Strain and Race Identification
Content on this page:
- The APS – ISF Initiative to Standardise Identification of Plant Pathogen Strains and Races
- What are Differential Host Sets and Reference Strains Races?
- System Background and Inoculation Protocols
- Availability of Differential Host Sets and Reference Strains
How does your local pathogen strain compare with other reported strains?
Race or strain names can vary from region to region. In some instances there is a single system of naming pathogen races/strains in use all around the world, as in the case of leaf mould in tomato (Ff) and near wilt in pea (Fop). But often there are different systems. This causes no problems to breeders when there is no overlap in the names, as in anthracnose in bean (Cl) in Europe and the USA, or when the naming systems complement each other through the use of the same or similar host differential sets, as in the case of downy mildew in lettuce (Bl) in Europe and the USA. Sometimes, however, there is an overlap in strain names, e.g. in Fusarium wilt in tomato (Fol 0, 1 and 2 in Europe vs. Fol 1, 2 and 3 in the USA) and downy mildew in spinach (Pfs).
Incorrect identification of pathogen races/strains gives rise to inconsistent disease resistance claims by companies, a situation that harms the seed industry. The question the seed industry has struggled with is where or with which organization the responsibility for identifying pathogen races and strains should reside.
In an effort to address inconsistencies in identifying pathogen strains and races the international seed industry has joined hands with the American Phytopathological Society (APS) to develop a system to standardize the identification of pathogen strains and races.
The goals of this initiative are to develop
- A standard system based on host differentials and established procedures in peer-reviewed scientific publications that the seed industry and researchers would use to identify pathogen races and strains
- A system for maintenance and long-term storage of pathogen reference cultures and/or seeds of host plant differentials that can be accessed by the international community
- A US-based network of seed companies, and private and public research programs for distribution of seeds of differential host sets and reference cultures of plant pathogens to facilitate the identification of pathogen races and strains.
The network will complement existing systems in Europe such as the International Bremia Evaluation Board (IBEB), the International Working Group on Peronospora (IWGP), MATREF in France and the Plantum / Naktuinbouw Isolate Group in the Netherlands, and will comply with US regulatory requirements (USDA Animal and Plant Health Inspection Service).
Differential hosts are sets of plant varieties used to define strains of plant pathogens based on susceptible and resistant reactions. Reference strains are known characterized isolates of a given pathogen.
A differential set for a pathogen is defined by varieties from within one or several plant species that are hosts to the pathogen. For example, races of Bremia lactucae causing downy mildew in lettuce are determined solely by using lettuce cultivars. But in the case of root knot caused by Meloidogyne spp. the set is made up of several host species - tobacco, cotton, watermelon, tomato, pepper and peanut. The hosts utilized within differential sets are often existing varieties or experimental species known as indicator hosts.
Different varieties or lines with the same resistance gene(s) can give the same reaction to a given race or strain of pathogen. Therefore, the differential varieties or lines used by various researchers may differ. The differential sets presented here may be different than those found in the scientific literature and other sources.
To meet the goal of a standardized system of identifying pathogen strains based on differential hosts, the APS-ISF Initiative has described the pathogen and the reaction of differential hosts to known strains or races of the pathogen causing four diseases (see below). For each disease, a protocol to screen for resistance is also provided.
There may be other protocols that differ from those recommended by the APS-ISF Initiative in elements such as the incubation temperatures used, number of days required for incubation after inoculation and plant age at inoculation. The protocols recommended by the Initiative have been demonstrated to be effective at identifying strains/races of the pathogen in question and resistance traits of the host cultivars.
Tomato mosaic virus
International cooperation in identifying pathogen strains and races goes hand-in-hand with researchers around the world being able to access differential host sets and reference strains. The APS-ISF Initiative aims to provide seed of differential host sets and reference races and strains of pathogens in the disease background documents listed above.
Seed of the differential hosts for each disease can be ordered online through the USDA Germplasm Resource Information Network (GRIN). Refer to the GRIN links noted in the disease background document.
For some host differentials, a Material Transfer Agreement (MTA) may be required to order seed. The GRIN order form indicate for which differential hosts an MTA is needed and the name of the person to be contacted for arranging an MTA.
Contact the ISF Secretariat for reference pathogen strains and races. It is the responsibility of those requesting pathogen strains to ensure they have the necessary permits to receive the strains. Contact USDA-APHIS for additional information.
Researchers from all over the world are invited to join this initiative and use the differential host sets provided to identify new pathogen races and strains. If you have used any of the information or resources provided by the APS-ISF Initiative, your feedback on new strains identified, views on the inoculation protocols, differential hosts, or any related matter is welcomed. Contact the ISF Secretariat.
If you are interested in contributing towards developing a document for adding other diseases to this system, please contact the ISF Secretariat.
ISF and members of the APS-ISF Initiative have done their best to provide information that is up-to-date and published in refereed journals and, therefore, accept no liability for the use of this information.
The inoculation protocols provided have been demonstrated to be effective at identifying strains and races of the pathogens in question and resistance traits of the host cultivars. As they will be updated at regular intervals, it is the responsibility of the user to verify that the latest version of the system background and inoculation protocol is being used.