Diseases can occur at any stage during the course of plant growth. The rapid, accurate diagnosis of the cause of a disease, along with the implementation of a rapid treatment, is essential to ensure the protection of the crop.

diseases affecting crops in kenya

Certain infectious diseases caused by living, microscopic organisms have the potential to rapidly ruin a crop. However, for any particular vegetable, these diseases are not that numerous and, so, it would not be difficult for a grower to become familiar with them and take proper preventative action. Diseases caused by nonliving things (i.e. not infectious) can be much more difficult to diagnose. Usually, it is easier to rule out an infectious agent as the cause of a disease before investigating possible nonliving (abiotic) causes.

This stresses the need for the farmers to become familiar with the more common infectious diseases that can occur on the crop. This post provides an overview of the science of diagnosis and treatment of vegetable diseases.

Why Is There Disease?

Disease is the outcome of an interaction between the host, the disease agent, and their environment. If the cause of infectious disease, the pathogen, is next to the host, nothing will happen unless environmental factors are favorable for its infection and development within the plant. With foliar pathogens, there is usually a minimal period of leaf wetness required to stimulate spore germination and infection. For some soilborne pathogens, infection occurs in combination with high soil moisture and certain critical soil temperatures.

Knowledge of conducive environmental factors for the more important vegetable diseases presents an opportunity for more effective management: the disease can prevented by altering some of the environmental factors, or, when such factors cannot be altered, steps can be taken to minimize the impact (e.g. fungicides could be applied in advance of a period of sustained rain which would favor foliar diseases.)

Diagnosing Diseases of Vegetables

Not all diseases are caused by pathogenic organisms. Determining whether a disease is caused by a pathogen, or has nonliving (abiotic) causes requires not only the examination of individual plants, but also, noting the pattern of symptom occurrence in a field. Examine individual plants for unusual symptoms, such as leaf spots, wilts, stunting, fruit rots, misshapen leaves, cankers and stem blight. Roots should be examined for galls, root rot and necrosis (dead areas). Fields should be observed to determine if the problem is widespread and whether different plants species in and around the field are affected, which could indicate an abiotic cause.

Symptoms with a nutritional or physiological cause have a more widespread occurrence within a field than infectious diseases. Initially, most disease causing pathogens will be isolated in areas and spread outward from those areas. Also, weeds or nonrelated crops are not typically affected. Soilborne pathogens are even more restricted within a field than foliar pathogens.

Diagnosis of Diseases Caused by Different Types of Pathogens


Fungi are multicellular microscopic organisms that can grow to their food, usually in the form of filamentous strands. Their growth pattern is radial, so on surfaces such as plant leaves, the effects of their growth may be seen as circular spots. However, fungal infections of other plant parts, such as roots, may produce no visible structures. Some symptoms can indicate these infections. For example, browning of the water-conducting tissues of the stem, in combination with wilt, can indicate infection by the Fusarium wilt fungus.

Other disease symptoms, such as blight (a general death of tissue), which can have a variety of causes, may require laboratory testing to confirm fungi as a cause. Fungi can produce specialized structures, such as spores, which are used for reproduction, dissemination through space and time, and survival. Sclerotia are structures that function in the long term survival of many soilborne pathogens. The southern blight fungus which infects many vegetables forms sclerotia resembling mustard seeds.

Most fungi that infect leaves require free moisture to initiate infection, with the exception of powdery mildew fungi, which need only high humidity to initiate infection.


Bacteria are single celled microscopic organisms, which survive by becoming dormant. The most notable exception to this is the pathogen that causes common scab on potato: this is a filamentous, multicelled bacterium that produces spores. They can be transported by wind driven rain, by insects, or the movement of infected plant parts, including seed. Bacteria that infect leaves may cause circular spots, but irregular shaped lesions that donโ€™t extend beyond veins are more characteristic for bacterial infections.

They can also cause soft rots of vegetative parts that are usually characterized by a foul smell. Other bacterial diseases that produce symptoms such as wilt require laboratory analysis for diagnosis.

Mycoplasmas are bacteria-like, only structurally simpler and smaller than bacteria. They are transmitted by leafhoppers. The most notable disease of vegetables caused by a mycloplasma is aster yellows, which affects carrots, celery and related plants. The symptoms of aster yellows are distinctive: leaves have a bronzed appearance and flowers are abnormal (leaf-like tissue grows from them, instead of petals.)

