Diseases of Field Crops: Alfalfa Diseases


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Pub 811: Agronomy Guide >Diseases of Field Crops> Alfalfa Diseases

Order OMAFRA Publication 811: Agronomy Guide for Field Crops


Seedling Diseases

Pythium Seed Rot
Pythium Damping-off
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 weather.

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 plant tissue.

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 growth
  • 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.

Plate 140. Verticilllium wilt initially affects each stem, causing stems to wilt, curl inward and become bleached. Growth is stunted.

Photo showing how phytophthora root rot infection begins as the plants emerge. Infected seedlings are stunted and begin to wilt.

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 or die.

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)
(Colletotrichum trifolii)
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 injury.

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.

Plate 141.Fusarium root rot appears as rusty, dark brown strands in the xylem of the root.

Photo showing how fusarium root rot appears as rusty, dark brown strands in the xylem of the root.

Leaf Diseases

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.

Plate 142. 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.

Photo showing how 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 of the 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 www.ontario.ca/crops.

Plate 143. Verticilllium wilt initially affects each stem, causing stems to wilt, curl inward and become bleached. Growth is stunted.

Photo showing how verticilllium wilt initially affects each stem, causing stems to wilt, curl inward and become bleached. Growth is stunted.


For more information:
Toll Free: 1-877-424-1300
E-mail: ag.info.omafra@ontario.ca
Author: OMAFRA Staff
Creation Date: 13 May 2009
Last Reviewed: 13 May 2009