability analysis, etc.) problems of cattle breeding. ...
... Most studies have been performed on local and transboundary cattle breeds with a wide breeding range, helping address both applied (characterization and monitoring of animal genetic resources) and fundamental (genome mapping, phylogeny, molecular genetics classification, gene geography, genetic variability analysis, etc.) problems of cattle breeding. For example, a meat traceability system has been developed for indigenous breeds of Chinese cattle to ensure meat safety and to solve adulteration issues [23]. For distinct ecotypes of Nguni cattle adapted to very different environmental regions of South Africa, a close genetic relationship has been reported [20]. ...
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
... The number of microsatellite alleles at each locus has been used to assess genetic diversity and between-breed relationships (Egito et al., 2007;Mateus et al., 2004;Suh et al., 2014;Stevanovic et al., 2010). The overall mean allele number per locus was comparable with previous results, which varied from 5 to 16 (Egito et al., 2007;Freeman et al., 2004;Mateus et al., 2004;Stevanovic et al., 2010;Suh et al., 2014, Zhao et al., 2017. Additionally, it has been suggested that individual microsatellite markers that are used to assess genetic diversity should have at least four alleles in order to generate reliable information (Barker, 1994;Shi et al., 2010). ...
... In general, the levels of heterozygosity (H e and H o ) that were observed in this study are similar to previous reports (Agung et al., 2019;Egito et al., 2007;Freeman et al., 2004;Suh et al., 2014;Zhao et al., 2017). Given that these observed levels of heterozygosity were greater than 0.5, this indicates that the 10 microsatellite markers are suitable for genetic diversity studies in the three dairy breeds (Sheriff & Alemayehu, 2017). ...
The aim of this research was to assess genetic diversity of Korean-Holstein, Korean Hanwoo, and Ugandan-Holstein dairy cattle. DNA was extracted from either blood or hair of Korean-Holstein (n=74), Korean-Hanwoo (n=75) and Ugandan-Holstein (N=77) using AccuPrep® PCR purification kit. The DNA samples were amplified by multiplex polymerase chain reaction, using GeneTrack M Hanwoo genotyping kit and assayed using ABI genetic analyser 3130XL. Number of alleles, expected heterozygosity (He), observed heterozygosity (Ho), and the polymorphism information content (PIC) were estimated from 10 microsatellite loci in the three breeds. In addition, F-statistics for each of the 10 microsatellites in the three cattle breeds were estimated using fstat version 2.9.3.2 computer program. GENETIX (v.4.02) was used to perform factorial correspondence analysis (FCA) from the allele frequencies and multi-locus clustering was done using STRUCTURE analyses. A total of 124 alleles were detected. The number of alleles per locus varied from eight (TGLA126) to 22 (TGLA122), with an overall mean of 12.2. Expected heterozygosity ranged from 0.617 (SPS115) to 0.854 (TGLA53) and averaged 0.761. Observed heterozygosity ranged from 0.6 (SPS115) to 0.859 (TGLA53); and averaged 0.761. The mean PIC was 0.723; and means of the F-statistics FIT, FST and FIS were 0.077, 0.076 and 0.001 respectively. Although FCA revealed clear differentiation of Uganda-Holstein, Korean-Holstein, and Hanwoo, clustering assignments showed genetic admixture between Ugandan dairy cattle (Uganda-Holstein) and Hanwoo. In conclusion, the allelic variation present at the 10 loci was sufficient to categorize these cattle into distinct breed groups.
... The mean number of alleles across 12 loci was 10.5. The allele range (7 to 16) corresponded to those determined previously, which ranged from 4 to 16 (Peelman et al., 1998;Maudet et al., 2002;Visscher et al., 2002;Machado et al., 2003;Sodhi et al., 2006;Van Eennenaam et al., 2007;Stevanovic et al., 2010;Zhao et al., 2017). It should be noted that the animals used in the study are related and higher number of alleles will be expected if larger samples of unrelated cattle are used (Table 2). ...
... The expected heterozygosity (He) ranged from 0.581 (ETH225) to 0.873 (INRA23). The He and Ho range corresponded to those reported previously (Peelman et al., 1998;Maudet et al., 2002;Visscher et al., 2002;Machado et al., 2003;Sodhi et al., 2006;Van Eennenaam et al., 2007;Stevanovic et al., 2010;Zhao et al., 2017). ...
The study was undertaken with an objective to develop and validate a panel containing maximum number of microsatellite markers that can be amplified in a single PCR reaction for precise parentage verification in Indian HF cattle population. The study was based on a total of 210 HF cattle (100 calf, 100 dam and 10 sires). Genomic DNA was extracted from blood and semen samples. A panel of 12 microsatellite markers (BM1824, BM2113, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH10, ETH225, BM1818, ETH3, TGLA53) was amplified in a single multiplex reaction and analyzed by capillary electrophoresis on an automated DNA sequencer. The observed heterozygosity (Ho) of 12 markers ranged from 0.607 (TGLA53) to 0.904 (BM2113) while the expected heterozygosity (He) ranged from 0.581 (ETH225) to 0.873 (INRA23). Eleven out of 12 microsatellite loci revealed relatively high polymorphic information content (>0.6). The results suggest that multiplex microsatellite panel can be effectively used to verify the
parentage as well as to assign the putative sire to daughters under progeny testing.
... As Limousin and Japanese Black are not native cattle breeds of China, their genetic distance is larger relative to the other breeds, and the Anduo yak breed has previously seen genetic information exchange between the native yellow cattle to improve their heredity and environmental resistance (Qi, Jianlin, Wang, Rege, & Hanotte, 2010). For the Jiaxian, Luxi, and Nanyang breeds, they all possess a long history in Chinese agricultural development, and the genetic distance between them is much closer ( Zhao et al., 2017). As such, the cluster analysis did not easily separate these three breeds from each other. ...
... Additionally, we used PLS-DA analysis for the discrimination of the six cattle breeds, and the results were consistent with the cluster analysis for the Limousin, Japanese Black, Anduo yak, and the three yellow cattle breeds. However, the PLS-DA method did demonstrate accurate differentiation between the three yellow cattle breeds, which was better than the 16 SSR markers used in our earlier study (Zhao et al., 2017). The results of the two types of DNA markers for distinguishing individuals and breeds indicated that different genetic markers could complement each other to achieve superior results, similar to how prior studies have converted the AFLP markers to SNP markers for achieving different research goals and practical conditions ( Sasazaki et al., 2004Sasazaki et al., , 2006). ...
