1
|
Jasielczuk I, Gurgul A, Szmatoła T, Radko A, Majewska A, Sosin E, Litwińczuk Z, Rubiś D, Ząbek T. The use of SNP markers for cattle breed identification. J Appl Genet 2024; 65:575-589. [PMID: 38568414 DOI: 10.1007/s13353-024-00857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/10/2023] [Accepted: 03/12/2024] [Indexed: 08/09/2024]
Abstract
A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods ("delta" and two FST-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure.
Collapse
Affiliation(s)
- Igor Jasielczuk
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1C, 30-248, Kraków, Poland.
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1C, 30-248, Kraków, Poland
| | - Tomasz Szmatoła
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1C, 30-248, Kraków, Poland
| | - Anna Radko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Anna Majewska
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Ewa Sosin
- Department of Animal Nutrition and Feed Science, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Zygmunt Litwińczuk
- Sub-Department of Cattle Breeding and Genetic Resources Conservation, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Dominika Rubiś
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| |
Collapse
|
2
|
Zhao J, Li A, Jin X, Pan L. Technologies in individual animal identification and meat products traceability. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2019.1711185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Jie Zhao
- Department of Agri-food Safety, Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing, PR China
- Department of Agri-food Safety, Risk Assessment Laboratory for Agro-products (Beijing), Ministry of Agriculture, Beijing, PR China
| | - An Li
- Department of Agri-food Safety, Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing, PR China
- Department of Agri-food Safety, Risk Assessment Laboratory for Agro-products (Beijing), Ministry of Agriculture, Beijing, PR China
| | - Xinxin Jin
- Department of Agri-food Safety, Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing, PR China
- Department of Agri-food Safety, Risk Assessment Laboratory for Agro-products (Beijing), Ministry of Agriculture, Beijing, PR China
| | - Ligang Pan
- Department of Agri-food Safety, Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing, PR China
- Department of Agri-food Safety, Risk Assessment Laboratory for Agro-products (Beijing), Ministry of Agriculture, Beijing, PR China
| |
Collapse
|
3
|
Aguiar JDP, Fazzi-Gomes PF, Hamoy IG, Dos Santos SE, Sampaio I. Tracing individuals and populations of the tambaqui, Colossoma macropomum (Cuvier, 1818), from Brazilian hatcheries using microsatellite markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2998-3004. [PMID: 30478936 DOI: 10.1002/jsfa.9513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND In recent years, tracing of alimentary produce of animal origin has become increasingly important, for economic, food safety and ecological reasons. The tambaqui, Colossoma macropomum, is the native fish most farmed in Brazil. The reliable identification of the origin of tambaquis (wild or farmed) offered for sale to the general public has become necessary to satisfy regulatory norms and uphold consumer confidence. Molecular methods based on the analysis of DNA sequences have often been used to evaluate the potential for tracing farmed fish, given their reliability and precision. RESULTS Full likelihood and Bayesian approaches proved to be the most efficient for the identification, respectively, of individuals and populations for most of the fish sampled from seven hatcheries and one wild stock. The exclusion method and genetic distances were the least effective approaches for the identification of individuals and populations. The Bayesian method identified correctly more than 99% of the fry from most stocks, except those of the Santarém hatchery and River Amazon wild stock, which presented the best results for individual identification. CONCLUSIONS The identification of populations was effective for most hatcheries, although the identification of individuals from most stocks was hampered by the reduced genetic variability. © 2018 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jonas da Paz Aguiar
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
| | - Paola F Fazzi-Gomes
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Igor G Hamoy
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Sidney Eb Dos Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Iracilda Sampaio
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
| |
Collapse
|
4
|
Soglia D, Sacchi P, Sartore S, Maione S, Schiavone A, De Marco M, Bottero MT, Dalmasso A, Pattono D, Rasero R. Distinguishing industrial meat from that of indigenous chickens with molecular markers. Poult Sci 2018; 96:2552-2561. [PMID: 28419370 DOI: 10.3382/ps/pex077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/17/2017] [Indexed: 11/20/2022] Open
Abstract
The aim of investigation was to evaluate a traceability system to detect industrial chicken meat among indigenous products, considering issues that could affect assignment accuracy. The dataset included 2 Italian indigenous meat breeds, namely Bionda Piemontese (2 ecotypes) and Bianca di Saluzzo, one broiler line, and 3 layer lines. Assignment tests were performed using a standard panel of 28 microsatellite loci. To evaluate effects of inbreeding and substructure on assignment accuracy, a simulated dataset was prepared. Broilers and layers belong to homogeneous populations and never enter the clusters of indigenous breeds. Ambiguity or misallocation are expected between the Bionda ecotypes and between the 2 indigenous breeds, but it is unlikely that niche products provided by Bionda and Bianca will compete with one another. Non-random mating reduces accuracy, but only populations having weak genetic differentiation are involved, namely those that are less interesting to discriminate. The dataset can be used as a reference population to distinguish commercial meat from indigenous meat with great accuracy. Misallocations increase as number of loci decreases, but only within or between the indigenous breeds. A subpanel of the most resolving 14 loci keeps sufficient informative content to provide accuracy and to correctly allocate additional test samples within the reference population. This analytical tool is economically sustainable as a method to detect fraud or mislabeling. Adoption of a monitoring system should increase the value of typical products because the additional burden of molecular analyses would improve commercial grade and perception of quality.
