Guide to Seed Saving

Here’s almost everything you want to know about saving seeds, starting seedlings indoors, and making sure your stored seeds last.

Spilled seed packets

Old film canisters or desiccant packs also make great seed storage.

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With 40 years of gardening experience under her belt, Linda Gilkeson has written the book Backyard Bounty, a guide chock-full of down-to-earth advice for Pacific Northwest gardeners. Whether a novice or seasoned grower, looking to start a garden or grow more in the one you have, and no matter where you live, this book offers adaptable tips on garden planning, soil preparation, growing healthy seedlings, and simple pruning and planting guides. Make gardening less challenging and less time-consuming with this seasonal wisdom and these practical tips.

This chapter covers how to start your own seedlings indoors for transplanting to the garden later. It also describes basic seed-saving methods for anyone interested in trying this rewarding aspect of gardening.

Should You Start Your Own Seedlings?

For beginning gardeners, I recommend starting off with transplants from garden centers or farmers markets. These local sources usually sell robust varieties known to do well in a range of conditions. While there are many reasons for growing your own transplants, to be successful, you have to provide good growing conditions and be prepared to give them daily care for 5 to 10 weeks. This is definitely for the advanced class!

Starting Seedlings Indoors

There are several reasons for starting vegetables several weeks to months before they can go out in the garden:

• Heat-loving plants, such as tomatoes, peppers, winter squash and cucumbers, take too long to ripen a crop in the cool coastal climate. There really isn’t enough time to sow them directly in the garden and have much of a crop.

• Some cool-season plants, such as leeks, Spanish onions, celery and celeriac, also need an especially long growing season. These are usually started indoors in February to early March.

• Summer varieties of cabbage, broccoli and cauliflower are ready to harvest much earlier if they go into the garden as transplants.

• Plants with large, starchy seeds (mainly peas and beans) are attractive to pests and prone to disease in cool soil. Pre-sprouting them indoors cuts down considerably on losses.

The most compelling reason to start your own seedlings is to have the widest choice of varieties. If you are a tomato enthusiast, for example, there are many more varieties to choose from as seeds than you would be able to buy as transplants. Given the high cost of seeds, however, if you only want one or two plants of many different tomato varieties, it might make more sense to buy plants — if you can get the varieties you want. Although most garden centers now carry a large selection of tomato varieties, they rarely have more than a couple of varieties of other crops. Some vegetables may only be labeled by the crop name (e.g., “leeks” or “celeriac”). Without knowing the variety, the following year you won’t know which one to look for if it was successful or avoid if it wasn’t. This is particularly annoying for leeks because some varieties are much less cold hardy than others. I hate to think of an unsuspecting gardener deprived of the joy of harvesting a fine, fat leek in February!

Other reasons for starting your own seedlings: to make sure they are grown organically and to avoid bringing pests from nurseries to your garden (this is usually a low risk). Starting seedlings can also save cash if you need a large number of transplants, but it will cost you in terms of labor.

Pre-sprouting Large Seeds

Unlike starting transplants, pre-sprouting peas and beans is easy. Presprouting these big starchy seeds is a way to get around the fact that they are highly attractive to pests. Birds and rodents love to dig up them up, and pillbugs, wireworms, slugs, climbing cutworms and soil fungi attack them too. In typical spring weather it is often very hard to achieve a good stand of seedlings. Rather than losing time replanting over and over, I think it is well worth the effort to pre-sprout these.

Both peas and beans can be started in trays of vermiculite indoors: peas from March onward, beans starting in early May. Every seed seems to germinate, and there is little risk of root rot as the vermiculite doesn’t hold excess water. The seedlings can grow for 2–3 weeks (until they are a couple of inches high) on the food stored in the seed, so they don’t need soil.

How to pre-sprout seeds: I cram 30 seeds (enough for a 10-foot row or one bean tepee) into a container made from a quart (1-liter) milk carton.

• Lay the carton on one side, cut out the top side and punch drainage holes in the bottom. Fill the carton with vermiculite, and poke the seeds about an inch deep.