... However, these methods are often subjective, lack standardized criteria, and are prone to inaccuracies, especially when dealing with breeds that exhibit similar external traits but possess significant genetic differences (Ceccobelli et al., 2016). To address these challenges, molecular biology techniques combined with various algorithmic models have been employed to identify livestock genetic resources, including chicken (Peng et al., 2019;Rikimaru and Takahashi, 2007; Van and Nel, 2000;Huang et al., 2016), cattle (Bertolini et al., 2015;Blott et al., 1999;Pei et al., 2018;Zhao et al., 2017),sheep (Arranz et al., 2001;Bitanyi et al., 2011;Niu et al., 2012), pigs (Fan et al., 2005) and dogs (Radko and Podbielska) breeds, with promising results (Wayne et al., 1996). In 2013, Iquebal et al established the world's first web server for goat breed identification, utilizing a Bayesian algorithm and microsatellite DNA markers, achieving 98.7 % accuracy for 22 goat breeds (Iquebal et al., 2013). ...
Accurate identification of chicken genetic resources is crucial for biodiversity conservation and the development of breeding programs. Traditional morphological identification methods face significant challenges due to phenotypic similarities among breeds and the increasing complexity of global genetic resource exchanges. This study aims to develop a high-throughput, accurate molecular identification system for chicken genetic resources by integrating advanced genomic analysis with machine learning approaches, addressing the pressing need for reliable breed authentication tools in both research and industry applications. To achieve precise molecular identification, we analyzed whole-genome resequencing data and 600 K-chip data from 3,798 individuals representing 132 chicken genetic resources. Maximum likelihood phylogenetic trees were constructed to assess sample accuracy and identify outliers, ultimately retaining data for 127 breeds. Genetic differentiation between chicken genetic resources was assessed using the fixation index (Fst). The 100 loci with the highest genetic differentiation index from each genetic resource were selected, and a gradient-boosting tree model was employed to assess the importance of these loci. The accuracy of various models was compared. The results indicate that each variety possesses loci that exhibit near-complete differentiation. MLR proved the most effective machine learning model for identifying chicken genetic resources, achieving 99.45 % accuracy with 2,000 SNPs. The system provides user-friendly, web-based access for chicken genetic resource identification through uploaded vcf or gvcf files. The system's versatility allows for the incorporating whole genome resequencing and SNP micro-array data. Additionally, a data upload function facilitates the continuous expansion of the chicken genetic resources database, enabling broader identification capabilities. This system offers a rapid, accurate, and cost-effective approach to chicken genetic resources identification, facilitating informed decision-making for conservation and innovative utilization, thereby supporting the sustainable development of the poultry industry.
... To solve a number of tasks related to the scientific support of breeding work, in particular regarding the certification of animal breeds, determining the level of consolidation of created groups and the degree of genetic differentiation of populations, a separate class of molecular genetic markers -microsatellites -is widely used (Debrauwere H. et al., 1997, Senan S. et al., 2014). Due to the high level of polymorphism of microsatellite markers (SSR, Simple Sequence Repeat), which is reflected in a larger number of alleles per locus compared to classical biallelic systems, microsatellites can be used as a rather subtle and effective tool for studying genetic variability, which allows successfully solving the entire range of these issues (Shelyov, 2015;Mishra S. et al., 2017, Zhao J. et al., 2017. SSR markers are considered to be selection-neutral and, due to their wide localization in the genome, are of interest for controlling genetic processes that occur in artificially reproduced animal populations (Shelyov, 2017, Al-Jubori & Senkal, 2023. ...
The article presents the results of a study of the genetic and population structure in herds of Ukrainian Black-and-White and Red-and-White dairy breeds kept in the Kharkiv region (DPDH “Hontarivka”). The analysis of genetic variability in the experimental groups of animals was carried out using 10 microsatellite loci recommended by FAO-ISAG: ETH225, BM2113, ETH3, BM1818, BM1824, ILSTS006, INRA023, TAGLA053, TAGLA12, ETH10. The amplification products were separated in native polyacrylamide gels of different concentrations (5 – 8 %). All studied loci were found to be polymorphic. The number of detected alleles per locus ranged from 4 to 8 (on average 5 alleles per locus) the size of which ranged from 115 bp (ETH3) to 307 bp (ILSTS006). The vast majority of studied loci belong to informatively valuable markers (PIC > 0.5). The most polymorphic loci for both breeds were TGLA053 (8 alleles), BM2113 (6) and ETH3(6). The main population genetic parameters were calculated for the studied loci. The highest values of heterozygosity indices (He) and effective number of alleles (ne) were characteristic of the BM2113 locus (He=0.80-0.81, ne=5.1-5.3). The minimum values of expected heterozygosity were established for the ETH3 loci (0.53-0.55; Ukrainian Black-and-White and Red-and-White dairy breeds) and BM1818 (0.59, Ukrainian Black-and-White dairy breed). For most microsatellite loci, an equilibrium state between the actual and expected genotype frequencies is characteristic. A probable deviation in the form of a deficit of heterozygotes was established only for the BM1818 locus in both experimental populations (Fis = 0.37; p < 0.05). Changes in the genetic structure of the experimental cattle population (Kharkiv region) were analyzed in comparison with data from previous years of research, other regions, and with data from the initial forms involved in the creation of these breeds. Analysis of genetic changes that occurred during the reproduction of experimental cattle populations indicates a narrowing of genetic variability and the need to control genetic processes in breeding work.
... Они служат значимым источником информации о состоянии генетических ресурсов, способствуя повышению эффективности процессов анализа генетического разнообразия и генетической чистоты, а также способны генерировать информацию для планирования скрещиваний и выбора генотипов в программах генетической селекции [21,22]. Кроме того, микросателлиты являются ценными инструментами для анализа достоверности происхождения [23,24,25,26], породной принадлежности [27, 28,29] и установления степени инбридинга в определенных группах и стадах [30,31]. ...
