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811: Agronomy Guide >Diseases
of Field Crops> Alfalfa Diseases
OMAFRA Publication 811: Agronomy Guide for Field Crops
Pythium Seed Rot
Pythium Seedling Blight (Pythium spp.)
Incidence: Pythium seed rot, damping-off or seedling
blight is predominantly an early-season fungal disease of alfalfa.
Infection of alfalfa plants most often occurs from the time of planting
to several weeks after emergence.
Appearance: Infected seeds may rot. Severely infected
seedlings may wilt, collapse and die. Look for wet or watery lesions
on the roots and hypocotyl of infected plants. A girdling, pinching
or damping-off of the stem at the soil line may be seen, causing
the seedling to fall over and die. Fields are most often affected
by the disease in circular or irregular patches.
Disease Cycle: Pythium seed rot, damping-off or
seedling blight is closely related to phytophthora root rot. Both
produce mobile spores that move through the water film between soil
particles to locate and subsequently infect alfalfa roots.
Management Strategies: Drain excess soil moisture
and avoid compaction. Plant when soil and weather conditions favour
rapid emergence and early growth of seedlings. Increase plant populations
to compensate for any plant losses. Seed treatments will provide
some protection to vulnerable seedlings.
Phytophthora Root Rot (Phytophthora medicaginis)
Incidence: Phytophthora root rot is an important
and common disease of alfalfa. The disease shows up mainly on poorly
drained soils or on clay loam soils during extended periods of wet
Appearance: Infection occurs as plants emerge,
so new seedlings are most at risk. As the stand gets older, the
risk declines somewhat. Infected seedlings are stunted, grow slowly
due to a reduced root system and eventually begin to wilt (See Plate
140). A girdling, pinching or damping-off of the stem at the
soil line may be seen, causing the seedling to fall over and die.
The field is often affected by the disease in circular or irregular
patches. In older seedlings or on established plants, a reddish-brown,
water-soaked lesion may develop on the roots. In severe cases, root
lesions become black, and the taproot may rot entirely. Since the
plant is unable to supply water and nutrients, the plant wilts and
dies. Lower leaves are yellow at first and as the disease progresses
may turn reddish-brown.
Disease Cycle: Phytophthora root rot is a soil-borne
disease that can cause root injury or plant death. The fungus survives
as thick-walled spores that produce mobile spores in the spring
that migrate and infect the plant roots. Water is important since
these mobile spores move in the water film between soil particles.
Disease development is favoured when moderate to high temperatures
occur (21°C-32°C) during humid or wet conditions. Fields
that are compacted or poorly drained are especially prone to the
disease. The fungus is able to survive for many years in infected
Management Strategies: For fields with a history of phytophthora
root rot, use highly resistant varieties and seed treatments. Consult
the current edition of the Ontario Forage Crop Variety Performance
Report, available from an OMAF Resource Centre, for variety
ratings for phytophthora root rot. Other management practices that
help in managing this disease include:
- maintaining good soil fertility, that will promote lateral root
- removing excess moisture through improved tile drainage and
ensuring reduced compaction
- avoiding other stresses such as leaf-feeding insects, weeds
and untimely cuttings that may stress the plants making them more
susceptible to phytophthora root rot. Crop rotation has little
effect on this disease.
Verticilllium wilt initially affects each stem, causing stems to
wilt, curl inward and become bleached. Growth is stunted.
Aphanomyces Root Rot (Aphanomyces euteiches)
Incidence: Aphanomyces root rot (ARR) is a potential
economically significant alfalfa disease that is considered a major
disease in alfalfa seedlings, particularly in wet, saturated soil
conditions. ARR also affects surviving adult alfalfa plants and
can dramatically reduce yield and vigour of established stands.
Appearance: Infected seedlings are stunted but
remain upright, and have yellow leaflets and cotyledons. Roots and
stems are grey and water-soaked in appearance. Severely infected
seedlings turn light to dark brown.
Classic symptoms in established stands are stunted, yellow plants.
Look for the absence of the fine, fibrous roots. Lateral roots are
often rotted and even absent. Affected established stands are typically
thin, yellow and weedy, and show reduced rhizobia nodulation. Symptoms
appear similar to nitrogen deficiency. Regrowth is slow with poor
vigour, and therefore yields are low. Because of the stunted root
system, infected alfalfa stands do very poorly during seasons with
extended dry weather.
Phytophthora tends to kill seedlings more quickly and extensively
than ARR by attacking the tap root. However, aphanomyces is considered
more chronic, less likely to cause seedling death but more likely
to result in stunted, low-yielding alfalfa crops.
Disease Cycle: The fungus survives in the soil
on infected plants or debris. For the initial infection to occur,
the soil must be saturated. Disease development is favoured when
moderate to high temperatures occur (16°C-30°C) during humid
or wet conditions. Fields that are compacted or drain poorly are
especially prone to the disease.
Management Strategies: Aphanomyces root rot is
best managed by using resistant varieties, similar to what has been
done with phytophthora-resistant alfalfa varieties. Race 1 and race
2 isolates of aphanomyces have been identified. Race 2 is more virulent.