• Set the container somewhere warm and keep the vermiculite moist. As soon as tips of sprouts show, move the carton to a windowsill with good light and grow them for two more weeks. For better light, you could put them in a coldframe during the day and bring them in at night.

• At planting time, gently disentangle the roots in the loose vermiculite, and set them out. Plant bean seedlings so the shriveled seed leaves remain above the soil surface. These are the starchy remnants from the seed, which are so attractive to pillbugs and other pests.

Requirements for Starting Seeds Indoors

The better the light, temperature and moisture conditions you provide, the healthier your seedlings will be. Providing sufficient light is usually the most challenging of the three — and it is the most critical.

Light: To grow good seedlings indoors requires the highest light levels you can manage. If you do not have an indoor grow-light set-up, you will need a greenhouse, sunroom or south-facing window that receives full sun. If you are making do with a south window, line up the individual pots or flats in a single row along the windowsill because only the seedlings right up against the window will receive adequate light. As soon as the weather permits, move seedling trays outside for the day to a coldframe or unheated greenhouse so they receive full, bright light.

If you don’t have good window light and really want to grow seedlings, you will need to set up grow lights. Buy special, full-spectrum grow lights, or use four 40-watt fluorescent tubes supplemented with one or two incandescent light bulbs to balance the light spectrum. To achieve the high light intensity required, the light tubes must be less than 6 inches (15 cm) away from the top leaves of the seedlings. If you rig the light fixture on a pair of chains, it is easy to raise it as the seedlings grow taller. This light setup is not a perfect substitute for sunlight, so as soon as possible, move the seedlings to a coldframe or greenhouse during the day.

Temperature: Most vegetable seeds germinate well at 70–86 degrees F (21–30 degrees C). The top of the refrigerator or hot water heater used to be a good place to germinate seeds, but not in this day of energy-efficient appliances. If you don’t have a warm place to set seedling trays, investing in a bottom-heat unit for seedlings is well worth it. Because bottom heat is only needed for the germination period, you can cycle a lot of seedlings through one bottom-heating unit the size of a standard seedling tray (about 10 × 20 inches/25 × 50 cm).

Good air circulation over the surface is essential, so do not cover the seed trays with those plastic covers that often come with the bottom-heat units. After the seeds sprout, move the trays to cooler, bright conditions. The best temperature for growth is 60–68 degrees F (16–20 degrees C), which is about 10 degrees Fahrenheit lower than germination temperatures.

Moisture: The soil should be moist, but not wet. Many seeds can germinate in barely damp soil because they are able to take up enough water from the humid air between soil particles (corn, cabbage family and squash family seeds do this). More people go wrong over-watering rather than with underwatering seeds. They often lose their seedlings to damping off, which thrives in wet soil.

So, water seed trays sparingly. I soak the soil mix before sowing seeds and then don’t usually have to water again for a couple of days. When the surface starts to dry out, water seed trays from the bottom by setting them in a shallow pan of water for a short time (10 minutes or so). Don’t leave them so long that the soil surface becomes waterlogged.

Once the seedlings are a couple of inches tall, they take up water at an increasing rate and should be checked daily. It is fine to water sturdy, well-grown seedlings from above because they are past the high risk stage for damping off. If the soil is allowed to dry out, it kills fine root hairs and stunts future growth, but you don’t want the roots to sit in waterlogged soil either.

Containers: You can use any kind of clean container for seedlings: egg cartons, milk cartons, cottage cheese containers, fast food “clam shells,” etc. Just be sure to punch two or three holes in the bottom to allow water to drain.

It doesn’t take long for gardeners to end up with a miscellaneous collection of pots and seedling trays. These just need to be cleaned to be reused. Soak the pots in a bucket of water to loosen the soil, then scrub with a brush to clean them. Optional step (but I highly recommend it): soak the pots in a bleach solution for 15 minutes, then rinse well. Mix 10 parts water to 1 part hydrogen peroxide (better for the environment than chlorine bleach). For best results, pots should be clean when you put them into the bleach.

New seedling trays made of recycled plastic are also available. They are inexpensive and with care last for several uses. The ones with individual cells for each seedling produce good results because roots suffer less disturbance during transplanting.