Over a few past decades, theoretical, analytical, and methodological advances in genetics have revolutionized population genetic research, providing a better understanding of evolutionary processes and the history of populations and species. Methodologically, this progress is largely due to the invention of polymerase chain reaction technology and the introduction of microsatellite DNA markers. This review discusses trends in the use of microsatellite markers as effective tools for solving a wide range of issues in population genetics, conservation and evolutionary biology of the only species of the genus Rangifer – reindeer. Based on the analysis of both experimental and review publications (78 sources) of the scientific teams of the Russian Federation, Canada, the United States of America, Ireland, Japan, China, Norway the first works on the successful amplification of reindeer microsatellites have been summarized. There has been demonstrated the significance of the data of markers for studying intra- and inter-population diversity, differentiation, genetic relationships, the impact of anthropogenic factors on genetic diversity and genetic isolation of populations, as well as for reconstructing the evolutionary history of the various reindeer forms.
... In addition, the use of microsatellites to trace the source of meat has become an essential trend to protect the health of consumers (Dalvit et al., 2008). Previous studies used seven highly polymorphic microsatellite loci obtained to genotype six beef cattle in the Chinese market and found that the genotype coincidence probability of blood and corresponding tissues of each individual was 100% (Zhao et al., 2017). These studies indicated that the use of microsatellites plays an important role in the identification of breeds as well as individuals, and the discrimination power continues to increase with the gradual increase in the number of microsatellite markers (Herraeza et al., 2005) The effects of individual and breed visual errors were excluded using microsatellite analyses (Cunningham and Meghen, 2001). ...
South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, Breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the Structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, and improve cultivar protection, and new germplasm construction.
... They also reported the average observed number of alleles per locus ranged from 0.619 ± 0.824 in Shahabadi cattle to 6.571 ± 0.732 in Hariana cattle with the mean allele number across all the loci of 8.784 ± 0.25. Zhao et al.18 studied Japanese cattle using 16 microsatellite loci and reported number of alleles per locus varied from 7 (ILSTS005 and ...
In countries where farming is largely subsistence, no pedigree records of farm animals are maintained at farmers' herd and scientific mating plans are not observed which leads to the accumulation of inbreeding and loss of production potential. Microsatellites have been widely used as reliable molecular markers to measure inbreeding. We attempted to correlate autozygosity estimated from microsatellite data with the inbreeding coefficient (F) calculated from pedigree data in Vrindavani crossbred cattle developed in India. The inbreeding coefficient was calculated from the pedigree of ninety-six Vrindavani cattle. Animals were further grouped into three groups viz. acceptable/low (F: 0-5%), moderate (F: 5-10%) and high (F: ≥10%), based on their inbreeding coefficients. The overall mean of the inbreeding coefficient was found to be 0.070 ± 0.007. A panel of twenty-five bovine-specific loci were chosen for the study according to ISAG/FAO. The mean FIS, FST, and FIT values were 0.0548 ± 0.025, 0.012 ± 0.001 and 0.0417 ± 0.025, respectively. There was no significant correlation between the FIS values obtained and the pedigree F values. The locus-wise individual autozygosity was estimated using the method-of-moments estimator (MME) formula for locus-specific autozygosity. The autozygosities ascribing to CSSM66 and TGLA53 were found to be significantly (p < .01 and p < .05, respectively) correlated with pedigree F values.
... Microsatellites or SSRs (Simple Sequence Repeats) are highly polymorphic and specific molecular markers. They have been used for animal identification and parentage determination in cattle (Zhao et al., 2017), sheep (Rosa et al., 2013) and horses (Kang et al., 2016) as well as in studies of population genetics (Zhou et al., 2015;Sheriff et al., 2018) and evolution (Oliveira et al., 2006). Although some opinions are controversial, the majority of researches admit that SSR are neutral markers of evolution (Tachida and Lizuka, 1992;Shriver et al., 1993;Valdes et al., 1993;Di Rienzo et al., 1994). ...
Background: The study of the homology of loci between different species has allowed the improvement of specific genetic knowledge and the development of several fundamental concepts. Thanks to this method, Wright discovered the correspondence between a gene and an enzyme (Wright, 1917). In ruminants, this correspondence between loci of different species has been demonstrated for a very long time (Lauvergne, 1979). In fact, the objective of this work was, initially, to use microsatellites recommended for sheep (FAO, 2011) for the amplification of bovine DNA to show that these loci are homologous and, then, to study the genetic diversity and population structure of three groups of each of the two species in Tunisia. Methods: In this study, we used three microsatellite markers (OarFCB304, OarFCB193 and MAF209) to verify whether they can be amplified in both sheep and cattle. For that, we considered 28 samples of sheep species from 3 different populations and 17 samples of cattle belonging to three breeds. The data obtained were also used to study their genetic diversity and population structure. Result: We have demonstrated the existence of microsatellite regions common to sheep and cattle. Regarding genetic diversity, we observed a heterozygous deficiency in all the studied breeds. Nei’s genetic distances were greater between breeds of cattle than between breeds of sheep.
... The present study demonstrated for the first time that an ultra-small panel of~20 SNPs can generate unique genotype profiles for all individuals in genetically heterogeneous data of 2106 animals and in a commercial dataset of nearly 80 000 purebred Australian Angus cattle. Previous studies in cattle, goats and sheep have shown that a small number of SNPs ranging from 5 to 48 markers can distinguish individuals with a high accuracy (Heaton et al. 2002;Werner et al. 2004;Goffaux et al. 2005;Allen et al. 2010;Zhao et al. 2017). However, none of the studies achieved 100% matching probability because genetic markers were pre-selected from published literature and then validated in the experimental samples. ...
Context
Genomic profiles are the only information source that can uniquely identify an individual but have not yet been strongly considered in the context of paddock to plate traceability due to the lack of value proposition.
Aim
The aim of this study was to define the minimum number of single nucleotide polymorphisms (SNP) required to distinguish a unique genotype profile for each individual sample within a large given population. At the same time, ad hoc approaches were explored to reduce SNP density, and therefore, the size of the dataset to improve computing efficiency and storage requirements while maintaining informativeness to distinguish individuals.
Methods
Data for this study included two datasets. One included 78 411 high-density SNP genotypes from commercial Angus cattle and the other 2107 from a research data (1000-bull genome data). In a stepwise approach, different-size SNP panels were explored, with the last step being a successive removal resulting in the smallest set of SNPs that still produced the maximum number of unique genotypes.
Key results
First study that has demonstrated for large datasets, that ultra-small SNP panels with 20–23 SNPs can generate unique genotypes for up to ~80 000 individuals, allowing for 100% matching accuracy.
Conclusions
Ultra-small SNP panels could provide an efficient method to approach the large-scale task of the traceability of beef products through the beef supply chain.
