Diagnosing alfalfa stand establishment and seedling growth problems in the fall

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Where soil moisture was good in August as a result of rainfall or irrigation, some producers planted alfalfa. Since then, it has been unusually hot and dry again. The stands, especially on dryland fields, may be struggling a bit in some cases until the weather becomes more favorable again. There may be issues with either stand establishment or seedling growth. The goal is to have about 15-20 vigorously growing seedlings per square foot before winter.

The following are some suggestions for diagnosing stand establishment and seedling growth problems from a fall seeding.

Stand establishment problems.

  • Planting depth. Alfalfa seed is very small, and the margin for error on seeding depth is also very small. Ideally, alfalfa seed should end up about ¼ to ½ inch below the soil surface. If the seed were placed on the surface of a firm, mellow seedbed and pressed with a roller or press wheel, this should have positioned the seed correctly within the soil. But it the seed end up more than ¾-inch deep, they probably will not be able to emerge well. Seed that remain on the soil surface may germinate, but the seedlings will be weak.
  • Poor seedbed. It is very difficult to get uniform, shallow seed placement in a rough, cloddy seedbed. Those seed that end up too deep in the soil may not emerge. 
  • Dry soils. With wheat and most other crops, seed can be planted down into moisture and emerge even if there is no rain after planting. Alfalfa seed is planted in the very top half-inch of soil, which is almost always dry at the time of planting and does not have enough moisture to germinate the seed. As a result, alfalfa seed requires a rain after planting to germinate and emerge. For best stand establishment, soils should have adequate moisture about 1 to 3 inches below the soil surface so that seedlings can survive even if the seed germinated as a result of only a very light rainfall.
  • Poor quality seed. Poor emergence can be caused by using seed with poor germination, although this almost never happens anymore with commercial seed.
  • Seedling diseases. Several fungi, including Phytophthora, Pythium, Aphanomyces, Fusarium, and Rhizoctonia, can attack alfalfa seedlings. Traditionally, Phytophthora and Pythium have been considered the primary pathogens in Kansas. Seedling diseases should be suspected when emergence is poor and/or there are obviously stunted, discolored, or dead seedlings. Alfalfa seedling diseases are more severe in cold wet conditions. Planting good quality seed when conditions are favorable for rapid germination and growth is important in reducing losses to seedling pathogens. Using varieties that are resistant to Phytophthora is your best bet for avoiding this disease. However, the resistance genes may not be expressed when the plants are very small and it is a good idea to protect the seed treatment with a fungicide such as Apron or Allegiance that is effective against Pythium and Phytophthora.

Seedling growth problems.


  • Poor seed inoculation. Unless the seed is pre-treated with an inoculant, alfalfa must be treated with a rhizobium inoculant that is specific to alfalfa. If the seed was inoculated, but seedlings are still chlorotic, it could be because the inoculant had died during storage. Heat, direct sunlight, and drying can all affect survival of rhizobia. Inoculants should be frozen or stored in a cool place. Prolonged storage can also reduce the viability of rhizobium.
  • Low soil pH. Alfalfa grows best in soils with a pH of 6.5-7.2, and does not like acid soils. If seedlings are weak and do not seem to be growing and developing well, check the soil pH for acid soil conditions. This condition should have been corrected before planting. If lime was surface-applied before planting, it may not have had enough time to work down into the topsoil and correct a low-pH condition.
  • Herbicide carryover. Sulfonylurea herbicide carryover can result in severe stunting of new alfalfa seedlings.
  • Allelopathy. If alfalfa is seeded into an old alfalfa stand, the new seed will emerge but the seedlings often have poor early vigor and eventually die.
  • Low soil nitrogen levels. About 10-20 lbs per acre of soil nitrogen is needed for seedlings to develop leaves and roots while the rhizobium is becoming established in the roots. Usually, there is enough soil nitrogen available on the kinds of good soils into which alfalfa is typically planted. But on poorer soils, or in no-till systems, there early-season yellowing may be caused by nitrogen deficiency. If the seed was properly inoculated, the plants should grow out of this before winter.
  • Insects. Spotted alfalfa aphids can cause patches of yellow areas due to a toxin it transmits to the plants. Even low numbers of this insect (1 or 2 per seedling) can cause significant damage to alfalfa seedlings, and should be controlled. The blue alfalfa aphid can be just as damaging to new alfalfa seedlings, but this insect does not cause yellowing. Other insects can also damage new alfalfa stands in the fall by chewing the leaves off. These include grasshoppers, cutworms, yellowstriped armyworm, corn earworm, fall armyworm, and alfalfa webworm. These insects can quickly destroy all plant tissue above the soil surface. Cutworms are an especially serious threat under dry fall conditions. The army cutworm feeds at or below the soil surface, cutting or defoliating plants. Infestations of 2-3 worms per square foot and 1-2 grasshoppers per square yard can be used as a general threshold in seedling alfalfa.
  • Seedling diseases. (See discussion in “Stand establishment” section above.)

Jim Shroyer, Crop Production Specialist

Erick DeWolf, Extension Plant Pathologist

Jeff Whitworth, Extension Entomologist