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Varietal Genetic Methods

 
 
Traditionally, fruit varieties are identified based on visible characteristics such as shape, color, or taste. However, these phenotypic traits alone are often insufficient for precise identification. This is where genetic fingerprinting comes in: it enables accurate variety identification by comparing genetic data with reference databases.

A key advantage of this molecular genetic method is its flexibility. The analysis can be performed regardless of the season or the plant's growth stage. Even small amounts of plant material such as leaves, bark, or roots (excluding seeds and flowers) are sufficient for the examination.

In Switzerland, the Federal Office for Agriculture (FOAG) has established or is in the process of building reference databases for various fruit types. To ensure compatibility with these databases, all analyses must follow the same method — using microsatellite marker sets.

Ecogenics employs this standardized procedure and aligns its approach with the FOAG guidelines. This ensures reliable and consistent genetic data analysis for the clear identification of fruit varieties.

 
 

Overview



Variety Identification Service

Our variety identification service supports two possible scenarios:

  • Direct Comparison: Two samples are compared, with one sample serving as a reference variety based on previous genetic and/or phenotypic descriptions.
  • Database Comparison: The unknown genetic fingerprint of a sample is compared with a reference database for identification.


Variety Identification for Small Sample Quantities
Twice a year, we offer variety identification for smaller sample batches (1–39 samples per fruit type). The deadlines for these analysis rounds are June 15 and September 15. To ensure your samples are included in the respective round, they must arrive at our facility before the deadline. Late submissions will be stored and processed in the following analysis round.

Sample Material and Fruit Types
We accept leaves only as sample material for analysis. Our variety identification service is available for the following fruit types:

  • Apple
  • Pear
  • Cherry
  • Apricot/Nectarine/Peach
  • Plum/Prune
  • Quince


For more information on the marker systems used, visit our Marker Systems page. Details on reference lists can be found under Databases.

Analysis and Results
We generate a genetic fingerprint for each sample and compare it with the relevant database. You will receive the genetic data along with information on potential matches. Results are delivered within 2 to 3 months after the respective deadline.

Contact
Would you like to learn more about our variety identification service or the ordering process? Please fill out our contact form.

 

Marker Systems

Available Marker Systems for:

Appel

PCR DB
Pos		 Marker Name Alleles of gene group “485”, MUNQ “448”, variety “Delicious
A1 01 CH01H01 107/109
  02 CH04C07* 132/132
  03 CH01H10 115/115
A2 04 CH05F06 181/181
  05 CH01F03b 207/207
  06 GD147* 121/121
  07 CH02b10* 120/130
  08 CH05c06* 87/91
  09 EMPc117* 113/117
  10 GD96* 173/173
  11 EMPc11* 143/149
  12 GD142* 164/164
  13 CH01d09* 133/147
  14 CH01d08* 240/282
  15 CH03g07* 240/240
  16 CH01f07a* 183/189

The analyses for all apple markers are conducted in accordance with the guidelines of the 'Fruit Network' of the 'European Cooperative Programme for Plant Genetic Resources (ECPGR)' (https://www.ecpgr.org/).

Pear

PCR DB
Pos		 Marker Name Alleles of the gene group “861”, PUNQ “134”, variety “Frühe aus Trevoux”
A1 01 CH01H01 107/109
  02 CH04C07* 132/132
  03 CH01H10 115/115
A2 04 CH05F06 181/181
  05 CH01F03b 207/207
  06 GD147* 121/121
P1 07 CH02b10* 120/130
  08 CH05c06* 87/91
  09 EMPc117* 113/117
P2 10 GD96* 173/173
  11 EMPc11* 143/149
  12 GD142* 164/164
  13 CH01d09* 133/147
P3 14 CH01d08* 240/282
  15 CH03g07* 240/240
  16 CH01f07a* 183/189

* The analyses for all pear markers are conducted in accordance with the guidelines of the 'Fruit Network' of the 'European Cooperative Programme for Plant Genetic Resources (ECPGR)' (https://www.ecpgr.org/).

