Genomics

The Laboratory of population genetics and traceability of animal organisms

The laboratory of population genetics and traceability of animal organisms, led by the Associate Professor Alexandros Triantafyllidis, supply genetic and genomic services and it is established in the Aristotle University of Thessaloniki Campus as well as in the new facilities of the Center for Interdisciplinary Research and Innovation of the Aristotle University. The laboratory’s equipment includes a SeqStudio Genetic Analyzer System (AppliedBiosystems) as well as StepOne Real-time PCR machines (AppliedBiosystems).

The provided services are mainly associated with:

  • Genetic identification of species in food products
  • Traceability of animal species in food products
  • Genetic counselling for the conservation and management of wild and farmed populations
  • Origin traceability of wild and hatchery individuals
  • Genomic characterization of livestock species

In this context, the lab has successfully accomplished, among others, the following projects:

  • Qualitative analyses of species composition in fish food
  • Qualitative and quantitative genetic analyses of species composition in meat products
  • Controls for the substitution of fish species in Greek and Bulgarian seafood and food samples
  • Genetic control, DNA identification and management of animal species populations
Genetic identification of species in food products

The authenticity of fish products is important, especially when it is known that there are phenomena of involuntary or deliberate mislabelling in the European and global market as well (Marko et al., 2004). Additionally, the adulteration or the mislabelling may be dangerous due to the unknown toxic or allergenic substances which may be present in a product (Ward et al. 2008, Wong & Hanner 2008, Holmes et al. 2009). Unfortunately, species identification is not always easy. Many fish species have a similar taste or morphological characteristics and sometimes may lack diagnostic parts of their body (e.g. skin, head, tail, fins) or they have been processed and being sold as fillets or slices.  The DNA techniques used for food analysis can enhance the safety and the authentication of products on the market and can also increase their commercial value.

DNA barcoding:  A fast and flexible method

Our laboratory has developed a “DNA barcoding” method for the genetic identification of fish species. Specifically, DNA sequencing and universal primers are used for the species determination in different fish products (fresh, frozen, processed, etc).

Commonly consumed fishes that can be detected:

AmberjackSalmon
CodSardine
DentexSea bass
EelSea bream
GrouperSole
HakeSwordfish
MackerelTrout
PerchTuna
Redfishand many more

Advantages

  • Reliable results
  • The universal approach enables the identification of all commonly consumed fish species
  • No prior knowledge about the expected species necessary
  • Highly experienced staff
  • Handling multiple samples per day
  • Special tests for difficult samples (closely related species, highly processed samples)
Traceability of animal species in food products

The nutritional scandal in 2013, underlined the significance of the genetic tests in meat products. Our laboratory provides services for species identification in meat products to verify their safety and authenticity. Nowadays, the need for such controls is more urgent taking into consideration the increasing consumers’ demand for safe products and accurate information on the labels.

Fast and reliable results

Reliable genetic tests of meat products can play an important role in their authenticity and can increase their commercial value. Our laboratory is equipped with the appropriate expertise and can provide reliable solutions to various queries. Services of both qualitative and (semi)-quantitative genetic species identification are offered using species-specific approaches and conventional and real-time PCR. We are at your disposal to find out the most appropriate method depending on your query.

Applicability of the methods

The used methods can be applied for the analysis of a variety of products (raw, processed, cooked). These methods can also be used to analyse highly processed products with degraded DNA.

These methods can be used for the genetic identification of the following species:

PorkGoat
SheepChicken
BeefHorse

Both conventional and real-time PCR can be used for the identification of animal species with a low limit of detection. The used methods are both specific and sensitive even in products which are mixtures of different animal or plant species.

Advantages

  • Reliable results
  • Different approaches depending on the query
  • Qualitative and (semi) quantitative determination of any fraud
  • The low limit of detection
  • Highly experienced staff
  • Handling multiple samples per day
Genetic counselling for the conservation and management of wild and farmed populations 

The laboratory uses classic DNA markers, i.e. protein genes, mitochondrial DNA, microsatellites, as well as NGS markers like SNPs depending on the questions asked. We have provided genetic analysis and counselling on many conservation and management projects for various species: dog, brown bear, wild boar, red deer, bovine, ovine, donkey, horse, hare, ferret, ground squirrel, rock and grey partridge, lizards, lobster and various fish species.

Origin traceability of wild and hatchery individuals

A large number of genetic markers has been used in the past for the genetic identification of the origin. Nowadays, the Single Nucleotide Polymorphisms (SNPs) is the state-of-the-art marker for such an analysis. In collaboration with European projects, we have established a large genomic reference database for the genetic comparison and identification of the origin for the two most commercial fishes in Europe, the sea bream and the sea bass. In particular, for these two species, we have developed an efficient, high fidelity and cost-effective genomic traceability tool for the identification of the origin stock (natural/farmed).

Genomic characterization of livestock species

Livestock species (e.g. sheep and goat) constitute an important economic sector for our country. The genomic improvement of the interest species regarding their products, such as milk yield and quality, meat, wool etc. is widely performed through single nucleotide polymorphisms (SNPs) which scan the whole genome to identify regions associated with the desirable phenotypic characters. In the framework of a European program, we analyze the genome of the Chios Greek sheep breed which is well known for high milk yield as well as fertility.  

Publications

Clusa, L., Ardura, A., Gower, F., Miralles, L., Tsartsianidou, V., Zaiko, A., Garcia-Vazquez, E. (2016). An easy phylogenetically informative method to trace the globally invasive Potamopyrgus mud snail from river’s eDNA. PloS one, 11(10), e0162899.