Peat pots and pellets are still sold, and since they have been on the market for decades I guess they must work for someone. I found that seedlings didn’t get their roots through the pot, the pots dried out easily, and I ended up ripping off the hardened remnants of the pots to plant the seedling anyway. Reusable plastic pots for me!

Soil mixes: Back when you couldn’t buy commercial organic soil mixes for seedlings, I used to make my own mix. Now, I am happy to buy a bag of commercial mix, certified by OMRI (Organic Materials Review Institute) for general use by organic growers. It saves a lot of time and effort and gives consistent results.

Look for products, such as Sunshine Organic Planting Mix or Seasoil Potting Mix, that state they are for seedling production. Check the labels of other commercial “potting soil” products before you buy. Some are intended as soil substitutes for use in containers and don’t have nutrients. Seeds germinate in these mixes, but stop growing as soon as they run out of the food stored in the seed itself. Seedlings in such mixes need regular applications of liquid fertilizer or should be transplanted into a fertile soil mix as soon as they have two leaves.

Are Your Seedlings Getting Enough Light?

Compare the stocky seedlings that come up in a bed outdoors with the seedlings grown indoors. The ones grown outdoors have hardly any distance between the soil surface and the first pair of leaves. Indoor seedlings that grow tall, lean toward the light, and have long, pale stems below the first pair of leaves are not getting enough light. They are also very susceptible to damping off because of the weak stem. Depending on how elongated the stem has become, they may or may not be salvageable. Try to get them into better light as soon as possible.

Is It Necessary to Pasteurize Soil Mix?

The purpose of heating soil to 140 degrees F (60 degrees C) is to kill soil-borne diseases (mainly damping off ). A soil mix made with finished compost, however, contains beneficial soil fungi that help suppress damping off — and these are also killed when the soil is heated. When I used to make seedling mixes, I actually had better results when I stopped pasteurizing the soil and concentrated instead on providing warm germination temperatures and avoiding overwatering (certainly easier than trying to heat a soil mix evenly in a kitchen oven!).

Steps for Starting Seeds Indoors

• Fill containers with potting mix, lightly pressed down to firm the mix. I like to soak the soil mix at this point, before seeding.

• Sow the seeds. Using a pointed chopstick, open a little hole in the mix and drop in the seed and close it up. Or, don’t quite fill the container with soil mix, place the seeds on the soil and cover with another layer of soil. If you are using a denser mix, for good results cover the seeds with vermiculite instead of soil mix. Sow 2 or 3 seeds in individual pots or in each cell of a seedling pack. Sow 8–10 seeds in small trays where you intend to grow 4–6 seedlings.

• Set the containers on bottom heat or in a warm spot, aiming for 70–86 degrees F (21–30 degrees C). Don’t cover the containers. Water from below when the top of the soil dries out.

• As soon as any seedlings show the tip of a shoot above the soil surface, move the tray to high intensity light and cooler temperatures (60–68 degrees F/16–20 degrees C).

• When seedlings are about an inch high, choose the best ones and pull out or clip off the extras.

• Grow on the seedlings. If possible, put them in a coldframe or greenhouse on sunny days. Bring them indoors at night until the minimum temperature at night stays above 54 degrees F (12 degrees C).

• If seedlings are growing too large for their pots and it is still too cold to put them out, repot them in bigger containers and keep them growing vigorously.

Hardening Off Seedlings

Seedlings that are grown under lights, in greenhouses, or on windowsills will have soft stems and tender leaves with thin cuticles (the thin, waxy coating on leaf surfaces). They have to gradually get used to direct sun, wind and cooler nights before they are sent out into the world. Through this process of “hardening off,” their growth slows a little as food reserves build up in the roots, and the cuticle on the leaves thickens up to protect them from sunburn.

The hardening off process is simple: get seedlings used to outdoor conditions gradually, starting with an hour in the sun the first day (or longer in cloudy weather). Move them back under glass or into light shade for the rest of the day. Over about a week, expose them to direct sun for longer periods, until they are outside all day.

