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How to Prevent Alfalfa Plant from Rotting

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by Dean Malvick, Assistant Professor of Plant Pathology Department of Crop Sciences University of Illinois at Urbana-Champaign

A goal for many forage producers is to plant alfalfa and clover, harvest high yields on an appropriate schedule, and retain stands for many years. Numerous obstacles, however, prevent this ideal scenario. Of those obstacles, diseases are among the most damaging. Diseases affect yield, persistence, and quality of forage crops and frequently force premature reestablishment of stands. Many disease affect roots, leaves, stems of alfalfa and red clover from the seedling to established stages. Three diseases that are particularly damaging will be emphasized in this presentation: Aphanomyces root rot of alfalfa, crown rots of alfalfa, and clover yellow mosaic virus.

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Alfalfa is an important forage crop for livestock farmers and a staple of agricultural production across many regions. However, this versatile plant can be susceptible to rotting, which poses a major threat to yields and profitability. In this article, we’ll explore the causes of alfalfa rot and provide actionable tips to prevent it.

What Causes Rotting in Alfalfa Plants?

Several factors can lead to the rotting of alfalfa plants

  • Excess Moisture – Waterlogged soils and poor drainage promote fungal and bacterial growth leading to rotting Flooding and heavy rainfall also contribute,

  • Compacted Soil – Restricted air flow and root damage in compacted soils create conditions conducive to rotting

  • Fungal Pathogens – Soil-borne fungi like Phytophthora, Pythium, Fusarium, and Rhizoctonia directly cause rotting of roots and crowns.

  • Bacterial Infections – Bacterial pathogens can also infect alfalfa and result in rotting. Common examples are Pseudomonas, Xanthomonas, and Streptomyces species.

  • Insufficient Air Flow – Lack of air circulation due to dense foliage or overcrowding enables persistence of moisture and pathogens.

  • Nutrient Deficiencies – Inadequate nitrogen slows regrowth and makes plants prone to rotting fungi after cutting.

  • Pests & Diseases – Alfalfa weevils, nematodes, and viral diseases weaken plants and predispose them to rotting.

8 Ways to Prevent Rotting of Alfalfa Plants

Here are some effective preventive measures to avoid alfalfa rot issues:

1. Ensure Adequate Drainage

  • Install drainage systems like tile drains in poorly drained fields.

  • Avoid low-lying areas and improve surface drainage through laser leveling.

  • Allow time between irrigations and rainfall events for soils to dry adequately.

2. Manage Soil Compaction

  • Limit equipment traffic on wet soils to prevent compaction.

  • Perform deep tillage to break up compacted layers if present.

  • Add organic matter like manure to improve soil structure.

3. Follow Proper Cutting Practices

  • Avoid cutting alfalfa when soils are saturated to prevent root and crown damage.

  • Allow adequate regrowth of at least 6 inches before next cutting to build carbohydrate reserves.

  • Leave higher stubble height of 3-4 inches after cutting to retain growing points and protect crowns.

4. Use Resistant Varieties

  • Choose alfalfa varieties bred for resistance against prevalent rot pathogens in your area.

  • Consult local extension resources for best variety recommendations.

5. Improve Air Circulation

  • Avoid overcrowding plants during establishment.

  • Conduct timely pruning and weed control to enhance air movement within foliage.

  • Wider row spacing also improves air circulation around plants.

6. Implement Crop Rotation

  • Rotate alfalfa fields annually or every 2-3 years with non-host crops like corn or small grains.

  • Rotation helps disrupt disease cycles and reduce root rot inoculum levels over time.

7. Apply Balanced Fertilizer

  • Soil test regularly and apply recommended phosphorus and potassium.

  • Top dress with nitrogen fertilizer after cuttings to aid regrowth.

  • Healthy, vigorous plants are less prone to rot issues.

8. Control Alfalfa Pests

  • Scout for alfalfa weevil, nematodes and signs of viral infection. Take timely control measures.

  • Their damage predisposes plants to secondary rot diseases.

Rotting can significantly impact yields, stand persistence and forage quality of alfalfa. By adopting proactive management practices like improving drainage, managing soil compaction, following proper cutting schedules, using resistant varieties, enhancing air flow, implementing crop rotation, applying balanced fertilizer, and controlling pests, alfalfa growers can prevent and minimize losses from rot issues. Being vigilant and addressing problems promptly also helps curb rot development in alfalfa fields.

how to prevent alfalfa plant from rotting

The Race is On for Aphanomyces Root Rot

One of the first diseases that often occurs after planting is Aphanomyces root rot. This disease, caused by the fungal-like pathogen Aphanomyces euteiches causes death and poor growth of seedling alfalfa in slowly drained fields. It also can be a chronic disease of established plants that may result in significant yield reduction. Aphanomyces root rot is similar to, and may occur in a complex with, Phytophthora root rot and Pythium damping off, diseases which also occur in wet or slowly drained soils (3). Plants infected with Aphanomyces usually are stunted and chlorotic before they wilt and die, whereas Phytophthora and Pythium tend to kill seedlings quickly before plants become severely chlorotic. Another clue to a potential problem with Aphanomyces is stunting and poor nodulation of an alfalfa cultivar that is highly resistant to Phytophthora. Aphanomyces root rot has also been related to increased damage to alfalfa from winter root heave damage (9). Perhaps because root rot of alfalfa that occurred in slowly drained soil was attributed to Phytophthora, Aphanomyces root rot was not recognized as a serious problem until the early 1980’s. Aphanomyces root rot is known to be a widespread problem for alfalfa in Wisconsin (4). Although Aphanomyces can infect red clover, it appears to be a minor problem on that crop (2).