Implications
Genomic tools could enhance supply-chain traceability.
... However, the requirement of a costly and complex instrumental system and highly trained operators constitutes a non-indifferent drawback of such a technique (Drivelos & Georgiou, 2012;Wadood et al., 2020). The accessibility to thousands of DNA markers and diverse sequencing methods make undoubtedly DNA-based approaches relevant to address many authenticity issues, including the discrimination of species and variety, geographical origin, mode of production, and the identification of genetically modified species, and uncontrolled admixtures both in plant and animal products (Voorhuijzen et al., 2012;Martins-Lopes et al., 2013;Zhao et al., 2017). Nevertheless, many shortcomings encountered during the experimental procedure (e.g., DNA fragmentation and cross-reaction of DNA from similar species present in the same food sample) could significantly alter the outcome (Lo & Shaw, 2018;Wadood et al., 2020). ...
Traceability has established itself as an essential tool of the agri-food business to improve consumers’ safety and confidence and support regulatory authorities in food control and fraud detection. Indeed, traceability has extensively demonstrated to profitably unmask frauds in terms of adulteration, species or even cultivar substitution, and not least, product provenance, by combining a variety of advanced analytical techniques with chemometrics. In this chapter, the state-of-the-art of Opuntia ssp. traceability is discussed with particular emphasis to the species Opuntia ficus-indica (L.) Miller and its cultivars, originating from the Mediterranean area. At an earlier stage, studies chemically characterized fruits of the prickly pear cactus and its derived products (i.e., fruit juice and seed oil), already pointing out peculiar compositional profiles in dependence of the geographical provenance or even cultivar. However, only recently, the screening of minerals, volatile and phenolic compounds, was combined with the multivariate statistical analysis in an attempt to purposely trace the geographical origin of O. ficus-indica, as well as the cultivar it belongs. Overall, the traceability platforms designed so far may play a vital role in the product quality and safety assurance system. They revealed to preserve the authenticity of products from O. ficus-indica successfully, thus, protecting consumers against mislabeling and false information.
... In animal differentiation studies, SSR markers have been considered as "markers of choice" for a long time (Scarano & Rao, 2014). According to the International Society for Animal Genetics (ISAG), 12 SSRs is the recommended number of markers for bovine genetic identification, which in this case would be a more expensive assay (Scarano & Rao, 2014;Zhao et al., 2017 with low-cost methods that could be widely employed in routine food analysis laboratories. Among the simplest methods, SNP-based detection, was recently applied to measure the genetic variation and its application in food analysis. ...
To guarantee food safetyand sustainability, it is necessary to verify meat authenticity. This study focused on the development of single nucleotide polymorphism‐based polymerase chain reaction‐restriction fragment length polymorphism (SNP‐based PCR‐RFLP) and forensically informative nucleotide sequence (FINS) methodologies based on PCR amplification of the mitochondrial 12S rRNA gene for discrimination of six red meat species, that is, cattle, buffalo, goat, sheep, camel, and donkey. FINS allowed the unambiguous identification of all species analyzed. In addition, six SNPs, where a restriction site for TasI could be localized using a preliminary in silico analysis, gave a unique RFLP pattern for each species. The results revealed a low level of species substitution (8%) in the tested meat samples. In particular, one buffalo and goat samples have been substituted with cow and sheep, respectively. Finally, the developed techniques herein showed high potentials to be routinely used as reliable and fast tools to avoid meat species substitutions.
Practical Application
This research deals with genetic techniques to trace meats. This kind of research helps the concerned agencies to build capacity to safeguard consumer sentiments as well as providing better market access and better food price and quality for the consumer.
... The misidentification can arise from the mixing of records of animals on the farm, and during grazing mixing of animals can cause miscellaneous data, mixing of the labels, and sometimes mixing the artificial semen can cause mixing of genetic material between animals. Therefore, it is essential to establish the true parentage of the animals before establishing the breeding programs for expected gains (Sharma et al., 2015;Zhao et al., 2017). The people living in high altitudes depend upon Yak for their dairy needs, and mostly the feeding behavior of yak in these areas is grazing which can cause the mixing with other animals. ...
Conventional breeding programs have limitations while working with quantitative traits and traits with low heritability. Furthermore, the identification of defective genes that can cause the development of a disease cannot be identified through conventional strategies until the development of the disease. The Discovery of molecular markers has made it easier for animal breeders and animal geneticists to enhance the productivity of animal breeding programs. Different kinds of molecular markers, RAPDs, SNPs, AFLPs, QTLs, and SSR are being used in animal breeding for gene mapping, phylogenetic studies, disease resistance studies, genetic conservation, and genetic diversity. Molecular markers also provide the advantage of working with low heritability and complex quantitative traits. QTL markers are being used for quantitative traits like milk production meat production because they are linked to quantitative trait genes. Marker-assisted breeding has helped the breeding programs to increase the efficiency of the breeding programs. Molecular markers like SNPs can be used to detect the mutation in genes at an early age. Microsatellites have been used at a very large scale for phylogenetic identification. In this review, we will discuss the importance and application of molecular markers in animal breeding and genetics.
... Therefore, knowing the origin of cattle is a significant determining factor about the health status of cattle and the quality of the meat products. Moreover, Zhao et al. (2017) argued that confirming the health of the living cattle and identifying diseases early is important for increased consumer awareness as well as food safety in the supply chain. Cattle traceability does not only help in controlling the spreading of diseases, but also increases the opportunity for beef exports. ...
... Moreover, Zhao et al. (2017) argued that confirming the health of the living cattle and identifying diseases early is important, for increased consumer"s awareness and source demands, food safety in the supply chain. Cattle traceability does not only help in controlling the spreading of diseases, but also increase chances for beef exports. ...
... Microsatellite marker-based identifications allows effective breed identification without phenotypic information from living animals. A large number of studies based on microsatellite markers were reported in cattle breed identification (Zhao et al., 2017), pork traceability (Gvozdanović et al., 2020;Oh et al., 2014), tea variety identification (Hu et al., 2014), strawberry cultivar identification (Honjo et al., 2011), meat species identification (Song et al., 2017), etc. ...