Characteristics to evaluate when Diagnosing Diseases

General SymptomsSpecific SymptomsPossible Causes
Distribution in the FieldSymptoms observed over a wide area on several cropsSoil Problem
Low Fertility
Insect Injury
Physiological Problem
Symptoms observed over a wide area on a single cropSoil Problem
Low Fertility
Insect Injury
Foliage Pathogen (advanced stage of epidemic)
Symptoms observed scattered over a field on a single cropSoilborne Root Rot Fungi
Soilborne Wilt Organisms
Foliar Pathogens
Soil Problem
Insect Injury
Foliage symptomsGeneral yellowingWet Soil
Low Fertility
Root Rot Pathogens
Necrotic spots on leavesSpots Generally Round (Fungal leafspot)
Spots Generally Angular (Bacterial leafspot)
White powdery substance on leaf surfacePowdery Mildew
Light yellow spot on upper leaf surface downy growth on lower surfaceDowny Mildew
Ruptured areas on lower leaf surfaceWhite in center of ruptured area (White Rust)
Reddish brown to orange in center of ruptured area (Rust)
Light and dark green areas on a leafAppears in a random pattern in the field (Virus)
Appears in rows (Nutrient Deficiency)
Leaves distortedVirus
Leaves with holes or chewed areasInsect Injury
Leaves yellow, wilt and dieRoot decayed (Root Rot)
Brown ring in vascular portion of root (Fusarium Wilt)
Roots cut or damaged by feeding (Insects; Gophers or Moles)
Damage in low areas of field (Root Rot; Poor Drainage)
Root SymptomsRoots decayedRoot Rot
Poor Drainage
Roots with discoloration beneath outer layerFusarium Wilt
Swellings on roots and stemLarge swelling (Crown Gall Bacterium)
Small swellings which appear in a random patter on roots (Root Knot Nematode)
Small swelling at root tips (Dagger Nematode)
Root tips deadIsolated areas (Nematodes; Fertilizer Burn)
Affected area is in a pattern or over the general field (Fertilizer Burn)
Roots dead with white fungal strands around the stem at the soil lineSouthern Blight
Fruit SymptomsFruit decay scattered over fruit surfaceWatery soft decay, foul odor (Bacterial Soft Rot)
Firm to watery soft rot (Fungal Decay)
Hard black decay at blossom endBlossom end rot (Nutrient and Water Problem)
Fruit distortedVirus
Faint rings visible on fruitVirus
Light colored blotchy appearanceInsects
Dark raised areas on fruitBacterial Leafspot
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Viruses are submicroscopic entities that can only replicate inside living plant cells. They require agents such as insects to transmit them to plants. A typical virus symptom is a mosaic pattern on leaves, but viruses may cause other symptoms, such as necrotic lesions and stunting, which can have other causes. Insect vectors of viruses include by aphids, leafhoppers, white flies and thrips. Viruses often have wide host ranges, including weeds that are not botanically related to the crop, and symptoms are not always produced in these plants.

Although some viruses can tentatively be identified by symptoms produced on plants (particularly mosaic or ringspots), accurate diagnosis requires laboratory testing.


Nematodes are microscopic roundworms that feed on the roots of plants. The root knot nematode produces root galls and deformed roots on a wide range of crops. Heavy infestation can lead to wilting and death of plants. Nematodes can also cause stubbiness, necrosis and stunting of roots, but these symptoms are not distinctive. Soil or root analysis is required to confirm diagnosis.

Environmental Factors Affecting Plant Pathogens


Soil temperatures that are suboptimal for seed germination and seedling growth can favor the development of damping off pathogens, such as Pythium and Rhizoctonia. Often, the impact of these pathogens can be reduced by delaying planting, until the soil temperature increases. Foliar pathogens have different optimal temperatures for development. Symptoms of bacterial diseases on leaves are produced at high temperatures, at which a fungal disease like downy mildew might be halted. These temperature requirements are known for many diseases and with a disease like late blight of potato, can be used to accurately apply fungicides when they are needed.


Moisture is the driving force for foliar diseases. Free moisture on the plant surface is necessary for growth and infection of many bacteria and fungi. There is usually a minimum, critical time requirement. Moisture can also infect spore production by fungi. This characteristic is the basis of a predictive system for fungicide choice for management of purple blotch of onion.

Saturated soil moisture conditions can create an environment conducive for root-rotting pathogens such as Pythium or other fungi that cause fruit rot.

Soil pH

Soil pH affects the activity of some soilborne pathogens. Diseases caused by the cotton root rot fungus tend to occur in alkaline soils, while Fusarium wilt diseases are more prevalent in acidic soils. The growth of the common scab pathogen of potato is reduced in acidic soils. However, it is generally not feasible to alter soil pH to manage disease.

Disease Control Methods

Cultivar Selection

In some cases, vegetable cultivars may be resistant or tolerant to important diseases. Resistant cultivars have no or low severity of disease, while tolerant cultivars may become diseased without incurring yield loss. The use of these cultivars does not necessarily eliminate the need for other disease management approaches, such as the use of fungicides.