Aphanomyces root rot of alfalfa can best be managed by avoiding slowly-drained soils and by using Aphanomyces-resistant alfalfa varieties. Fungicides are not available for control of Aphanomyces. Phytophthora and Pythium seed and root rots can be controlled with fungicidal seed treatments such as Allegiance-FL, ApronXL, or Apron-FL. These seed treatments are not effective against Aphanomyces. Alfalfa varieties rated highly resistant (HR) or resistant (R) to Aphanomyces root rot should be planted where slowly-drained soils occur and where Aphanomyces may be a problem (6, 8). Management of Aphanomyces root rot clearly became more challenging when different races of this pathogen were discovered.

Aphanomyces root rot of alfalfa is caused by two races of Aphanomyces. One race (race 1) was initially discovered and was used for development of most alfalfa cultivars with Aphanomyces resistance. Another race (race 2) was discovered that can kill and stunt cultivars that have resistance only to race 1. The frequency of race 1 and race 2 isolates were studied from 13 fields in Wisconsin (5). Aphanomyces isolates (total number = 405) were collected from the fields. The race of the isolates was determined by inoculation of Saranac (susceptible to races 1 and 2) and WAPH-1 (resistant to race 1) alfalfa varieties. The populations of the two races of Aphanomyces varied among the different Wisconsin fields. For example, 51 percent were race 2 in a field never used for alfalfa production and 27 percent of isolates were race 2 from a field used for pea production, while 43 percent of all isolates from fields with a history of alfalfa production were race 2. Race 2 isolates appear to be widespread in Wisconsin and other Midwestern states and this race of Aphanomyces occurs in fields with varied cropping histories.

Alfalfa varieties with resistance only to race 1 are vulnerable to Aphanomyces root rot in many areas due to the presence of race 2. Of eight alfalfa cultivars evaluated for resistance to both races in a recent study, all except those selected for R2 resistance were susceptible to R2 isolates (5). Several commercial alfalfa varieties are available that have resistance to both races of Aphanomyces. Race 2 isolates may represent a widespread risk to alfalfa cultivars with resistance only to race 1.

Crown Rots in Alfalfa: Perils to Persistence

Crown rot of alfalfa can be as damaging as it is frustrating to manage. This disease complex occurs in nearly every established stand of alfalfa. The older the stand, the more crown rot that typically occurs (7). Typical initial symptoms of crown rot include brown dead tissue in the crown and root cortex, and this may spread to kill the entire root core and crown buds. While it is difficult to prevent crown rots, we can gain understanding of what causes them, what factors favor development of crown rot, and what management steps we can take to reduce or delay their development.

Several fungi are commonly associated in a complex with crown rot disease. They include Phoma spp., Colletototrichum trifolii, Fusarium spp., Pythium spp, and Rhizoctonia solani. These pathogens can also cause other symptoms/diseases including root rots and stem infections. Thus, they may infect plants months or even years before crown rot develops, and isolation of these pathogens from plants does not mean that crown rot will develop.

These pathogenic fungi may only cause crown rots under specific, stress conditions. Plant stresses that may favor crown rots include poor fertility, low soil pH, other diseases, harvesting too often or too late in the season, and grazing animals or wheel traffic that damages the crowns. Because of the complex nature of this disease, alfalfa varieties with high levels of specific resistance to crown rots have not been developed. Crown rot damage can be reduced by choosing and planting adapted varieties that have resistance to multiple diseases, and by maintaining sound management practices that consider the stresses related to crown rots noted above.

How to Combat Alfalfa Seedling Diseases

FAQ

How do you treat alfalfa root rot?

The best way to manage Aphanomyces root rot is to plant Aphanomyces-resistant alfalfa varieties and improve soil drainage. Monitor at-risk fields for disease to inform management, which can also include planting non-host crops. Mefenoxam and metalaxyl seed treatments are not effective against A. euteiches.

Can a rotting plant be saved?

The best you can do is to take the plant out of its pot, remove the parts of the plant that are affected (including the roots) and repot into fresh compost. If the rot is visible on most of the plant’s roots and foliage, it’s unlikely that you will be able to save the plant.

What causes alfalfa to turn brown?

Brown root rot is caused by the fungus Phoma sclerotioides and can contribute to winterkill. Circular brown lesions form on roots and cause girdling in taproots, lateral roots, and feeder roots. Lesions will occasionally have black borders, which is indicative of brown root rot.

How do I know if my alfalfa plant has rot?

To evaluate stands, dig several alfalfa plants in the fall and look at the condi-tion of the root. This will give an idea of stand vigor and future life span. Some crown rot will be visible in most older stands. Look for the number of crowns and roots with rot and the degree of infection.

What diseases affect alfalfa plants?

Three diseases that are particularly damaging will be emphasized in this presentation: Aphanomyces root rot of alfalfa, crown rots of alfalfa, and clover yellow mosaic virus. One of the first diseases that often occurs after planting is Aphanomyces root rot.

How do you control Aphanomyces root rot in alfalfa?

Aphanomyces root rot of alfalfa can best be managed by avoiding slowly-drained soils and by using Aphanomyces-resistant alfalfa varieties. Fungicides are not available for control of Aphanomyces. Phytophthora and Pythium seed and root rots can be controlled with fungicidal seed treatments such as Allegiance-FL, ApronXL, or Apron-FL.

Does alfalfa have crown rot?

This disease complex occurs in nearly every established stand of alfalfa. The older the stand, the more crown rot that typically occurs (7). Typical initial symptoms of crown rot include brown dead tissue in the crown and root cortex, and this may spread to kill the entire root core and crown buds.

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