Cherry

PCR DB
Pos		 Marker Name Alleles of gene group “105”, CHUNQ “45”, variety “Hudson"
C5 01 EMPaS12 144/153
  02 UDP98-412 129/129
  03 EMPaS10 162/171
  04 EMPaS02 146/151
C6 05 CPPCT006 190/192
  06 BPPCT037 147/153
  07 PceGA34 162/166
C7 08 EMPaS14 206/208
  09 CPPCT022 253/253
  10 EMPaS06 210/212

 

Apricot, Nectarine/Peach

PCR DB
Pos		 Marker Name Alleles of gene group “1001”, variety Apricot “Orangered" Alleles of the gene group “P8”, peach variety “RedHaven”
T1   UDAp404 156/156 0/0
    PaCITA16 129/143 139/159
    PaCITA7 192/216 170/170
    PaCITA5 124/136 104/104
T2   MA040a 207/209 235/253
    MA027a 145/157 147/147
    UDAp419 146/146 0/0
    UDAp413 184/184 94/106
T3   BPPCT037 0/0 153/159
    BPPCT007 0/0 146/152
    BPPCT039 0/0 149/149
T4   BPPCT040 0/0 136/136
    BPPCT014 0/0 201/201

 

Prune/Plum

PCR DB
Pos		 Marker Name Alleles of gene group “8”, variety plum “Elena”
Z1 01 CPSCT005 186/190/192/198/204
  02 CPSCT012 161/167
  03 CPSCT006 124/128
  04 CPSCT039 100/106
Z2 05 CPSCT044 171/177/201/213
  06 CPSCT026 173/189/200/204/210
  07 CPSCT035 193/199/202
  08 CPSCT024 165/169/171/179/180
Z3 09 BPPCT007 123/127/133/135/137/139
  10 BPPCT040 124/128/132/146
  11 BPPCT034 215/223/237/273
  12 UDP98-407 164/168/180/186/192
Z4 13 UDP96-005 105/113/136/153
  14 BPPCT014 186/204/218/222/238/258
  15 BPPCT039 126/132/136/144/152/162
  16 PacA33 171/180/188/198

 

Quince

PCR DB
Pos		 Marker Name Alleles of gene group “1”, variety “Ronda"
Q1 01 Hi02c07 110/149
  02 CH04c07 128/140
  09 Ch01h10 96/98
Q2 03 CH05c06 111/113
  04 EMPc117 102/102
  10 CH01f02 167/182
Q3 06 EMPc11 141/145
  08 Gd142 135/135
  05 IPPN18 311/346
  07 CH01d08 276/276

 

Databases

Databases



Data Source:

*The genetic data collected as part of your variety testing is used by the Federal Office for Agriculture (BLW) to further develop and maintain the databases. However, all data is fully anonymized, ensuring that no personal data is published.


Reference Lists

Apple

  • Entries: > 1600 gene groups
  • Data Source: BLW, DGO
  • Comment: Samples analyzed through our variety testing service are compatible with the published DGO database. Color mutants cannot be differentiated.
  • Status: 01.01.2025

 

Pear

  • Entries: > 700 gene groups
  • Data Source: BLW, DGO
  • Comment: Samples analyzed through our variety testing service are compatible with part of the published DGO database (12 out of 16 markers). Samples analyzed from 2025 onward are not compatible with analyses conducted before 2025. If you wish to have your samples analyzed exclusively with the DGO marker set or match older data sets, please contact us via the Contact Form Offer.
  • Status: 01.01.2025

 

Cherry

  • Entries: > 480 gene groups
  • Data Source: BLW, DGO
  • Comment: The sweet cherry marker data from the DGO database has been adjusted to align with the marker data from the BLW database and combined. Samples analyzed through our variety testing service are not compatible with the published DGO database for sweet cherries. If you wish to have your samples analyzed exclusively according to the DGO system, please contact us via the Contact Form Offer.
  • Status: 01.01.2025

 

Apricot, Nectarine/Peach

  • Entries: > 70 gene groups
  • Data Source: BLW
  • Comment: Combined marker systems for apricot, nectarine/peach. The database was built using marker systems specific to apricot and nectarine/peach. Therefore, some data points may be missing.
  • Status: 01.01.2025

 

Plum/Prune

  • Entries: > 300 gene groups
  • Data Source: BLW
  • Comment: As plum/prune is a polyploid fruit type, data analysis can be challenging, potentially resulting in ambiguous data matches.
  • Status: 01.01.2025

 

Quince

  • Entries: > 20 gene groups
  • Data Source: BLW
  • Comment: In some cases, the marker system used may not provide sufficient precision to clearly differentiate between varieties.
  • Status: 01.01.2025