Propagation - My Set up and Methods

To propagate native seeds, you don’t need anything fancy! Depending on the scale of your propagation project you might not need all of these items. Recycled clear plastic clam trays with slits cut in the bottom can replace the growing trays and humidity domes for small propagation project.

Equipment Needed

  • Growing trays both with and without drainage holes
  • Vented Humidity Domes. These domes need to fit the growing trays.
  • Deepots (D40H) and stand. These are purchased from Steuwe & Sons
  • 2.5” pots
  • 5-6” pots
  • Shelving unit and/or table
  • Grow lights. These can be created from work light fixtures and Grow lights from a discount home supply store.
  • Potting mix
  • Perlite, vermiculite, coconut coir, or Bio-Fiber (I used to use peat moss but this isn’t environmentally friendly)
  • Labels with black marker
  • Cold frame (optional), This isn’t necessary but makes life easier. Without one plan to spend time moving trays in and out of your garage.
  • Grow mats are useful in the cold frame when my growing space in the house is filled and it is below 50° outside

My Set Up

My propagation set up is in the mechanical room. I use a 6’ table with Grow lights on chains hanging from the ceiling and a 3-shelf unit with Grow lights hanging underneath each shelf. Once the seeds are stratified and ready to germinate, they are moved here. They stay here until they are large enough to survive hardening off (the process of moving them outside for acclimation to natural weather elements).  I harden off in the cold frame or in the garage. See Hardening Off for more info on this process.

One photo shows a 6′ table with plants. I’ve fenced it to keep the curious cats from gnawing on the plants.

The photo on the right is the set up using a shelving unit. It has deer netting to prevent “cat interference.” 

This is the 6' table configuration. Because I have cats, I fence off the table.
Propagation shelf set up.

Seed Germination

This can be the tricky part!! Norman Deno scientifically documented many seed germination needs. Not all native seeds have the same germination requirements. These evolved differences enhance their germination rates. It helps to think like a seed and you can read more about by clicking the button below.  Prairie Moon Nursery provides a recommended germination guide with each purchased seed species.

Many native forbs require a period of cold, moist stratification. Generally this is 3 months of 40° followed by a period of 70° but this is a guideline and cannot be applied universally. Some seeds need only light to germinate; others need an alternating cold, warm, cold; some need to be inoculated; some need a special plant hormone called Gibberellic Acid-3 (GA-3); some need warm temperature only; and others need cold temperatures only. To be successful, it’s necessary to understand the species seed germination requirements.

Grasses will germinate at 70° without any prior treatment.

Scarification and Inoculants

I have tried various scarification methods such as sandpapering and nicking. Scarification is usually suggested with hard-coated seeds such as legumes but I have found it ineffective. Using the proper inoculate and cold moist stratification is all that is necessary. Legumes have a mutually beneficial relationship with a specific Rhizobia species. Legume seeds need to be innoculated prior to sowing them with the correct Rhizobia; this is a very easy process. Most reputable companies will provide the inoculate. If you have collected your own seed, Prairie Moon will sell the inoculate for the seed.

2 Stratification Methods

1. The Paper Towel Method

One way is by placing the seeds on one half of a paper towel, then folding the towel over and spraying it until it is moist. Once moist, place it in an unsealed baggie then place the baggies in a container with the open end up. The advantage to this system is the amount of room necessary for stratifying. The biggest disadvantage I’ve found with this system is with damp paper towels, it’s sometimes difficult to get the seeds off the paper towel.

I use the plastic container show to the right to control the water spray.


Propagation, stratification
Propagation, stratification
Propagation, stratification
Propagation, stratification

I take 2 paper towels, fold them half, and place the seeds on half. Then I spray the seeds with water to moisten.

The empty half of the paper towel is folded over the seeds and moistened. Then they are placed in quart size bags. Be sure to leave them unsealed.

The plastic bags are placed upright in a container before going into the refrigerator. I can easily open and spritz them to keep them moist.

2. Sowing Directly into the Substrate

This is my preferred method. Once the substrate is mixed (see below), fill your tray nearly full. Sprinkle it with 3 Tbsp kelp, mix gently, then tamp it down. To create a row for the seeds, take a ruler and wiggle out a shallow “V” (1/4-1/2” deep) about 3” apart. Place the seeds uniformly inside the “V” but without any spacing. The reason is many native seeds are not “pure live seed”; some are viable, some are not. The crowding is OK just don’t layer the seeds, if possible. With the super small seeds, such as Heuchera richardsonii (Alumroot), you can’t be exact.