For hardy plants, such as onions, leafy greens and cabbage, hardening off gets seedlings used to direct sun and cooler temperatures. Small seedlings (for example, cabbage with fewer than five leaves) can get used to quite low temperatures. For seedlings larger than that, however, exposure to temperatures under 40–50 degrees F (5–10 degrees C) for a couple of weeks may cause them to go to seed in mid-summer.

Hardening off tender crops, such as tomatoes, peppers, cucumber, squash and melons, mainly means getting them used to direct sun. Cucumbers, for example, can be seriously set back or even die from sunburn if they are abruptly moved from indoors into full sun for a whole day.

Coldframes are excellent tools for hardening off plants. As the weather warms, plants gradually become used to the sun as the frames are opened a little more each day for ventilation. By the time plants are ready to be set out, they are used to the sun and outdoor conditions and don’t need any more special treatment.

The tricky thing is that over-hardening plants can slow their growth so much that they may never recover, delaying and reducing the total harvest. Transplants become over-hardened if they are held too long in pots and become root-bound, or are stressed by uneven watering or lack of nutrients. Transplants for sale have usually been hardened off enough by the time they reach the market. They risk becoming over-hardened if kept too much longer in their pots.

Ideally, you have timed seeding dates so transplants are the perfect size to plant out when the weather is right. Given the difficulty of predicting spring weather on the coast, however, that doesn’t always happen. Be prepared to move seedling into larger pots to avoid over-hardening if it isn’t warm enough to put them out.


A traditional coldframe is handy to have for producing good quality seedlings if you don’t have a greenhouse or plastic tunnel to use. Make a simple coldframe from four boards for sides and an old window (or clear plastic) as the cover. Set it so that the glass faces south and is slanted downward at the front to allow in light. Use a stick to prop up the window to ventilate the frame during the day, because it quickly overheats inside when the sun comes out. You can build or buy much more elaborate designs, including frames made entirely of rigid clear plastic and frames with automatic openers to lift the covers. When I lived in eastern Canada, I used an extensive collection of coldframes to give seedlings a good start and to extend the growing season for various plants. When I moved to the West Coast, however, I soon found that one small coldframe was all I needed.

How to Tell If Plants Are Root Bound

Lift the pot and look for roots coming out of the drainage holes. A few roots showing is okay, but a straggly beard of roots trailing out of each hole is a bad sign. Another way to check is to gently slide a seedling slightly out of the container: the more roots you can see wrapping around the sides of the root ball, the more root bound the plants are. If you can’t get the root ball to slide out easily, it is probably extremely root bound.

Seed Saving

I think everyone should know how to save seeds — at least the easy ones. When it comes to seed saving, coastal gardeners have an enormous advantage because many vegetables are biennials and have to be kept over the winter before they will flower. This takes special management where winters are cold, but on the coast most biennials are hardy enough to stay in the garden all winter. It is just a matter of waiting until the next summer and letting them get on with flowering and setting seeds.

Saving seed cuts down on costs, of course, and with plenty of seeds on hand, you can sow extra to ensure a good stand despite pests. It also gives you surpluses to trade with other gardeners. And, when you find a variety you really like, you might be able to keep it going yourself, long after it disappears from seed catalogs.

Most seeds keep for years if stored properly, so you only need to save seeds from a few different vegetables each year to end up with a good collection of varieties. Aside from remembering not to save seeds from hybrid varieties, the main issue to be aware of is the risk of flowers being cross-pollinated by a different variety (or in some cases by related weeds).

Only Save Seeds from Open-pollinated Varieties

Don’t save seed from hybrids (if a variety name has “F1” after it, it is a hybrid). Unlike hybrids, open-pollinated (OP) varieties come relatively true from seed because both parents are the same.

Basic Seed-Saving Methods

Isolate blooming plants in space or time: That sounds like science fiction, but all it means is this: if you want to save seeds, either put some physical distance between varieties or don’t allow different varieties of the same vegetable to bloom at the same time in your garden. There is also a third alternative for plants that are self-fertile, such as peppers and eggplants: you can cover plants with a floating row cover or screen cage to keep out bees and other pollinators (you will have to pollinate these flowers by hand).