Many alfalfa varieties are resistant to race 1, but far fewer are
resistant to race 2. Consult with seed company representatives or
see the Ontario Forage Crop Variety Performance Trial Report
or the website at www.ontario.ca/crops
for current information on available ARR resistant varieties. Fungicide
seed treatments are not effective against ARR.
Brown Root Rot (Phoma sclerotioides)
Incidence: Brown root rot was confirmed in Ontario
during the 2007 growing season. It is most likely widespread in
the province. It most often occurs in areas with severe winter conditions.
The disease is often associated with winterkilled areas, plants
that are slow to produce spring growth (slow emergence from winter
dormancy) and yield loss.
Appearance: The tap roots, lateral roots and/or
crown have characteristic sunken brown lesions (almost black), and
in severe cases the tap root is rotted completely. The fungus does
not infect the above-ground parts of the alfalfa plant.
Disease Cycle: The brown root rot pathogen thrives
when soil temperatures are 15°C or less. Therefore, the fungus
is most active in the fall and spring when environmental conditions
are favourable for infection and the plants are dormant. Infection
of the roots and/or crowns can have a detrimental impact on over-wintering
health and promote other diseases, winterkill, stand decline and
yield loss. Since the fungus grows very slowly, damage is not often
noticed until the second or third year when plants become stunted
Management: Resistant varieties for Ontario are
not available. Management strategies to help reduce losses and increase
stand longevity include:
- avoiding fall harvest during the critical harvest period (reduce
plant stress going into winter)
- maintaining proper soil fertility and rotating out of alfalfa
for at least 3 years
Other Crown and Root Rots
Stresses such as leaf diseases, insects, frequent or untimely harvests,
winter conditions and low soil pH, increase the severity of crown
and root rots. Stresses during the growing season render the plants
more susceptible to winter stress. Good crop management practices,
especially a good harvesting schedule, and maintenance of adequate
soil fertility and proper pH, help reduce disease severity. Control
leafhoppers in alfalfa. Avoid mechanical injury of the crowns as
much as possible. Crowns are easily injured by machinery and by
livestock tramping, especially when the soil is wet.
Anthracnose (in alfalfa)
Northern Anthracnose (in red clover) (Kabatiella caulivora)
Incidence: In alfalfa, anthracnose occurs mostly
in the extreme southwest portion of the province. Northern anthracnose
is more widely distributed in red clover fields. Losses in both
alfalfa and red clover due to anthracnose can be as high as 25%.
Appearance: Although symptoms can occur on the
stem and leaves, it is the damage to the crown area that is most
important. Stem symptoms on resistant varieties are small, black,
irregular-shaped lesions. Lesions on susceptible varieties are large,
sunken and oval to diamond-shaped. These lesions have a tan to straw-coloured
centre, with a dark-brown border. When the fungus reproduces, the
centre of those stem lesions produced on susceptible varieties will
contain small, black, fruiting bodies. These can be easily seen
with the eye or a simple hand lens. In severe cases, the lesions
will join together and eventually girdle the entire stem, causing
wilting or killing of the stem. Dead stems and leaves (shoots) become
white and have a characteristic shepherd's hook appearance. These
are scattered through the field. They are often confused with two
other diseases (rhizoctonia crown rot or fusarium wilt) or frost
Damage to the crown appears as a blue-black discolouration of
the crown tissue. Infected plants are easily broken at the base.
If the diseased tissue is light brown, the cause is most likely
not anthracnose but either rhizoctonia crown rot or fusarium wilt
(See Plate 141). Crown infection results
in fewer stems per plant and eventually plant death.
In red clover, northern anthracnose can be very destructive. In
addition to most of the symptoms described for alfalfa, infection
can result in cracking of the stem surface.
Disease Cycle: The fungus thrives during moderate,
humid weather conditions and survives in diseased stems, leaves
or debris. Spores produced in the spring are spread by rain. The
rain causes splashing, which moves spores from infected plants to
neighbouring plants. The fungus can be spread from field to field,
through equipment, soil and water erosion.
Management Strategies: Varieties with moderate-to-high
resistance to anthracnose are available. Clean harvest equipment
between fields. Crop rotation has been found to have limited success
in managing the disease in alfalfa, but has had better success in
red clover, which does not have the same degree of resistance.
root rot appears as rusty, dark brown strands in the xylem of the
Common Leaf Spot (Pseudopeziza medicaginis)
Leptosphaerulina (lepto) Leaf Spot (Leptosphaerulina trifolii
or L. briosiani)
Incidence: Although both these leaf spot diseases
occur in Ontario, common leaf spot is more destructive. Leaf spot
infection can cause premature leaf loss and thereby reduce the quality
of forage, yield, health and vigour of the crop.
Lepto leaf spot can be confused with common leaf spot since leaf
symptoms begin as small, black spots (1-2 mm (1/16 in.)) that have
a light tan or brown centre. A yellow halo usually surrounds the
leaf spots. Unlike common leaf spot, these lesions will join together
to form larger lesions (See Plate 142).
