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• Pathogen Coding
• Recommended Codes
• Strain Denomination

 

Consistency in terminology is highly recommended for companies when communicating with their clients/customers. The Vegetable and Ornamental Section adopted a paper in 2005 wherein it defined terms describing the reaction of plants to pests or pathogens and to abiotic stresses for the vegetable seed industry.

In addition, a subgroup of the ISF Vegetable and Ornamental, and Cereal Crops Sections, the Pathogen Codification Working Group, has devised codes for pest organisms affecting vegetable and cereal crops that can be used by seed companies worldwide on their catalogues and other communication with customers.

Guidelines for Coding Pest Organisms in Vegetable and Cereal Crops

Nomenclature and codes

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 new name only

The transition from Step 1 to Step 2 and thereafter to Step 3 is 5 years. The transition time allows 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 when viruses are assigned to (new) groups.

A pest organism affecting more than one crop receives one code.

Viruses

• Codes as adopted by ICTV are used. They are in capital letters, except in cases where a letter (in lower caps) 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 as 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 are used. For example: Fusarium oxysporum = Fo.
• For more than species within a genus all causing the same disease, the abbreviation of the genus may be used. For example, in the case of Verticillium wilt disease, both Verticillium albo-atrum (Va) and V. dahliae (Vd) have been found to be causal agents. Then Va + Vd can be indicated by V.
• The use of a single code for different pest organisms within one crop is avoided. In such cases the second or any other relevant letter of the species name is added to the code. For example: Corynespora cassiicola and Cladosporium cucumerinum are two different diseases in gherkin and the assigned codes are: Cca and Ccu.
• For different subspecies of a pest organism in the same crop causing different diseases, the subspecies has been defined with a small letter. For example Fol and For, respectively for Fusarium oxysporum f.sp. lycopersici and Fusarium oxysporum f.sp. radicis-lycopersici in tomato.

Separators

• It is also recommended that the following separators be used:
• / (slash) to separate pest organism codes
• : (colon) to separate the species code from the strain/race/pathotype code(s)
• , (comma) to separate strain codes

Using the above convention resistance to Ua and Cl strains 1 and 2, for instance, will be denoted as Ua / Cl:1,2. Fol:1,2,3 indicates resistance to strains 1, 2 and 3, and Cl:α,β,δ indicates resistant to strains α, β and δ.

Links:

American Phytopathological Society

International Society of Plant Pathology