Once sowed, pinch the “V” together and tamp down. Do not put much soil on top of the seeds. If the seeds require light to germinate, I just sprinkle substrate on top and tamp down. It’s imperative you tamp the soil; you need seed-to-soil contact.

Label each row. The easy labeling method is to use the first 3 letters of the genus and the first 3 letters of the species. For example, Gentian alba would be GEN ALB. I keep a spreadsheet of each species sown; it shows the date stratifying began, the date transferred to 70°, and the date of germination.

I place the growing tray on our screened-in porch. Occasionally, when it snows, I throw snow on top of them. You don’t want these to dry out. We have cats, so I have to place screens over the trays so the kitties don’t dig in them!

Propagation, germination trays

Once the 3 month cold, moist stratification is complete, the seeds are moved to 70 degrees and a humidity dome is placed over them.

What Substrate to Use

Substrate is the growing medium. Once the seeds are stratified, they are ready for germination.

I use two types of medium or substrate. One for initial sowing/ stratification and germination and one when transplanting the seedlings to separate, individual pots. When stratifying in the trays, I use equal amounts of peat 

moss, Perlite, Vermiculite, and potting soil. This mix is designed for water holding capacity and allowsample air space to maintain aerobic conditions.

When repotting from the germination tray, I use a 3:1 mix of potting soil and Perlite.

Some Other Considerations

Applying inoculate

This method works great whether you are planting a small native garden or acres! Mix the sugar water – a quart of sugar (or stale non-diet soda) to 1 cup of water. Place one seed species in a plastic container and put the sugar water in a spray bottle. Spritz the seeds until they are damp, then sprinkle on the inoculate stirring to ensure thorough coverage; let them dry. If you are using the paper towel method of stratification, wait to do this until you sow the seeds in the substrate.

If you are using GA-3, apply it before you put the seeds in your paper towel or substrate. Read the directions on how to use the GA-3.

Seeds in Fruits

To propagate seeds covered with pulp requires removing the pulp as it contains germination inhibitors. In nature, the fruit is eaten and the seeds later pooped out. Using GA-3 usually has no effect on seeds with fruit.

Drying the berries and scraping them over hardware cloth screens is a non-messy, efficient process for pulp removal.

Heat and Lights

The soil temperature needs to be 70° regardless of the ambient temperature. With my set up, the Grow lights are sufficient heat to warm the soil in the trays. If you have an area with sufficient natural light using the heat mats underneath the trays is a good option. The mats are on a timer to maintain the 70° temperature.

Transplanting Seedlings

Transplant to 2 ½” pots when four true leaves develop. Great success means you can have numerous plants tightly fitting in a row. Tease these apart and plant them individually. Hold the seedling by the leaves to protect the stem and roots. I sprinkle mycorrhizal into the soil to give them an added boost. 

Milkweeds have long taproots and need special pots called Deepots. Knowing the root structure (taproot, fibrous, rhizomes, stolons, etc.) of the plant you are propagating helps when transplanting.


Propagation, germination, transplants
Propagation, milkweed, deepots
Top view of Deepots with milkweed

Feeding and Watering

Check your plants daily. Don’t assume they are doing fine. I made this mistake and never will again!!

When germinating, keep the soil moist, not saturated. Much like stratification, germination depends on sufficient moisture. Adequate moisture creates necessary humidity.

Once transplanted into separate pots, water only when they need it. Plants in the same tray will have different water needs!

Feeding every 2-3 weeks helps. I use a hydrolized fish emulsion but only for those plants that aren’t hardening off outside. For those outside, I use an odorless option such as a compost tea. I also use this tea when I plant them into the prairies, woods, or savanna. The odorless option doesn’t attract raccoons and skunks who dig the plants up.

Hardening Off

Hardening off is the process of transitioning the plants to an outdoor environment. A couple rules of thumb to know when to do this: 1) the plants must be at least 2” tall, and 2) the nighttime weather needs to be above 40°. If I’m using the cold frame, I raise the lid during the day and lower it at night to maintain the daytime built up solar heat. If I’m using the garage, (ours is heated and never gets below 40°) the plants are placed near the doors. The plants get sunlight from the open doors and protection from the nighttime closed doors. Eventually, I’ll move these plants outside during the day and back in during the night. I don’t let the plants in the garage or the cold frame get rained on during this time as I want to control the water.

I don’t rush this process and for some plants, they stay in their individual pots and are overwintered rather than planted. In general, it takes 2-4 weeks, but is is weather based. I do not plant until the nights are consistently above 50°.


Whether you overwinter the plant or transplant it the first year is  based on how healthy and strong you think the plant is. I have better success when I overwinter and plant as second-year plants.

