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Varietal Genetic Methods
In order to describe a variety it is necessary that genetic information in addition to the phenotypic characteristics is available, i.e. a genetic fingerprint. The advantage of having a genetic fingerprint is that a variety can be uniquely defined allowing one to compare varieties against a reference database. Provided that a variety is phenotypically and genetically described, a further variety determination of a plant does no longer require an in-depth expert knowledge, rather the genetic fingerprint is compared against the reference database. Moreover, the analysis can be carried out regardless of the season and the growth of the plant (fruit stage), since smallest amounts of all plant parts (except seeds and flowers) are sufficient to perform a genetic analysis.
In Switzerland, the BLW (Federal Office for Agriculture) established and/or is in the process of setting up reference databases for different fruit types (apple, pear, cherry, plum, quince). In order to ensure compatibility of new analyzed data with the databases, the same method (microsatellite marker sets) must be used for each analysis. Ecogenics has aligned the genetic fingerprinting for variety identification with the BLW approach and can therefore ensure the necessary consistency of the genetic data analysis.
Overview
Two scenarios are conceivable for the identification of varieties. Either two samples can be compared, where one of the samples is considered as the reference variety due to previous genetic and/or phenotypic description. Or the unknown genetic fingerprint of a variety is compared to the reference database.
Methods
Genotyping & Database Matching
With this method, you can send us a sample of your fruit of interest, have it genetically analyzed and a database search is performed to identify the closest matching variety in the database.
We offer a sample collection date twice a year (June 15 and September 15), by which time your sample will have to arrive at ecogenics. Please note, for these analysis rounds we only accept leaf material. For detailed information of sampling and sending the samples please contact us.
You can contribute to the construction of the database. The database comparison is currently available for apple, pear and cherry. Many databases are very extensive including several hundred varieties, however it may occur that a genetic fingerprint of a variety is not yet represented in the database. In that case, the BLW will decide if this new fingerprint of your variety can be added to the database.
If you would like to do an analysis outside of the given time frame or if you would like to send us some other source material, do not hesitate to contact us and we will be happy to make you a project based offer.
Genotyping & One-to-one Comparison
This method is suitable for the verification of varietal authenticity. Especially in cutting gardens, the molecular genetic varietal authentication is very efficient and replaces the phenotypic characterization in certifications.
In order to determine the variety of your sample, there is a need for a second sample which serves as reference material with known variety origin. We kindly ask you to organize the reference material before submitting your samples.
We offer a sample collection date twice a year (June 15 and September 15), by which time your sample will have to arrive at ecogenics. Please note, for these analysis rounds we only accept leaf material. For detailed information of sampling and sending the samples please contact us.
If you would like to do an analysis outside of the given time frame or if you would like to send us some other source material and variety not listed in our available marker systems, then do not hesitate to contact us and we will be happy to make you a project based offer.
Bioinformatics Database Matching
Datasets with genetic fingerprints are often very large and the search for similar or identical fingerprints is prone to errors and is very time consuming. With our validated in-house bioinformatics pipeline we compare the datasets with the genetic fingerprints for you.
Marker Systems
Available Marker Systems for:
- Apple
- Pear
- Sweet – and sour Cherry
- Plums
- Quinces
- Apricot
- Peach/Nectarine
- Grapes
- Nuts
If you have not yet found a suitable marker system for your variety, please do not hesitate to contact us. Marker systems have already been developed for many varieties and details can often be found in the literature. Besides, ecogenics is specialized in the development of marker systems and we would be happy to work with you on your project. Get in contact with us to see how we can enrich your research.