Disease-Free Planting Material

Several pathogens can be spread by contaminated seed, for example, the bacteria causing leaf spot of pepper and tomato, black rot of crucifiers and fruit blotch of watermelon; and fungi causing gummy stem blight and anthracnose on watermelon. Some seed companies indicate whether seed lots have been tested for these pathogens. However, low levels of seed contamination could increase if transplants are produced from the seed. Infected transplants may have slight or no symptoms. The use of a soilless mix and good sanitation practices during the production of the transplants will greatly reduce the risk of infection by soilborne pathogens.

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The risk of introducing a foliar epidemic, such as gummy stem blight, can be minimized by inspecting transplants and making preventative applications of fungicides or bactericides (copper-based) early in the season.


Many pathogens which cause diseases survive in the soil, on crop residue. Rotation with nonsusceptible crops, or fallowing, can reduce the pathogen population. Rotation is not a practical alternative for some soilborne fungi, such as Fusarium wilt fungi and the southern blight fungus, because their survival structures persist for years in soil. White rust, an important fungus disease of spinach, mustard, turnip and swiss chard, forms survival structures in the leaves of diseased plants that require 2 to 3 years to die out.

Burial of crop residue can augment the beneficial effects of crop rotation. Many foliar pathogens can survive in crop residue, but only for one or two years. Burial of crop residue decreases pathogen survival and physically removes their access to the new crop. Shredding of crop residue can speed up the decomposition of certain pathogens. For example, the bacterium that causes black rot of cabbage can survive in plant residue for nearly a year, but if the residue is shredded, the survival time decreases to less than 2 months.

A pathogen that attacks one member of a plant family frequently will infect other members of that family or group. Table VII-2 lists vegetables which are susceptible to similar diseases. A standard rotation program should use only one member of each group on a site in a 2 to 3 year period. An exception to this recommendation is the Fusarium wilt fungus. There are variants of this fungus that infect one crop only. Thus, the Fusarium wilt fungus that infects watermelon will not infect cantaloupe or other cucurbits and these crops can be grown in soils where Fusarium wilt of watermelon was a problem.

Rotation is important in the control of root knot nematodes. If susceptible crops are grown repeatedly on nematode infested land, production levels decrease until susceptible crops are no longer economical. Onions, shallots, garlic, leek or sweet corn should be grown on sites where root knot nematodes are a known problem. Fallowing can also reduce populations, but the fallow land must be kept weed free, since many weeds are also hosts for this nematode.