Collapse
|
5
|
El Sheikha AF, Mokhtar NFK, Amie C, Lamasudin DU, Isa NM, Mustafa S. Authentication technologies using DNA-based approaches for meats and halal meats determination. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2017.1369886] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Aly Farag El Sheikha
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, Shibin El Kom, Egypt
| | - Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Products Research Institute, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Ceesay Amie
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shuhaimi Mustafa
- Laboratory of Halal Products Research Institute, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| |
Collapse
|
6
|
Protected Designation of Origin (PDO), Protected Geographical Indication (PGI) and Traditional Speciality Guaranteed (TSG): A bibiliometric analysis. Food Res Int 2017; 103:492-508. [PMID: 29389640 DOI: 10.1016/j.foodres.2017.09.059] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/16/2017] [Accepted: 09/21/2017] [Indexed: 11/22/2022]
Abstract
Despite the importance of the literature on food quality labels in the European Union (PDO, PGI and TSG), our search did not find any review joining the various research topics on this subject. This study aims therefore to consolidate the state of academic research in this field, and so the methodological option was to elaborate a bibliometric analysis resorting to the term co-occurrence technique. Analysis was made of 501 articles on the ISI Web of Science database, covering publications up to 2016. The results of the bibliometric analysis allowed identification of four clusters: "Protected Geographical Indication", "Certification of Olive Oil and Cultivars", "Certification of Cheese and Milk" and "Certification and Chemical Composition". Unlike the other clusters, where the PDO label predominates, the "Protected Geographical Indication" cluster covers the study of PGI products, highlighting analysis of consumer behaviour in relation to this type of product. The focus of studies in the "Certification of Olive Oil and Cultivars" cluster and the "Certification of Cheese and Milk" cluster is the development of authentication methods for certified traditional products. In the "Certification and Chemical Composition" cluster, standing out is analysis of the profiles of fatty acids present in this type of product.
Collapse
|
7
|
Zhao J, Zhu C, Xu Z, Jiang X, Yang S, Chen A. Microsatellite markers for animal identification and meat traceability of six beef cattle breeds in the Chinese market. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.03.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
Breed traceability of buffalo meat using microsatellite genotyping technique. Journal of Food Science and Technology 2017; 54:558-563. [PMID: 28242954 DOI: 10.1007/s13197-017-2500-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/06/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Although buffalo has emerged as a major meat producing animal in Asia, major research on breed traceability has so far been focused on cattle (beef). This research gap on buffalo breed traceability has impelled development and validation of buffalo breed traceability using a set of eight microsatellite (STR) markers in seven Indian buffalo breeds (Bhadawari, Jaffaarabadi, Murrah, Mehsana, Nagpuri, Pandharpuri and Surti). Probability of sharing same profile by two individuals at a specific locus was computed considering different STR numbers, allele pooling in breed and population. Match probabilities per breed were considered and six most polymorphic loci were genotyped. Out of eight microsatellite markers studied, markers CSSMO47, DRB3 and CSSM060 were found most polymorphic. Developed technique was validated with known and unknown, blood and meat samples; wherein, samples were genetically traced in 24 out of 25 samples tested. Results of this study showed potential applications of the methodology and encourage other researchers to address the problem of buffalo traceability so as to create a world-wide archive of breed specific genotypes. This work is the first report of breed traceability of buffalo meat utilizing microsatellite genotyping technique.
Collapse
|
9
|
DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy. DIVERSITY-BASEL 2015. [DOI: 10.3390/d8010002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|