Most vegetables have a high risk of cross-pollination. Seeds of most are quite easy to save, but you do you need to make sure the flowers don’t receive pollen from other plants in your garden or nearby gardens. The best way to do this is to save only one variety at a time, and make sure no other closely related plants are flowering in the garden at the same time. Cut down flower stalks of other plants before the flowers open or remove the plants altogether so there is no stray pollen for wind or bees to move around. Gardeners in community garden plots might not be able to save pure varieties because there may be cross-pollination from plants in other plots. Some plants with very light pollen that blows on the wind can cross with plants from gardens as far away as a mile, though the risk of that happening is pretty remote.

Vegetables that are self-fertile and have a low risk of cross-pollination, are unlikely to cross if they are grown a short distance (30 feet/ 10 meters) from related plants in bloom at the same time. In home gardens, however, where plants grow closer together, wind or bees can move pollen between these plants, so it is still best to grow out only one variety at a time, and remove flowers of related plants during the blooming period.

Saving seeds of a few vegetables is definitely for the advanced class:

• Squash, cucumber and melon: Both male and female flowers have to be bagged or taped shut so they can be hand pollinated. Squash crosses produce notoriously inferior fruit.

• Sweet corn: It takes special methods to make sure there is no chance of unwanted wind-borne pollen reaching the silks.

• Cauliflower: Heads of cauliflower have to be maintained through the winter (usually in a greenhouse), so flowers can develop the following spring.

Decide which plants to use for seed: Choose parent plants based on whether they are showing the characteristics you want. It might seem logical to save seeds from the first plants that produce seed, but for some vegetables those are the very plants you don’t want to keep. For example, late seed production is a good thing in leafy greens that you want to harvest over a long period. The same goes for radishes, leeks and onions. On the other hand, you might want to save seed from bean and pea plants that produce pods earliest. Watch for plants that have other characteristics that you like, such as taste, size, vigor or color.

Save seeds from as many different plants of each variety as you can, as long as they have the characteristics you are looking for. Try to save seeds from at least three different plants at one time — from six to ten plants is even better — so you maintain a pretty good level of genetic diversity within the variety.

Label everything! Mark the parent plants when they are planted, and label seed heads the moment they are harvested. Tie labels onto the stalks or label the container. Don’t wait until later, because, believe me, seed pods of many plants look identical when they dry.

Allow seeds to mature on the plant: Seeds of most plants do not mature at the same time, so keep checking the plants or pods. It can take most of the summer for some seeds to ripen. You can open a test seed pod every week or two to check when seeds lose their green color and harden up. When seeds are easy to shell out of pods and look hard and dry, they are ready to harvest. Collect just the ripest pods or heads, leaving later seed to ripen on the plant. Practically, however, if you want to cut seed stalks only once, harvest them when the earliest third of seed pods have thoroughly matured. Much of the laterforming seed will still mature after the stalks are cut.

Here is when to expect seed heads to form:

• Annuals form seed their first year. Arugula, beans, summer broccoli, lettuce, peas, spinach, mustard greens, corn salad, Chinese cabbage, summer radishes, dill and cilantro are annuals. Tomatoes and pepper are perennials, but for seed-saving purposes are treated as annuals because they produce seeds the first year.

• Biennials don’t form seed until the following summer. Kale, Swiss chard, winter broccoli, Brussels sprouts, cabbage, celery, endive, parsley, leeks, sweet onions, carrots, beets, parsnips, winter radishes and turnips are some of the biennials that overwinter successfully on the coast.

Dry the seeds: You can do this in a garage, basement, back porch, shed, back room, top of refrigerator, etc. The seed stalks (or entire plants of some vegetables) can be cut and hung upside down to finish drying. I hang plants inside paper bags (with holes cut in the upper part of the bag for ventilation) to catch seeds that drop. You can also pick seed heads and pods and spread them on trays to dry. Corn salad seeds, for example, shatter out of the seed head very easily, so they should be dried on trays to avoid losing them. Never use a heat source over 90 degrees F (32 degrees C) to dry seed.