I overwinter by “planting” these in my vegetable garden. The first time overwintering was an intimating process. I had babied these plants to this stage and now I was putting them in the harsh elements of winter! I knew the natural process of freezing and thawing was necessary and eventually would strengthen those that made it through. And on that note, don’t expect that every plant will survive.

The plants are in trays with holes so the water will drain. Then I dig a section of the garden deep enough for the dirt to come to the top of the pots.


I dug sections deep enough to bury the tray with the pots up to the rim of the pot. The soil is an insulator so be sure it surrounds the pots. Flag the corners with flags to know where to dig your plants in spring and keep them moist until it freezes. Once the ground freezes and the plants have senesced, cover them with a few inches of straw.

The first year I overwintered, I used a permanent black marker on metal labels made from mini blinds. The marking wore off during the winter. To remedy this, I bought colored labels and I color code my plants, making a list of what is being overwintered, how many of each, and what color(s) labels they have.



When spring arrives and the ground thaws, I remove the straw and place them in the cold frame, propping the lid up during the day and down at night if the temperatures are under 40°. If I have plants that have overwintered twice, then I transplant them to the 5-6” pots once they begin to show their leaves. This ensures they have plenty of room for their roots to expand.

I color code the plants I overwinter. I never trust the writing will not fade over winter.

Propagation, label

Transplanting to Your Prairie

Mark them with a flag and mulch around each plant. Mulching holds the moisture. Provide each plant with a drink of compost tea then water the plant once it’s mulched.

For the first growing season, plan to water the transplants once a week, unless it rains, throughout the growing season. Depending on the temperatures and whether the plants are in the shade or full sun, we’ll water every 4 days or 6-7 days. That’s something you’ll need to decide. Since we’re usually putting out quite a few, we use the pumper unit for watering. We had this created for prescribed burns but it’s a good thing for watering, too!


Keep equipment clean and sanitized. I wash them with a liquid detergent and brush, then rinse them in a 10% bleach solution, allowing them to air dry in the garage.

When completely dry, I either package them into lidded plastic containers or wrap them in a plastic garbage bag, this keeps them from getting dirty. It’s so much more fun working with clean pots and having them ready when needed.

Creating a Propagation Garden

I have 3 propagation gardens (AKA prop gardens). These are used to nurture the uncommon native plants and for easy seed collecting of certain plants.

A 2-year process makes for the best gardens. The first year, mow very close, then herbicide the area to kill off weeds. If you have smooth brome in the area, be sure to use a grass-specific herbicide. Optionally, you can rototill and herbicide regrowth. Once the area is dead, place 2 layers of cardboard down, making sure to overlap the edges. Add a fairly thick layer of plain wood chip mulch. I chose cardboard instead of landscape fabric because cardboard would break down easily, feed the soil microbes, and let it become a “natural” planting. The goal was to let the plantings fill in and look like an intentional garden.

The second year is when I plant. I’ve found that because of the woodchip mulch I sometimes need to add some soil when planting so the plants are even with the top of the mulch. These plant also get a flag with their name written on it.

Propagation garden

This is my first prop garden. These can be made to appear as beautiful as any flower garden with non-native plants.

Propagation garden

This is Aster oblongifolius which is a loverly prop garden plant! Blooms late and the bees love it!

Cold Frames

Having a cold frame makes the hardening off process easier! There are many websites on how to build one. We placed ours next to our house so it would stay a bit warmer. One end is shaded in the late afternoon to accomodate savanna plants.

We made covers for it. Although it doesn’t often hail in Wisconsin , the possibility is there.

Two section show the covers on. They keep the weight of the snow from breaking the glass.


Propagation, cold frame


Bubel, Nancy. 1988. The New Seed Starters Handbook. Emmaus, PA: Rodale Press.

Cullina, William. 2000. Growing and Propagating Wildflowers of the United States and Canada. New York: Houghton Mifflin Company.

Deno, Norman C. 1993. Seed Germination Theory and Practice. Pennsylvania: Norman C. Deno. This has a couple of supplements that update the info and add new species to the original publication.

Heon, Al and Andy Larsen. 2003. Begin With a Seed. Newburg, WI: Riveredge Nature Center.

Phillips, Harry R. 1985. Growing and Propagating Wild Flowers. Chapel Hill: University of North Carolina Press.

Rock, Harold W. Prairie Propagation Handbook. Milwaukee: Wehr Nature Center.

Smith, Miranda. 2007. The Plant Propagator’s Bible. Emmaus, PA: Rodale, Inc.

Sperka, Marie. 1973. Growing Wildflowers: A Gardener’s Guide. New York: Charles Scribner’s Sons.