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How to identify potato varieties using their genetic fingerprints?

For the identification of varieties, lab molecular techniques (photo 1) are particularly efficient. Indeed, each variety contains specific DNA sequences able to generate unique fingerprint (or profile) likewise barcoding (photo 2).

The process is based on the analysis of specific DNA regions called microsatellites markers. They correspond to short repeated sequences; it is the number of repeats, specific to each variety, which makes DNA-profiling possible.

 

After DNA extraction from leaves, tubers or in vitro plantlets, markers are amplified in the lab and then revealed.
 

Each genetic fingerprint is then compared to the ones contained in a database named IdeAle.

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Photo 1. This is a laboratory method (©inov3PT).

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Photo 2. Genetic fingerprints are produced using large electrophoresis gels (©inov3PT).

Identify potato varieties for which purposes?

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Photo 3. Genetic fingerprints are complementary to visual inspections performed in the fields (production and national field set up every year) (©inov3PT).

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Photo 4. Genetic fingerprints also enable to control in vitro collections (©inov3PT).

This method is used for several purposes:

  • Description and validation of the identity of the material performed at the very beginning of the seed potato multiplication process

  • Check of the first steps of the multiplication process, as a complement to the visual inspections made in the production fields and to the national field set up every year to control trueness to type (photo 3)

  • Description of the genetic profile of each new variety obtained into the breeding stations

  • Test batches of ware potatoes

  • Control of collections of varieties like the ones maintained in BrACySol BRC (Biological Resource Center) by INRAE (photo 4)

Each year, around 3000 samples are analysed in the network, 80% of the analysis are made on the seed potato production material.

The labs network is coordinated by FN3PT/inov3PT

The laboratories of the partners are:

  • Labs owned by seed potato producers’ organisations (control and certification of seed potatoes)

    • Bretagne Plants

    • Comité Nord

    • Comité Centre et Sud

  • Service Commun des laboratoires (tests on ware potatoes)

  • Lab of INRAE/UMR Igepp (control of the BrACySol BRC collection).

The Swiss lab of Agroscope Changins is also associated to the French network.

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All members of the network use the same method and share information through the IdeAle database. The method was developed by FN3PT/inov3PT and is being used since 2017 for official analysis in the course of the seed potato certification. Nine ring tests have been organised since 2003 under the aegis of SOC (Official service for control and certification of seeds and plants). Ring tests consist in identifying de-identified tuber samples using their genetic fingerprints. These tests are performed to validate the strength of the method, the expertise of the labs and the database content.

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Photo 5. During ring tests, de-identified samples are re identified thanks to their genetic fingerprints. (©inov3PT).

IdeAle facilitates the transmission of information across the network

IdeAle is an internet platform secured by a login and a password. The system was built to share data but it can also deal with confidential data. The shared data consistency is checked by the super-administrator. Data are updated in real time and for the entire network simultaneously.

The database contains profiles for almost 2200 varieties and 900 hybrids or only numbered genotypes (as of June 2020).

It was built by FN3PT/inov3PT in collaboration with and for the seed potato producers’ regional organisations in the course of a project conducted with a grant of the French Ministry of Agriculture between 2008 and 2012. INRAE, the Service commun des Laboratoires, Gnis/SOC & Geves were also involved in the project (Marhadour, Dargier et al., 2014).

Contact details of the network members

Laboratories

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Contact details

inov3PT

43-45 rue de Naples

F-75008 PARIS

https://www.inov3pt.com

contact@inov3pt.fr

Bretagne Plants

Roudouhir

F-29460 HANVEC

http://www.plantsdebretagne.com/

bretplants@plantsdebretagne.com

Comité Centre et Sud

Station de Lavergne

BP3

F-87370 LAURIERE

https://www.comitecentresud.com/fr/accueil/

flore.madruga@comitecentreetsud.fr

INRAE UMR Igepp

Keraiber

F-29260 PLOUDANIEL

https://www6.rennes.inrae.fr/igepp/

IdEvol, a new project for our network

We are constantly working on improving our practices. Lab techniques are rapidly evolving, making the reduction of the analysis delay, the improvement of the working conditions and the reduction of the costs of the wastes processing possible.

We are currently working on the transfer of our method to another platform able to reveal our markers. The main constraint is that we want to keep using the huge amount of profiles contained in IdeAle, which implies to maintain the current coding system.

To do so, we were supported by the French Ministry of Agriculture by a grant obtained in the call for proposals “Casdar Semence et sélection variétale”.

Our project, handled between 2019 and 2023, was entitled AMS-IdEvol for « Technological evolution to identify potato varieties using microsatellites markers in support of the seed certification process » (photo 6). All the members of our network were involved. FN3PT/inov3PT coordinated the project.

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Photo 6. Qiaxcel advanced system was chosen to improve our process (©inov3PT).

To go further

Summary of the IdEvol project (download, in French)

Posters to download (in English): 

  • Marhadour S, et al. (2022) Genetic fingerprints using SSR markers to secure seed potato production in France: method and database improvement.  EAPR 2020, Krakow, Poland (presentation prepared for the EAPR 2020 Congress)

  • Marhadour, S., et al. (2017). Genetic fingerprints using SSR markers to secure the seed potato production scheme, improvement of the method and database in France. EAPR2017 20th triennial conference. Versailles, France (poster)

  • Marhadour S, (2014). Seed potato identification using SSR markers in France: organization, methods and database.  19th triennial conference, EAPR 2014 Brussels (presentation)

  • Marhadour, S., et al. (2013). Construction of an online database to improve management of DNA profiles dedicated to cultivar identification of seed potatoes in France. The 17th Joint Meeting of the EAPR Breeding and Varietal Assessment Section & EUCARPIA Section Potatoes, Héviz (poster)

  • Marhadour, S., et al. (2011). Potato variety identification using SSR in France and Switzerland. EAPR 2011, the 18th Triennal Conference of the European Association For Potato Research, Oulu, Finland (poster)

Papers in LPTF download (in French)

  • Marhadour S (2023) Projet IdEvol, l'identification variétale accélérée.  La Pomme de Terre Française, pp 44-45, article disponible ici

  • Marhadour S (2021) Projet IdEvol, faciliter le travail des laboratoires.  La Pomme de Terre Française, pp 50-51, article disponible ici

  • Marhadour, S. and Y. Le Hingrat (2018). Identification variétale, un réseau qui fait évoluer ses pratiques. La Pomme de Terre Française, pp 47-48, article disponible ici

Paper describing the setup of the IdeAle database (in French, abstract in English)

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