Shell out seeds: When seeds are thoroughly dry, shell them out of the pods or heads. Rub dry pods between your fingers to crack off shells, or pound them in a bowl with a pestle to free the seeds from pods. Shake them through a colander or a mesh screen to separate seeds from chaff. To remove finer chaff, winnow them gently in a breeze or roll the seeds down a piece of flannel, which catches the chaff. Some seed is very easy to pop out of hulls, while others, such as leeks, are tough to separate from their hulls. You do not need perfectly cleaned seed, so don’t spend a lot of time getting out every particle of chaff.

How to Store Seeds

Seeds stay viable (able to germinate) longest when they are kept cool and dry. Moisture is the enemy of seeds. As soon as a seed begins to absorb moisture, it begins to wake up from dormancy.

When seeds become too old, they are no longer able to germinate. How long this takes depends on the kind of seed and how well they have been stored.  If in doubt, you can always do a simple germination test (instructions below) to find out if the seed is still good.

With seeds now costing 2–5 dollars per packet, it is well worth taking good care of your investment. If stored properly, even seeds with a short storage life can be kept a couple of years longer than average. Here’s how:

Keep the air out: Put thoroughly dry seeds in labeled envelopes. Small paper envelopes work fine, but these should then be stored in airtight containers. Jars or plastic containers with tight seals work fine, as do heavy plastic zip-lock bags.

Store seed containers in a dark, cool, dry place. The ideal spot for your seeds might be in a cool cupboard in the basement or unheated back room or other place away from heat. You can store seeds in the freezer, but only if you are careful to let the contents return to room temperature before you open the container. If the container is opened while it is still cold inside, moisture in the air immediately condenses on the seed packages. This undoes the care you took to provide dry conditions. I store large quantities of seed in my freezer, but hold the quantities I want for planting this season in a cool cupboard.

The small desiccant packets that come in pill bottles, shoe boxes, etc., hold silica gel that keeps the contents of the container dry. You can reuse these or buy larger desiccant packs to put into the containers with your seeds. It is well worth the cost because it adds considerably to the life of the stored seeds. Sometimes seed suppliers include desiccant packs with seed orders or sell them separately. Lee Valley Tools sells reusable silica gel desiccant packs in a metal case for woodworkers (look up “dehumidifiers” in their catalog). One small pack (1.4 oz./40 g) is sufficient to dehumidify the interior of a closed container the size of a tool box, making it ideal for a big plastic box of seed packets. You can reuse desiccant packs for years by heating them for a couple of hours in the oven to dry out the silica gel granules.

A Simple Germination Test

When in doubt about the viability of old seeds, it is easy to do a quick germination test. If you do this in January, you will have time to buy fresh seed if necessary. Here’s how:

• Count out 20 seeds if you have a good supply. Count out 5–10 seeds, if you don’t have many left.

• Spread the seeds on the bottom half of a moist paper towel and fold the other half of the towel over the seeds to keep them moist. If you are checking several different kinds of seeds, they can be placed together in groups on the same paper towel. Be sure to label each group of seeds. Before you wet it, you can write on the paper towel with a waterproof pen or pencil. Put the moist towel with the seeds in a plastic container or plastic bag, label and cover/close loosely (not sealed closed).

• Put the container in a warm spot and check daily to make sure the paper towel doesn’t dry out. Most seeds will germinate within 3–5 days (carrots, parsnips and parsley take longer).

• Count how many seeds show a tiny little root sprout and calculate the percentage of viable seeds. For example, if 15 out of 20 seeds germinate, that is a 75 percent germination rate.

A germination rate above 75 percent is fine. If the percentage is lower, sow those seeds more thickly to make up for it. If less than half germinate, it is time to buy new seed or grow out a planting to save fresh seed.

Also learn how to utilize your garden all year long!

Reprinted with permission from Backyard Bounty: The Complete Guide to Year-Round Organic Gardening in the Pacific Northwest by Linda Gilkeson, published by New Society Publishers, 2011.