Common Diseases of Specific Vegetables and their Control

Beans, SnapSouthern BlightApply preplant soil fungicide
Deep burial of crop residue
Damping OffPlanting at soil temperature > 60ยฐF
Plant on raised beds
Plant treated seed
Apply preplant soil fungicide
Bean Mosaic (virus)Virus-free seed
Resistant cultivars
Bacterial BlightPathogen-free seed
Apply copper fungicides
Two year crop rotation
Cercospora and other Fungal LeafspotsApply fungicides as needed
Two year crop rotation
White MoldApply fungicides as needed
Wide row spacing and orientation to favor drying of the canopy
RustApply fungicides as needed
Crop rotation
Resistant cultivars
Cabbage, Cauliflower, Broccoli, KaleBlack RotPlant hot water treated seed
Plant resistant varieties
Plant on raised bed to avoid flooding
Two year crop rotation
Downy MildewPlant resistant varieties
Apply fungicides as needed
Alternaria LeafspotApply fungicides as needed
Cucurbits: Watermelon, Pumpkin, Cantaloupe, Squash, Cucumber, CushawFusarium WiltCrop rotation (5+ years)
Resistant cultivars
Powdery MildewResistant cultivars
Apply fungicides as needed
Downy MildewResistant cultivars
Apply fungicides on a preventative basis
Anthracnose (watermelon, cucumber, cantaloupe)Resistant cultivars
Crop rotation
Apply fungicides on a preventative basis
Alternaria Leafspot, Cercospora LeafspotApply fungicides as needed
Two year crop rotation
Angular LeafspotPathogen-free seed
Apply copper fungicides
Avoid overhead irrigation
Bacterial Wilt (cucumber)Control beetle vector
Resistant cultivars
Fruit Blotch (watermelon)Pathogen-free seed
Copper fungicides
Two year crop rotation
Avoid overhead irrigation
Gummy Stem BlightTwo year crop rotation
Apply fungicides on a preventative basis
Choanephora Wet RotFrequent sprays of blossoms with copper fungicides
Keep fruit cool and dry after harvest
Virus DiseasesResistant cultivars
CarrotBacterial Soft RotMinimize injury during harvesting, grading and packing.
If carrots are washed after harvesting, they can be dipped in a 1:500 solution of sodium hypochlorite (5.25%)
Store at a temperature just above 32ยฐF.
Crown RotCrop rotation (4 to 5 years)
Cercospora or Alternaria Leaf BlightApply fungicides as needed
Aster YellowsControl leafhoppers
Control weeds in and around fields
Corn, Sweet & PopNorthern Corn Leaf BlightBurial of crop residue
Apply fungicides as needed
Rusts (Common, Southern)Resistant cultivars
Crop rotation
Burial of crop residue
Downy MildewMetalaxyl/mefenoxam seed treatment
Do not plant on land subject to flooding
Do not plant sweet corn following sorghum
Two year crop rotation
Common SmutResistant cultivars
Maize Dwarf Mosaic VirusResistant or tolerant cultivars
Eradication of johnsongrass in and around the field
EggplantSouthern BlightDeep burial of crop residue
Crop rotation (do not follow beans, tomatoes, southern peas, okra or peanuts)
Verticillium WiltSoak seed for 20 minutes in 120ยฐF water
Phomopsis BlightResistant cultivars
Pathogen-free seed
Three year crop rotation
Apply fungicides as needed
LettuceBacterial Soft RotsPlant in well-drained soil
Use furrow or drip irrigation
Downy MildewResistant cultivars
Three year crop rotation
Apply fungicides as needed
Bottom RotDo not plant lettuce following tomatoes, Irish potatoes, or beans
Plant on wide, raised beds
Deep burial of crop residue
Apply fungicides as needed
Sclerotinia DropFollow long rotations
Plant on well-drained soil
Use furrow or drip irrigation; Resistant cultivars
Apply fungicides as needed
Lettuce MosaicControl weeds in and around the field
Plant only Mosaic Indexed seed (MTO)
Resistant cultivars
Mustard, Turnip, RadishWhite Rust & Downy MildewApply fungicides as needed
Crop rotation
Burial of crop residue
Anthracnose & Cercospora LeafspotTwo year crop rotation
Apply fungicides as needed
Onion, Garlic, ShallotPink RootResistant cultivars
Purple BlotchCrop rotation
Apply fungicides as needed
Botrytis Leaf BlightApply fungicides as needed
Pea (English, Sugar Snap, Edible Pod)Fusarium and Pythium Root RotCrop rotation
Powdery MildewApply fungicides as needed
Resistant cultivars
Pepper (Bell and Hot)Phytophthora BlightPlant on well-drained soil
Plant on raised beds
Apply fungicides as needed
Cercospora LeafspotOne year crop rotation
Apply fungicides as needed
Powdery MildewApply fungicides as needed
Viruses (several)Control weeds in and around field
Resistant cultivars
Bacterial SpotResistant cultivars
Apply copper bactericides
PotatoBlack LegAvoid excessive irrigation
Avoid washing seed potatoes
Common ScabMaintain high soil moisture before and after tuber set
Early BlightApply fungicides as needed
Late BlightPreventative applications of fungicides
VirusesPlant virus-free seed
Spinach, Swiss ChardFusarium WiltLong crop rotation
White RustThree year crop rotation
Apply fungicides as needed
Burial of crop residue
Resistant cultivars
Downy MildewCrop rotation
Soil treatment with metalaxyl or mefenoxam Resistant cultivars
Burial of crop residue
Fungal LeafspotsApply fungicides as needed
Crop rotation
Burial of crop residue
Viruses (several)Resistant cultivars
Control weeds in and around the field
SweetpotatoScurfDo not use manure where sweet potatoes are to be planted
Plant slips from disease free roots
Crop rotation
Southern BlightDeep burial of crop residue
Crop rotation
Black RotPlant clean slips clipped 1 inch above the soil line
Crop rotation
TomatoFusarium WiltResistant cultivars
Southern BlightCrop rotation
Deep burial of crop residue
Apply soil fungicide as preplant treatment
Early BlightApply fungicides as needed
Septoria Leaf SpotCrop rotation
AnthracnoseResistant cultivars
Do not plant tomatoes following cabbage, lettuce, mustard and solanaceous weeds
Apply fungicides as needed
Stemphylium Leaf SpotApply fungicides as needed
Late BlightApply fungicides as needed
Use plastic mulch to prevent fruit from coming in contact with the soil
Avoid heavy irrigations just prior to and during harvest
Buckeye RotThree year crop rotation
Plant on raised beds
Avoid heavy applications of water just prior to and during harvest
Tomato Spotted WiltControl thrips
Rogue diseased plants
Do not plant tomatoes near Irish potatoes
Other VirusesResistant cultivars
Control weeds in and around field


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