Numerous influential animal breeds and plant varieties provide high-quality and nutritious foods for human. The popularity and high profit of premium foods usually accompany with adulterated products, which harmed rights of both consumers and law-abiding producers. So, it is necessary to build an effective breed identification system using genetic markers genotyped from meat products to safeguard public and increase confidence of consumers. To improve the accuracy of breed identification, six machine learning methods were evaluated using different number of breed tag single nucleotide polymorphisms (SNPs) and different size of training sets from 13 pig breeds. Herein, six machine learning methods were Naïve Bayes, Support Vector Machine (SVM), k-Nearest Neighbor, Random Forest (RF), Artificial Neural Networks and Decision Tree. Results showed that using breed tag SNPs increased identification accuracy compared with random SNPs. For SVM, accuracy of using 20 breed tag SNPs and 200 random SNPs were 99.30 (±0.14%) and 99.13 (±0.11%), respectively. Among the six methods, both RF and SVM methods were robust across all tested scenarios. Additionally, the accuracy of breed identification first increased with the size of training set and then remained stable in Test-in-training breeds test set. Overall, it can be deduced that breed tag SNPs, machine learning methods and training set size play important roles in ensuring the accuracy of breed identification.
... This can be achieved by analysis of sexual hormones (Draisci, Palleschi, Ferretti, Lucentini, & Cammarata, 2000;Hartwig, Hartmann, & Steinhart, 1997;Simontacchi, Marinelli, Gabai, Bono, & Angeletti, 1999) or gene amplification by polymerase chain reaction (PCR)-based procedures, for example, in pigs (Fontanesi, Scotti, & Russo, 2008). On the other hand, breed has been habitually assessed by genetic analyses such as genotyping, amplified fragment length polymorphism, single nucleotide polymorphism, and random amplification of polymorphic DNA, which have been employed in swine (Alves, Castellanos, Ovilo, Silió, & Rodrıfiguez, 2002;Fontanesi, Scotti, Gallo, Nanni Costa, & Dall'Olio, 2016;Zhao et al., 2018a), chicken (Du, Ding, Li, & Fang, 2017), and beef (Campos et al., 2017;Dalvit et al., 2008;Rogberg-Muñoz et al., 2014;Zhao et al., 2017). Other outspread techniques for breed determination purposes are spectroscopy-based, such as NIRS, which has been successfully used to discriminate beef meat from different breeds (Alomar, Gallo, Castañeda, & Fuchslocher, 2003). ...
With globalization and complex distribution systems, the increase of food adulteration has become a significant concern for manufacturers, researchers, governments, and consumers. A collective approach is needed to identify all stakeholders in the food supply chain, to verify their qualification, and to exclude those who do not meet the required standards through all levels of food supply and production. Food authentication is a broad range of efficient activities, which is rapidly growing due to increasing public awareness concerning food quality and safety. Food products can be verified based on their chemical composition, botanical sources, specified geographical origin, or possible adulterations by modern analytical methods. This chapter represents a detailed explanation about critical concepts including “authentication,” “traceability,” and “labeling” followed by a systematic discrimination of authentication on different food products. Classification of different food products is based on authenticity indicators providing insight into future developments. The most common adulteration methods have been explained for different categories of food products. This chapter also presents critically the analytical techniques that are used for authenticity assessment, their operation, together with their advantages and drawbacks, in order to show different strategies for food authentication. A wide range of the currently available multivariate pattern recognition tools for detecting food adulteration are also represented.
... By analyzing microsatellites, it has been possible to distinguish between different types of cocoa varieties [25]. Similar procedures exist for the differentiation of olive oil [84,85], wine [86], potato varieties [87], and meat [88]. ...
In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and thus the safety of food is one of the central questions for actors from science, politics and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis.
In the past five years, non‐targeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further non‐targeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding high‐resolution laboratory infrastructure and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of non‐targeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.
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... DNA-based identification could be extremely useful for traceability. However, the cost of using DNA analysis is one of its major limitations, and research has been carried out to develop fast and low-cost tests by using a low number of DNA markers [13][14][15][16][17]. Microsatellite markers or simple tandem repeats (STR), available for all livestock species, are commonly used for many applications such as parentage analysis and breed assignment [18]. ...
Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost.
... Despite the relatively higher price, yak meat and its products are still very popular, however yak meat is less available with seasonal variation and relatively lower output compared with more common cattle (Bos taurus) beef ( Li et al., 2015). A common problem is the fraudulent marketing and sale of cattle beef as yak meat for commercial profit ( Zhao et al., 2017), which not only hurts consumers' interests, but also undermines the normal market order. Thus, there is a growing need for an accurate and sensitive method that allows the discrimination of meat from yak and cattle, ensuring the quality of yak meat and its products and protecting the interests of consumers and yak meat producers. ...
... Through domestic and foreign literature analysis, it can be seen that the traceability information first uses the QR code, RFID tags, and DNA as product identifiers and then obtains product information through manual or semi-automatic methods. The improvement of information acquisition capabilities has significantly improved the quality and safety management capabilities of products, but at the same time, there are still many problems in information collection, such as the low degree of automation of information acquisition, the lack of seamless linking of information, and the acquisition of information with "large granularity" [14][15][16]. ...
In view of the problems existing in the processing of duck products, such as complicated technology, difficulties in information collection and information linkage, and lack of dedicated information collection equipment, the duck product traceability information of the Institute of Things automatic collection system was developed. Acquisition system is mainly composed of sensing terminals, bus structure, and host computer management system. Perceiving the terminal can automatically perceive the information of each link and transmit the perception information to the upper computer management system through the bus. The upper computer management system realizes the functions of storing the sensing information, intelligent analysis, and alarm prompting. The long-term operation results show that the system performance is stable and reliable; the collection of data is efficient, complete, and accurate; and the degree of automation of the system is high, which significantly improves the product quality and safety supervision capabilities of the company.
Rapid assays allowing for on-site or in-field testing can enable us to detect food contamination in a timely manner, thus facilitating the insurance of food safety. Isothermal nucleic acid amplification has emerged as a tool for rapid and high-efficiency signal amplification for both nucleic acid and non-nucleic acid targets. In this review, we outline how the features of isothermal amplification techniques have been leveraged for food safety analysis, and present the principles of isothermal amplification techniques. We then introduce isothermal amplification-based approaches for foodborne pathogen and authenticity analysis by detecting nucleic acid markers. Further, the techniques for heavy metal, mycotoxin and antibiotic detection by isothermal amplification combined with functional nucleic acids were reviewed. And particularly, imaging methods enabled by isothermal amplification for in situ analyzing foodborne pathogens are highlighted. Current limitations of these technologies, such as robustness and enzyme preservation, that hinder broad application, are also discussed.
