User:Somanypeople/Style guide for plant disease articles

Style guide for plant disease articles

I am currently hosting this style guideline on my user page until I can get some feedback as to it's usefulness. If it is determined that it is valuable contribution to the plant disease community, it will then be moved to a more appropriate location.

The purpose of this proposed style guide is provide authors of plant disease articles some guidance in formatting and structure.

Disease or pathogen article

A disease is the result of the infection of a host species by a pathogen. Many articles about commercial crops (Apple, Maize, Wheat, ) contain some information about plant diseases. However, more detailed information regarding a disease should appear in a disease article. The disease article should focus on the interaction of the pathogen and host species. Ideally, a separate article should contain information that is specific to the pathogen. Currently, the majority of plant disease articles combine information about the pathogen (in particular the taxobox) and disease in the disease article (see Chestnut blight, Citrus canker, Dutch elm disease, Fireblight, Grey leaf spot, Plum pox, Ryegrass bunt Sudden oak death, Texas root rot, Wheat leaf rust). All of these articles have re-directs to them from articles with the name of the pathogen that causes the disease. There are also a few cases where a disease is re-directed to a pathogen (Rice blast --> Magnaporthe grisea; Net blotch (barley) --> Pyrenophora teres; Burrowing nematode --> Radopholus similis).

In some cases, the pathogen and disesase articles are separate (Hemileia vastatrix - Coffee rust; Mycosphaerella fijiensis - Black sigatoka; Fusarium oxysporum - Panama disease; Rhynchosporium secalis - Scald (barley); Septoria tritici - Septoria tritici blotch (wheat)).

The need to separate disease and pathogen articles is further strengthened by the fact many pathogens not only infect a variety of different species, some can also produce different diseases on one species (Cochliobolus sativuus causes common root rot, spot blotch and head blight). Many aspects of these diseases are unique to the species and/or plant part infected and can be deserving of a separate article.

The name of the article

The name of the article should include both the common name (but which common name?) and the name of the host in parentheses (Bacterial blight (barley), Leaf rust (cereals). Articles that do not include the host name (Leaf curl, Blight) generally are concerned with symptoms that are produced by a wide range of pathogens or appear in a wide range of plant species by a single pathogen. The inclusion of the host species in the article is necessary since common names are not unique (specific to particular host-pathogen).

Redirects

Late Blight of Potato, Potato fungus, Potato blight, Potato late blight, Tomato late blight --> Phytophthora infestans

Drechslera graminea, Helminthosporium gramineum, Napicladium hordei, Pleospora graminea --> Pyrenophora graminea

Marssonia secalis, Rhynchosporium graminicola, Septocylindrium secalis --> Rhynchosporium secalis

When creating redirects for a different common name or the synonym for the causal agents, the redirect article should also include categories so the redirect with included in the category.

Example

#Redirect Scald (barley)
Category:Plant diseases
Category:Cereal diseases
Category:Barley diseases
Category:Wheat diseases

Suggested plant disease (and pathogen) article headings

The following is a suggested list of possible headings and topics that could be covered in plant disease articles. Whether something deserves its own heading or whether it should be considering under another heading is usually based on the amount of information that is included about that subject. Thus, it is certainly not suggested that all disesae articles include these headings or that they should be restricted to these headings. As the number of plant disease articles expands and the depth of individual articles increases, we will eventually begin to see separate articles addressing these headings on a disease specific basis. This list also includes a number of headings that are specific to the pathogen, not the disease. In the early stages in the development of plant disease article, this information may be contained within the article, however, I suspect that in most cases, this information will be migrated to articles focusing specifically on the pathogen.

(introduction, causal agent(s), host(s), overview, history)

Symptoms

Isolation
- Growth media
- Storage/Preservation (media, under oil, freeze-drying, silica-gel, sand, wheat-bran, cryopreservation)

Identification and diagnosis
- Characteristics / morphology
  - Asexual stage
  - Sexual stage
  - Mating types, anastomsis groups
  - Structures (sclerotia, chlamydospores
- Immunological techniques
- Nucleic acid probe-based methods (hybridization methods [nucleic acid probes], polymermase chair reaction, rapid amplified polymorphic DNA)
- Electron microscopy
- Dilution end point, thermal inactivation point, longevity in vitro

Biology
- Systematics
- Genomics
- Nuclear number and chromosome
- Extrachrosomal elements
- Transposable elements
- Somatic compatibility
- Heterokaryosis
- Linkages
- Synonyms
- Strains
- Pathogenic species
- Origins
  - Mutation
- Fitness
- Main diseases

Disease cycle
- Reproduction
- Replication
- Host species and alternate hosts
- Overwintering structures

Pathogenesis
- Infection process
  - Method of infection, penetration
  - Colonization
  - Histology
  - Biochemical