Appearance: Leaf spot diseases are first seen
on the lower leaves and then develop or move up the plant. Common
leaf spot produces small, circular (1-2 mm (1/16 in.)) leaf spots
that are brown to black. These lesions rarely join together to form
larger lesions. Lesions on the upper leaf surface often have a raised
centre. Within these raised centres, the black fruiting bodies (bumps)
are easily seen with a hand lens. To be sure, put some infected
leaves into a plastic bag with wet paper towels, to help speed the
production of these fruiting bodies. Infected leaves become yellow
(chlorotic) and drop prematurely.
Disease Cycle: Cool, wet weather favours leaf
spot development, so it is found primarily in the early cuttings
(spring and early summer) and regrowth (fall). These fungi survive
in infected leaves and on dead leaves found on the soil surface.
Spores produced on living and dead leaves are spread through the
air, where they infect new growth. Young leaves are the most susceptible
to leaf spot diseases.
Management Strategies: Timely harvesting of forages
is important to reduce leaf loss and minimize disease in the regrowth.
Some varieties tolerant of common leaf spot are available, but no
resistance or tolerance to lepto leaf spot has been found. There
are few practical control strategies available for leaf spot diseases
in forages. Leaf spots can reduce the protein level in legume leaves,
so it is important to balance the time of harvest between the optimum
stage for highest protein and the level of leaf spot disease.
Leptosphaerulina (lepto) leaf spot starts as small dark spots that
enlarge until spots join together. Spots will have a tan centre
and a yellow halo.
Bacterial Wilt (Clavibacter michiganensis)
Incidence: Bacterial wilt has historically been
one of the most important forage diseases, not only in Ontario but
anywhere forages are grown. The development of resistant varieties
has made the disease less common.
Appearance: Symptoms become apparent as the stand
gets older (3 or more years). Infected plants are stunted and have
a yellow-green colour. In severe cases, the plant has spindly stems
with small, distorted leaves. Infected plants that are stressed
by water, heat or both will wilt or die and are scattered throughout
the stand. Infection stresses the plant and increases its susceptibility
to winterkill. Cutting the taproot in half (in cross-section) will
show a light brown-to-yellow discolouration of the vascular tissue
near the outer edge.
Disease Cycle: This disease is caused by a soil
bacteria that survives in diseased alfalfa roots and in plant debris
for at least 10 years. Infection occurs through wounds to the roots
and crown or through cut stems. The bacteria causes the plant to
wilt since it grows in the vascular system of the plant, thereby
blocking water and nutrient movement in the plant.
Management Strategies: All recommended varieties
are resistant to the disease. Since the bacteria can be spread through
wounds, cut young, less-susceptible stands first and then move to
older stands. Harvest stands when the plants are dry. This will
limit or reduce potential spread from infected to non-infected plants.
The bacteria can be spread in seed and hay.
Verticillium Wilt (Verticillium albo-atrum)
Incidence: Verticillium wilt of alfalfa is a disease
that increases with stand age. It mainly occurs after the second
year of production. The fungus responsible for this disease can
be found in most areas of Southern Ontario. Farms with a history
of the disease may find dead plants in younger stands (second-year).
Verticillium wilt can reduce yields up to 50% and shorten the life
of the stand.
Appearance: Initially, a few stems are affected
and eventually, the leaves on infected plants wilt, curl inward
and become orange-brown or tan-brown (bleached) (See Plate
143). In the early stages of disease development, leaves will
exhibit a V-shaped yellowing of the leaflet tips. Growth is often
considerably stunted, and plants eventually die. Although all the
plant leaves may die, the stems remain green. The fungus enters
through the root or cut stems and is spread from older infected
stands to younger stands by harvest equipment, insects and manure
application. The disease causes a brown discolouration of the interior
root and stem (vascular) tissue. Cutting the stem in half will usually
reveal this browning.
Disease Cycle: The Verticillium fungus enters
the plant primarily through the roots. The fungus blocks or inhibits
the plant's ability to move water, resulting in wilting. The fungus
survives (overwinters) in infected plant debris. During cool, moist
conditions, numerous spores are produced on diseased tissue.
Management Strategies: The disease is best managed
by the use of varieties rated as resistant and highly resistant.
For variety ratings for verticillium wilt, consult the current edition
Ontario Forage Crop Variety Performance Report, available
at an OMAFRA Resource Centre and online GoForages.ca.
Treating seed with a fungicide will help reduce early infection.
The fungus is spread primarily on the cutting bar of forage harvesting
equipment. Before harvesting, clean the cutting bar with a 1% solution
of bleach followed by a clean water rinse and oil spray. Cut the
youngest non-infested fields first, working towards the oldest fields.
Early harvest can limit yield and quality losses and slow fungus
spread from field to field. Wait 2-3 years between alfalfa crops.
Maintain a good weed control program, since some weeds can be alternate
hosts. For additional information, see the OMAF website at
Verticilllium wilt initially affects each stem, causing stems to
wilt, curl inward and become bleached. Growth is stunted.