Nowadays, stable isotope technology, DNA technology, spectroscopic technology, volatilomics technology, metabolomic analysis, mineral elements analysis and fatty acid analysis have been used to trace the origin of beef. Stable isotope technique is often combined with mineral elements analysis. Both of them have the advantages of high accuracy and low detection limit. Stable isotopes may be affected by geography and dietary history. The mineral elements analysis has high requirements for experimental operation. DNA technology is not affected by geography and dietary history, so it has unique advantages. It faces the problem of selecting molecular markers. Spectroscopic technology and volatilomics technology based on electronic nose do not require sample pretreatment. The limitation is that infrared and Raman are insensitive, and the data processing of hyperspectral image is difficult. Raman is much less sensitive than Infrared. The use of electronic nose has higher requirements for environment. Volatilomics technology based on mass spectrometry (MS), metabolomic analysis and fatty acid analysis have been used to analyze organic components. They can provide comprehensive information, but they have higher requirements for sample preservation. Metabolomic analysis equipment is expensive. The research on traceability and authenticity of beef can help to ensure the security and quality of beef.
Traceability systems have become necessary, especially for beef products, to protect consumers’ health. Aims of this study were to validate and to test a set of 12 microsatellite (STR) markers for the assessment of a genetic traceability system in six cattle breeds. The probability to find, by chance, two individuals sharing the same profile at the studied loci, was computed considering different number of STR, pooling the alleles in each breed, in the total population and in the dairy and beef population separately. Best results were then obtained considering match probabilities per breed. In this study, genotyping the five most polymorphic loci, the probability of finding two identical animals was approximately five in one million. Match probability values increased when the pooled marker sets were used, but were still satisfactory; moreover, use of the pooled marker sets will reduce the cost of analyses.
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.
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.
DNA fingerprinting allows the verification of conventional methods used to implement beef traceability. At any point along the supply chain, the identity of an animal or piece of meat can be checked by comparison of its DNA profile with an initial sample. Practical application of DNA fingerprinting to trace beef requires a choice of DNA markers as well as the optimization of sampling methods. This has been achieved as the result of collaboration between meat technicians and geneticists over a period of 4 years. The discrimination power of nine highly polymorphic microsatellite markers was evaluated. We propose that three markers (with a 0.001 probability that two individual profiles match by chance) are adequate for routine tests. Two key points along the production-commercialization chain where sampling must be systematic were defined: (i) the tagging of the calf (identity control) and (ii) after slaughter (slaughter control), before the animal loses its external appearance. The identity control was blood collected on a filter paper adapted to the ear tag; the slaughter control was the tagged ear itself. These constituted the control samples, which were archived with a code matching the individual tag number. Test samples were obtained on a random basis from live animals, carcasses, and pieces of meat at cutting halls and at the retail outlet and in cases when the verification of identity was needed. The DNA profiles of the test samples and the controls were then obtained and compared, to verify either an individual identity or the origin of a piece of meat from the stated animal.
Microsatellites (SSR--simple sequence repeats, STR--short tandem repeats, SSLP--simple sequence length polymorphism, VNTR--variable number of tandem repeats) are the class of repetitive DNA sequences present in all living organisms. Particular characteristics of microsatellites, such as their presence in the genomes of all living organisms, high level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping and positional cloning of genes. The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions between inversely oriented closely spaced microsatellites; and (3) SAMPL (selective amplification of microsatellite polymorphic loci), which utilises AFLP (amplified fragment-length polymorphism) methodology, with one exception--for the second amplification, one of the starters is complementary to the microsatellite sequence. The usefulness of the three above-mentioned markers for numerous purposes has been well documented for plants.
Highly informative genetic markers are essential for efficient management of cattle populations, as well as for food safety. After a decade of domination by microsatellite markers, a new type of genetic marker, single nucleotide polymorphism (SNP), has recently appeared on the scene. In the present study, the exclusion power of both kinds of markers with regards to individual identification and parental analysis was directly compared in a Galloway cattle population. Seventeen bovine microsatellites were distributed in three incremental marker sets (10, 14 and 17 microsatellite markers) and used for cattle genotyping. A set of 43 bovine SNP was used for genotyping the same cattle population. The accuracy of both kinds of markers in individual identification was evaluated using probability of identity estimations. These were 2.4 x 10(-8) for the 10 microsatellite set, 2.3 x 10(-11) for the 14 microsatellite set, and 1.4 x 10(-13) for the 17 microsatellite marker set. For the 43 SNP markers, the estimated probability of identity was 5.3 x 10(-11). The exclusion power of both kinds of markers in parental analysis was evaluated using paternity exclusion estimations, and, in addition to this, by estimation of the parental exclusion probability in 18 Galloway family trios. Paternity exclusion was estimated to be over 99% for microsatellites, and approx. 98% for SNP. Both, microsatellite and SNP sets of markers showed similar parental exclusion probabilities.
Identifying genetic diversity patterns is fundamentally important for effective species management and conservation. In this study, we used five microsatellite loci to investigate the genetic diversity and population differentiation of Achyranthes bidentata in Dao Di and its surrounding region. Our analysis of microsatellite data indicated the level of genetic diversity of A. bidentata (HT = 0.333) was lower than other plants. The results showed no significant genetic diversity differences and population genetic differentiation between the Dao Di and surrounding region. Significant temperature differences (Bio2: mean diurnal range and Bio7: temperature annual range) were found between the Dao Di and surrounding region, which may improve the accumulation of medicinal ingredients of populations in the Dao Di. The populations of A. bidentata were divided into two genetic groups, which was caused by five temperature variables (Bio1, Bio4, Bio7, Bio9, and Bio11). This study thus provides an important case for over-collecting within limited ranges in affecting population diversity and bioclimate variables for different producing area in driving population differentiation.
The author explores the variations in the domestic livestock populations worldwide between 1961 and 1998, and observes a marked increase in the swine population, as compared to other domestic species. Trends in international trade of live animals over the same period are also analysed; international trade involved 1% of livestock world-wide and the international meat market constituted 10% of total meat production. The various stages of the food chain are analysed, from farm to fork, with emphasis on those elements to which the concept of traceability is applicable; from the composition of bovines, to slaughter, and through the various products and sub-products all the way to the final product consumed. Against this background, the characteristics of identification systems for individual animals and animal products is described, as well as applications to traceback and trace forward. To conclude, the author details the factors which influence the various processes of identification and traceability, and thus must be considered when choosing a system. The wide variability amongst systems world-wide is noted and attributed to the differences in sanitary and economic or socio-cultural criteria. The author therefore recommends that work should begin on international harmonisation of such systems.
