Pathogen Coding
Consistency in terminology is highly recommended for companies when communicating with their clients/customers. The Vegetable and Ornamental Section adopted a paper in 2005 which defines terms describing the reaction of plants to pests or pathogens, and to abiotic stresses.
The Working Group (WG) on Pathogen Coding (a subgroup of the ISF Vegetable and Ornamental, and Field Crops Sections) has proposed codes for pest organisms affecting vegetable and cereal crops that can be used by seed companies worldwide in their catalogues and other communication with customers.
Guidelines for Coding Pest Organisms in Vegetable and Cereal Crops
General rules
Every effort has been made to remain consistent with the nomenclature used by internationally recognised institutions such as the American Phytopathological Society (for fungi), the International Committee for the Taxonomy of Plant Pathogenic Bacteria (of the International Society of Plant Pathology (ISPP)) (for bacteria) and CAB International Bioscience (formerly the International Mycological Institute, IMI) (for fungi and bacteria), and the International Committee for Taxonomy of Viruses (ICTV) (for viruses). In case of any deviation a special note of explanation has been given.
Taxonomic changes to the Latin binomial may necessitate a change in the code. The following procedure has been established:
Step 1 List the old name and quote the new name between brackets, i.e. ”old name”
(now “new name”)
Step 2 List the new name and quote the old name between brackets i.e. ”new name”
(ex “old name”)
Step 3 Quote the new name only
The transition from one Step to the next is 5 years. The WG will use this 5-year transition period so as to allow companies and their customers worldwide to accustom themselves to the change. It also takes into consideration the fact that organisations such as ICTV meet only once in three years to evaluate proposed taxonomic changes. Companies may choose to use the new name and accompanying code in catalogues and other communication earlier, if they so wish.
A pest organism affecting more than one crop receives one code.
Viruses
- Codes adopted by ICTV will be used. They are in capital letters, except in cases where a letter in lower case is added to differentiate between two viruses with the same initials, e.g. TMV and ToMV.
- In case there is a deviation from the code used by ICTV, an explanatory note will be added to the text.
Fungi, Bacteria, Nematodes and Insects
- In general two letters corresponding to the first letter of the genus and species of the Latin name will be used, e.g. Fusarium oxysporum = Fo.
- The use of a single code for different pest organisms affecting a crop species will be avoided. In such cases the second or any other relevant letter of the species name is will be added to the code, e.g. Corynespora cassiicola and Cladosporium cucumerinum are two different diseases in gherkin and the assigned codes are Cca and Ccu, respectively.
- For different subspecies of a pest organism in the same crop species causing different diseases, the subspecies will be defined by a letter in lower case, e.g. Fol and For respectively for Fusarium oxysporum f.sp. lycopersici and Fusarium oxysporum f.sp. radicis-lycopersici in tomato.
Separators
The following separators will be used:
/ (slash) to separate pest organism codes
: (colon) to separate the species code from the strain/race/pathotype code. The colon is
followed by a space
, (comma) to separate strain/race/pathotype codes. The comma is followed by a space
- (hyphen) to indicate an uninterrupted series of strain/race/pathotype numbers
. (dot) to separate numbers defining a compound strain/race/pathotype name
Using the above convention, resistance in a variety to Ua and Cl strains 1 and 2 would be denoted as Ua/Cl: 1, 2.
A series of race numbers following a logical and uninterrupted order will be abbreviated in a 'from-to' mode and Fol: 1, 2, 3 would be noted as Fol: 1-3. Strains 1 to 25 of Bremia in lettuce will be noted as Bl: 1-25. An interrupted series will be presented in the following manner - Bl: 1-16, 21, 22-25.
An example of a virus strain with a compound name is PMMoV: 1.2.3.
Relevant Links
American Phytopathological Society