Devloo-Delva, F., Miralles, L., Ardura, A., Borrell, Y. J., Pejovic, I., Tsartsianidou, V., & Garcia-Vazquez, E. (2016). Detection and characterisation of the biopollutant Xenostrobus securis (Lamarck 1819) Asturian population from DNA Barcoding and eBarcoding. Marine Pollution Bulletin, 105(1), 23-29.

Garcia-Vazquez, Ε., Perez, J., Martinez, J. L., Pardinas, A. F., Lopez, B., Karaiskou, N., Casa, M. F., Machado-Schiaffino, G., Triantafyllidis, A. (2011). High level of mislabeling in Spanish and Greek hake markets suggests the fraudulent introduction of African species. Journal of Agricultural and Food Chemistry, 59, 475-480.

Gkagkavouzis, K., Karaiskou, N., Katopodi, T., Leonardos, I., Abatzopoulos, T. J., & Triantafyllidis, A. (2019). The genetic population structure and temporal genetic stability of gilthead sea bream Sparus aurata populations in the Aegean and Ionian Seas, using microsatellite DNA markers. Journal of fish biology.

Karaiskou N., Buggiotti L., Leder E., Primmer C.R.(2008). High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. Journal of Heredity 6: 688-693.

Karaiskou N., Lappa M., Kalomoiris S., Oikonomidis G., Psaltopoulou C., Abatzopoulos T.J., Triantaphyllidis C., Triantafyllidis A. (2011). Genetic monitoring and effects of stocking practices on small Greek Cyprinus carpio populations. Conservation genetics 5:1299-1311.

Karaiskou N., Moran P., Georgitsakis G., Abatzopoulos T.J., Triantafyllidis A. (2010). High allelic variation of MHC class II alpha antigen and the role of selection in wild and cultured Sparus aurata populations. Hydrobiologia. 638:11-20.

Karaiskou N., Triantafyllidis A., Katsares V., Abatzopoulos T.J., Triantaphyllidis C. (2009). Microsatellite variability of wild and farmed populations of Sparus aurata. Journal of fish biology. 74:1816-1825.

Karaiskou, N., Tsakogiannis, A., Gkagkavouzis, K., Οperator of Parnitha’s National Park, Papika, S., Latsoudis, P., Kavakiotis, I., Pantis, J., Abatzopoulos, J. T., Triantaphyllidis, C., Triantafyllidis, A. (2014). Greece: A Balkan subrefuge for mammal populations the case of the last remnant red deer (Cervus elaphus L.) population. Journal of Heredity, 105(3), 334-344.

Kavakiotis I., Triantafyllidis A., Ntelidou D., Alexandri P., Megens H.J., Crooijmans R., Groenen M.A.M., Tsoumakas G., Vlahavas I.(2015). TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data.”, Journal of Heredity, Wiley, 2015 Sep-Oct;106(5):672-6. doi: 10.1093/jhered/esv044. Epub 2015 Jul 2.

Maroso, F., Hillen, J.E.J., Pardo, B.G., Gkagkavouzis, K., Coscia, I., Hermida, M., Franch, R., Hellemans, B., Van Houdt, J., Simionati, B., Taggart, J.B., Nielsen, E.E., Maes, G., Ciavaglia, S.A., Webster, L.M.I., Volckaert, F.A.M., Martinez, P., Bargelloni, L., Ogden, R., AquaTrace Consortium, 2018. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Marine Genomics, 39, 64-72.

Minoudi, S., Papapetridis, I., Karaiskou N., Chatzinikos, E., Abatzopoulos, T. J., Triantaphyllidis, C., Triantafyllidis, A. (2018) Genetic analyses of brown hare (Lepus europaeus) support limited migration and translocation of Greek populations. PLoS One. 13(10): e0206327

Papakostas S., Dooms S., Triantafyllidis A., Deloof D., Kappas I., Dierckens K., Wolf T.D., Bossier P., Vadstein O., Kui S. et al. (2006). Evaluation of DNA methodologies in identifying Brachionus species used in European hatcheries. Aquaculture. 255:557-564.

Papakostas S., Michaloudi E., Triantafyllidis A., Kappas I., Abatzopoulos T.J. (2013). Allochronic divergence and clonal succession: two microevolutionary processes sculpturing population structure of Brachionus rotifers. Hydrobiologia 700, 33-45. (IF 1,985).

Tsaparis, D., Karaiskou, N., Mertzanis, Y., and Triantafyllidis, A. (2015). Non-invasive genetic study and population monitoring of brown bear (Ursus arctos) in Kastoria region – Greece. Journal of Natural History 49: 393-410.

Tsartsianidou V, Triantafillidou D, Karaiskou N, Tarantili P, Triantafillidis G, Georgakis E, Triantafyllidis A. (2017) Caprine and ovine Greek dairy products: The official German method generates false-positive results due to κ-casein gene polymorphism. J Dairy Sci. 100, 3539-3547.

Vlachavas A*., Karaiskou N.*, Kokokiris, L., Zampeta F.I. Drosopoulou E., Triantafyllidis A., (2018). Using genetic methods for analysis of fish meals and feeds employed in Greek mariculture. Aquaculture Research 50 (1): 312-322. *equal contribution. Yang, B., Cui, L., Perez-Enciso, M., Traspov, A., Crooijmans, R. P., Zinovieva, N., … & Triantafyllidis, A. (2017). Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution, 49(1), 71.

Minoudi, S., Karaiskou, N., Avgeris, M., Gkagkavouzis, K., Tarantili, P., Triantafyllidou, D., … & Triantafyllidis, A. (2020). Seafood mislabeling in Greek market using DNA barcoding. Food Control. 113:107213.

  

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