Cattle (Bos taurus) is an important meat food source for humans. STR loci have been extensively used for parentage testing in high demand by the animal breeding industry, but have also shown useful for forensic purposes to carry out identification of stolen animals or ones involved in traffic accidents. The International Panel of Microsatellites for Cattle Parentage Testing established 12 microsatellites for cattle parentage analysis (ISAG 2008). At present, there are few commercial kits for meat traceability and cattle parentage testing. In this study, based on a data set of 431 animals, an assessment of the Finnzymes Bovine Genotype™ panel with 12 STRs (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA122, TGLA126, TGLA227, and TGLA53) is reported for forensic investigations. Genotypes from STR loci were used to calculate the power of exclusion, matching probability, power of discrimination, and null allele frequencies and check the power of these loci as a minimum standard for identity and kinship analysis.
Breed assignment has proved to be useful to control meat trade and protect the value of special productions. Meat-related frauds have been detected in China; therefore, 95 SNPs selected from the ISAG core panel were evaluated to develop an automated and technologically updated tool to screen breed label fraud in the Chinese meat market. A total of 271 animals from four Chinese yellow cattle (CYC) populations, six Bos taurus breeds, two Bos indicus and one composite were used. The allocation test distinguished European, Japanese and Zebu breeds, and two Chinese genetic components. It correctly allocated Japanese Black, Zebu and British breeds in 100, 90 and 89% of samples, respectively. CYC evidenced the Zebu, Holstein and Limousin introgression. The test did not detect CYC components in any of the 25 samples from Argentinean butchers. The method could be useful to certify Angus, Hereford and Japanese Black meat, but a modification in the panel would be needed to differentiate other breeds.
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Current traceability systems are characterized by the inability to link food chains records, inaccuracy and errors in records and delays in obtaining essential data, which are fundamental in case of food outbreak disease; these systems should address the recall and withdraw of non-consumable products. The present paper provides a review of the various latest technological advancements such as innovative implementations of RFID that can make to increase the sales of wheat flour, or allowing the consumer to know the full record of the IV range products through the smartphone; knowing the food authenticity with an isotope analysis or by analysing the DNA sequences. There are also presented some conceptual advancements in the field of food traceability such as the development of a common framework towards unifying the present technical regulations, the interconnectivity between agents, environment loggers and products, all of them in the form of Internet of things system as well as the development of intelligent traceability, where it is possible to retrieve the temperature of a product or its remaining shelf-life.
In livestock, breed assignment may play a key role in the certification of products linked to
specific breeds. Traceability of farm animals and authentication of their products can
contribute to improve breed profitability and sustainability of animal productions with
significant impact on the rural economy of particular geographic areas and on breed and
biodiversity conservation. With the goal of developing a breed genetic traceability system for
Girgentana dairy products, the aim of this study was to identify specific microsatellite
markers able to discriminate among the most important Sicilian dairy goat breeds, in order to
detect possible adulteration in Girgentana dairy products. A total of 20 microsatellite markers
were analyzed on 338 individual samples from Girgentana, Maltese, and Derivata di Siria
goat breeds. Specific microsatellite markers useful for traceability of dairy products were
identified. Eight microsatellite markers showed alleles present at the same time in Maltese
and Derivata di Siria and absent in Girgentana and, therefore, they were tested on DNA pools
of the three breeds. Considering the electropherograms’ results, only FCB20, SRCRSP5, and
TGLA122 markers were tested on DNA samples extracted from cheeses of Girgentana goat
breed. These three microsatellite markers could be applied in a breed genetic traceability
system of Girgentana dairy products in order to detect adulteration due to Maltese and
Derivata di Siria goat breeds.
In livestock, breed assignment may play a key role in the certification of products linked to specific breeds. Traceability of farm animals and authentication of their products can contribute to improve breed profitability and sustainability of animal productions with significant impact on the rural economy of particular geographic areas and on breed and biodiversity conservation. With the goal of developing a breed genetic traceability system for Girgentana dairy products, the aim of this study was to identify specific microsatellite markers able to discriminate among the most important Sicilian dairy goat breeds, in order to detect possible adulteration in Girgentana dairy products. A total of 20 microsatellite markers were analyzed on 338 individual samples from Girgentana, Maltese, and Derivata di Siria goat breeds. Specific microsatellite markers useful for traceability of dairy products were identified. Eight microsatellite markers showed alleles present at the same time in Maltese and Derivata di Siria and absent in Girgentana and, therefore, they were tested on DNA pools of the three breeds. Considering the electropherograms’ results, only FCB20, SRCRSP5, and TGLA122 markers were tested on DNA samples extracted from cheeses of Girgentana goat breed. These three microsatellite markers could be applied in a breed genetic traceability system of Girgentana dairy products in order to detect adulteration due to Maltese and Derivata di Siria goat breeds.
The concept of food traceability can be traced back 5000 years to Egyptian society. Over the last decade, traceability has become recognized as an essential food safety and food quality tool. Food safety legislation and voluntary standards have delineated different traceability frameworks, which can be assigned to two models: a generic, low-warranty traceability procedure or a specific, high-warranty traceability procedure. The latter is based on the documentation of the material and information collected from an organization and among parties in a supply chain. A risk-assessment based approach is needed to determine the best traceability procedure for each food product produced by a specific organization. This paper focuses on a medium-sized enterprise case-study operating in the poultry meat supply chain. The benefits and difficulties of implementation of a traceability system were discussed. This surveyed case-study provides a partial explanation as to why traceability in this sector is mainly being driven by food safety regulations, even if it also has potential as a visible value-added marketing tool. The lack of process automation is the underlying reason for complex implementation of a specific high-warranty traceability tool. A perspective schematic of straightforward traceability implementation is finally illustrated.