Epidemiology
- Inoculum source
- Sporulation, spore release and dispersal (wind, splash ..)
- Transmission (mechanical, vector, ..)
- Environmental conditions
- Disease progress curve
  - Apparent infection rate
  - Monocyclic/Polycyclic (simple interest, compound interest)
- Disease foci, gradients
- Forecasting models
- Density-dependent and density-independent factors
- Spatial population structure, spatial distribution
  - Measurement (temperature, humidity, wind, leaf wetness, leaf area, soil moisture )

Disease assessment
- Incidence
- Severity
- Index
- AUDPC
- Remote sensing
- Digital image analysis
- Sampling methods
- Surveys

Host resistance
- Pathotypes
- Differentials
- Genetics
- Defense mechanisms (cell wall reinforcement, hydroxyproline-rich glycoproteins, lignin, pathogenesis-related proteins, phenolics, phytoalexins)
- Physiology of pathogenesis (Adhesion, nutrition, plant barriers, enzymes, toxins, phytohormones

lipase, cutinase) reactive oxygen species (ROS)/change in reodx potential

- Plant extracts (antimircobial action, induction of disease resistance)
- Signalling
- Seedling, adult resistance
- Temperature sensitivity
- Types of resistance
  - Horizontal
  - Vertical
  - Cultivar mixtures
  - Non-host immunity
  - Tolerance
- Breeding
  - Convential
    - Screen
  - Genetic engineering
  - In vitro
  - Sources of resistance
  - Breeding strategy
  - Screening methods

Geographical distribution and economic importance
- distribution
- crop loss
  - quality
  - quantity
    - yield components
- disease intensity-yield loss relationships
- effects on humans and animals

Management
- Monitoring
  - Environmental coniditions (forecasting models)
  - Spores
- Disease thresholds
- Cultural
  - Prevention,clean seed, virus-free, indexing
  - Inoculum, residue management (tillage)
  - Crop rotation, intercropping, catch crops
  - Environment modification, irrigation
  - Soil amendments (organic, nutrients), suppressive soil
  - Seeding density, plant density, pruning
  - Soil solarization
  - Hydroponics, UV treatment
- Host resistance
  - Resistance/Environment
  - Multi-variety
- Chemical control (Fungicides, Bactericides, Nematicides, Viricides, Insecticides [vector control])
  - Seed treatment
  - Foliar treatment
    - Application timing, rates, mixtures,
  - Fumigation
  - Pesticide resistance
- Biological control
  - Mycorrhiza
  - Microbial pesticides
- Quarantine
- Regulatory
  - Inspection
  - Certification
- Eradication

Current headings used in plant disease articles

The following is a summary of the headings that are currently used in plant disease articles and the articles in which they appear.

Overview Dutch elm disease

Symptoms Common bunt (wheat), Common root rot (wheat), Crown rust (barley), False loose smut (barley), Leaf rust (barley), Loose smut (barley), Crown rust (barley), Stripe rust (barley)
Infections and symptoms Oak wilt
Cause and symptoms Scleroderris canker
Hosts and symptoms Sudden oak death

Diagnosis Black spot (roses)
Detection Citrus canker
Identification Pyrenophora graminea
- Asexual stage Pyrenophora graminea
- Sexual stage Pyrenophora graminea
The two mating types Sudden oak death
Characteristics Erysiphales
Morphology Blumeria graminis, Hemileia vastatrix, Rhynchosporium secalis, Begomovirus
Systematics Blumeria graminis, Erysiphales
Genes Agrobacterium tumefaciens
Genonme Begomovirus
Primary and secondary structure of the PSTVd viroid

Potato spindle tuber viroid

Confugation Agrobacterium tumefaciens

Biology Phytophthora infestans, Plum pox, Potato cyst nematode, Phytophthora, Barley yellow dwarf, Botrytis cinerea

Citrus canker

Biology and pathology Magnaporthe grisea
Life cycle Corn smut, Pythiaceae
Life cycle of the fungus Ergot
Disease cycle Common bunt (wheat). Crown rust (barley), False loose smut (barley), Leaf rust (barley), Crown rust (barley), Stripe rust (barley)

Reproduction Pythiaceae
Replication Rhabdoviridae
Dispersal and spread Pyrenophora teres
Sources and spread Barley yellow dwarf
Transmission Sudden oak death, Begomovirus

Ecology Blumeria graminis, Erysiphales, Hemileia vastatrix
Pathology Plum pox, Citrus canker, Barley yellow dwarf
Method of infection Agrobacterium tumefaciens

Possible origins Sudden oak death
- Introduction as an exotic species Sudden oak death
- Hybridization events Sudden oak death
- A native organism Sudden oak death
Possible earlier occurrences Dutch elm disease