Development of DNA technologies makes today possible implementation of conventional beef traceability systems with molecular methods. In the recent past, microsatellites have been the most used marker for individual assignment, however single nucleotide polymorphisms (SNPs) is now replacing them. With the aim to provide a set of SNPs useful for bovine meat traceability we have tested 63 SNPs for the ability to identify single individuals in six European cattle breeds. Eighteen highly informative SNPs located in different genes, have been selected. By using this panel of SNPs the probability that one individual is incorrectly assigned ranges from 1.39 to 0.07 out of 1 million, depending on the breed.
Consumer concerns about beef demands instruments to assure its traceability. A methodology using DNA markers is proposed for beef identification focussing on a Spanish beef certification, Ternera de Navarra (Beef of Navarra). To validate this methodology the number of markers used and the implications of population structure in individual identification were evaluated. In order to get practical implementation, the sampling levels required, depending on the number of markers and amount of possible fraud, is also discussed. Using at least eight very informative markers the origin of retailed meat is always found independent of genetic population structure. The total control of fraud would be very expensive using large-scale application of DNA analyses and a strategy based on anonymous sampling is proposed.
To set up routine assays for molecular meat traceability along the food chain, the availability of a simple and low cost test for the identification of cattle carcasses is required. For this purpose, we evaluated 13 microsatellites for their ability in the identification of animals belonging to four Italian cattle breeds. Here we propose a criterion for a microsatellite-based test with the best reliability when reducing the number of loci to be analysed. The method is based on the observation that in the same loci breeds can show differences in frequencies and number of fixed alleles. This non-uniform distribution of alleles between breeds results in differences in the informative content of the same loci in different breeds. Taking into account these differences, it is possible to perform tests for the allocation of samples to specific animals utilizing a small number of microsatellites. The proposed approach allows cost reduction and ease in performing the analyses.
The polymorphism distributions of 14 microsatellite loci were detected using the Bovine Paternity PCR Typing Kit (including 11 X-STR) and 3 selected Y-STR microsatellite DNA markers. The genetic diversity were evaluated, and the feasibility of the application to individual identification and paternity testing were discussed. The results showed that all the 14 microsatellite loci had genetic polymorphisms in bulls, and the polymorphism information content (PIC) in loci MCM158 was the biggest (0.888), while the ETH10 was the lowest (0.482). Power of discrimination (DP) value of the 14 STR loci ranged from 0.715 to 0.968. The Cumulate DP (CDP) was 99.99%, and the Cumulate PE (CPE) also reached 99.99%. These results indicate that the 14 microsatellites can be applied to the individual identification.
We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.
The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are > 0.9999 in all four breeds when all 23 microsatellites are used and > 0.98 with only the two most polymorphic multiplexes.
The author explores the variations in the domestic livestock populations world-wide between 1961 and 1998, and observes a marked increase in the swine population, as compared to other domestic species. Trends in international trade of live animals over the same period are also analysed; international trade involved 1% of livestock world-wide and the international meat market constituted 10% of total meat production. The various stages of the food chain are analysed, from farm to fork, with emphasis on those elements to which the concept of traceability is applicable; from the composition of bovines, to slaughter, and through the various products and sub-products all the way to the final product consumed. Against this background, the characteristics of identification systems for individual animals and animal products is described, as well as applications to traceback and trace forward. To conclude, the author details the factors which influence the various processes of identification and traceability, and thus must be considered when choosing a system. The wide variability amongst systems world-wide is noted and attributed to the differences in sanitary and economic or socio-cultural criteria. The author therefore recommends that work should begin on international harmonisation of such systems.
Individual animals differ from each other on a number of biological levels. At the most basic level, the deoxyribonucleic acid (DNA) of each animal is different, and transcription of the DNA code yields variations at the protein level, which in turn give rise to individual diversity at the physical level. In recent years, accessing the primary genetic code of individual animals has become straightforward. The authors briefly review the development of biological identification technologies and then consider in more detail the application of current DNA testing technologies to issues of traceability of live animals and derived products. Although largely focused on cattle and beef traceability, the principles described are relevant to ovine, porcine and equine traceability. The accelerating pace of innovation and development within the field of molecular genetics suggests that the technologies described may soon be superseded. However, the principles of genetic identification will remain unchanged.
Since the 1980s, concerns about the safety and quality of food have increased at both governmental and consumer levels. The importance of traceability of animals and animal products has grown as food production and marketing have been removed from direct consumer control. Product traceability, which requires a transparent chain of custody to maintain credibility and to complete information transfer functions, has two components, namely: a unique identification system, and a credible and verifiable mechanism for identity preservation. Traceability systems can be subdivided into the following four categories: country of origin; retail; processor; and farm-to-retail identity. Although the availability of computers and electronic data devices can enhance the speed and accuracy of data acquisition and manipulation, a common set of developmental criteria exists, irrespective of data-handling processes. As data management technologies become more powerful and less costly, product traceability requirements will multiply. Public and private sectors should seize these opportunities to improve public health and quality parameters, or risk a narrowing of their markets.
The genetic diversity of 9 Chinese native cattle breeds and 3 introduced breeds were analyzed using 12 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations (FAO) and the International Society of Animal Genetics (ISAG) through fluorescence-multiple PCR. According to the allele frequencies of 12 microsatellite locus, mean heterozygosity (H), polymorphism information content (PIC) , DA and DS genetic distances were calculated for each breed. Cluster analysis based on UPGMA method indicated that 12 breeds were clustered into four groups. Group I belonged to the southern-China cattle including Enshi, Liping, Zhaotong and Chuannan Mountainous; Group II belonged to the central-China cattle including Jiaxian Red and Zaosheng, Pinglu Mountainous; Group III belonged to the northern-China cattle including Yanbian and Changbai; Group IV consisted of foreign breeds including Germany Yellow, Simmental and Charolais. The results may provide an academic basis for preservation and utilization of Chinese native cattle breeds.
Studies on population genetic diversity and microsatellite markers for growth traits in Luxi cattle
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Research on software architecture of food safety traceability system based on trust computing
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Individual identification of bulls based on microsatellite markers
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Introspection of import and export food safety supervision in China from meat adulteration case
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Current status and countermeasures of meat safety and risk in China
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Individual identification of the Yangtze finless porpoises Neophocaena phocaenoides asiaeorientalis inhabiting the Tian-e-Zhou Natural Reserve based on microsatellite fingerprints
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Effects analysis of two cattle pupolations in the west of China crossed by Limousin cattle
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The software of ModifiedePowerstates used in forensic biological statistics
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Study on genetic diversity and classification of the yak
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