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Seed Saving Instructions


For most of agricultural history, seed saving was a necessity. Gardeners and farmers carefully selected and stored the best seeds from their harvests, ensuring they had seed for planting in subsequent years. The knowledge of pollination, purity, harvesting and storage of seeds was all part of survival and learned within the family and community.

The rise of commercially available seed resulted in a trend away from seed saving. Farmers and gardeners simply purchased new seed every year. Growing concern regarding the loss of commercially available seed offerings however, led to a grass-roots movement in the late 70’s and early 80’s dedicated to seed saving.

Today, recognition of the importance of crop genetic diversity is exemplified by the many local, regional and national efforts devoted to conserving the heirloom, traditional varieties that were once so prevalent. For both home gardeners and seed bank operators, the fundamentals are the same in terms of saving seed and maintaining purity. What follows are some basics to get you started saving seeds.


Pollination is necessary to produce seed. When pollen from the male flower part (stamen/anthers) comes in contact with the female part (pistil/stigma), pollination occurs. Successful pollination results in a zygote, or fertilized egg, within the ovary that matures into a seed.

Perfect flowers have both male and female parts. Beans and chiles both have perfect flowers. Self-pollination occurs when pollen (male) is transferred to the stigma (female) within the same flower. Technically, self-pollination also occurs when pollen from one flower is transferred to another flower on the same plant. Some plants have specific mechanisms for ensuring self-pollination. In beans, pollen transfer happens within a flower before it even opens. Thus, by the time a bean flower opens, it has already been self-pollinated!

Imperfect flowers are either only male (no pistil or stigma) or only female (no stamens or anthers). These flowers require cross-pollination. Cross-pollination occurs when pollen is transferred by wind or insects from a male flower to a female flower. The flowers may be on the same plant (monoecious) or different plants (dioecious). Cucurbits (squash, melons, gourds) have separate male and female flowers (imperfect flowers) on the same plant (monoecious). Pollen must be transferred by insects between male and female flowers in order for fruit to be produced.


Guidelines for maintaining seed purity between cross-pollinating crops help growers prevent unwanted crossing from occurring. The “one-quarter mile” rule is the standard isolation distance to prevent pollen from one variety contaminating another during the growing cycle. This may be a bit extreme in the southwest’s arid climate. Corn pollen can easily survive in high humidity, but quickly desiccates in low humidity and drying winds. Insects carry pollen considerable distances, but must stay near a water source. Therefore, in hot, arid conditions, isolation can often be accomplished at distances of less than one-quarter mile.


All plants have a Latin name, known as their genus and species. The same plant can be known by different common, local, or regional names, so Latin names are used to make things universal and less confusing. Plants are given their Latin names based on their flower structure. Thus, plants of the same genus and species are very closely related and therefore cross pollinate. All corns, whether sweet, flour or popcorn, belong to the same species – Zea mays – and readily cross. Most of the peppers, or chiles, commonly grown in gardens are just one species, Capsicum annuum.

Generally, plants within the same genus, but different species, will not cross. Of the squashes, for example, Cucurbita pepo will not readily cross with Curcurbita argyrosperma, Cucurbita moschata or Cucurbita maxima. For this to be helpful, you have to know which species a particular variety belongs to.

For example, crookneck, zucchini, cushaw and hubbard represent 3 different species! It is rare, but not impossible, for plants from different genera (plural of genus) to cross. There are exceptions to the rules, and plant breeders have had some success with forced crossings.

Open-pollinated means that the variety is pollinated randomly, that is, pollination is not controlled in any way, such as that typically performed by plant breeders. Even self-pollinating crops, such as beans, are considered open-pollinated, though there is nothing particularly random about who pollinates whom. Technically, a plot of corn in your neighbor’s backyard is open-pollinated, unless he/she goes out every morning and hand-pollinates individual ears. The interesting twist is that the corn could be the product of controlled pollinations between two or more different corn varieties, i.e., a hybrid. Yet, unless your neighbor actually conducts his/her own pollinations, the corn plot will be considered open-pollinated. Hybrids are produced by specifically cross-pollinating two varieties to produce a unique, third variety, and are common in modern agriculture and commercial garden seeds. Seeds from hybrids often do not produce “true-to-type”, that is, offspring of hybrids often do not maintain the characteristics of their hybrid parents.


Purity means preventing the mixing of more than one variety. Contamination of seed stocks can occur both as a result of cross-pollination between varieties of the same species or by mixing different varieties as a result of poor labeling after they’ve been harvested. The easiest method for maintaining seed purity is to grow only one variety of any one species at a time. Always be aware of what other gardeners near you have planted and what “weeds” may have volunteered in your compost or grow along the roadway.

Hand pollinating is commonly used on a small scale to maintain purity. It can be time consuming and labor intensive, but it’s fun to play Mother Nature! When hand pollinating, you must physically act as the agent to transfer the pollen (male) to the stigma (female). You must also act to prevent any unwanted pollen from finding its way to the stigma.

Staggered planting times is another good practice to prevent crossing, especially for corn. Allow two, four or more weeks between planting of different varieties so that tasseling does not overlap. You must know how many days it takes each variety to mature for this to work; a second planting of an "early" corn that flowers while the first planting is still flowering will defeat the purpose.

Caging individual plants with window screening, or bagging flowers with cheese cloth, muslin or paper sacks can prevent insects from visiting and crossing varieties. This will work well, as in chiles, if flowers are capable of self pollinating. Otherwise, hand pollination may be necessary. Other physical barriers include buildings and plants to disrupt or prevent movement of pollen or insects. Some crops and trees can act as deterrents to insect pollinators, but it takes a comprehensive understanding of which garden insects visit your garden.



Corn, Zea mays, is wind pollinated. The tassel, at the top of the plant, is the male flower. Pollen is shed from the anthers, along the tassel branches. Pollen shed usually begins at the uppermost part of the tassel, progressing down the main branch and subsequently onto the branches. Thus, a tassel that has just started shedding pollen will only have anthers producing pollen near the tip of the main tassel branch while a mature tassel will produce pollen along all of its branches. The ear is the female flower part and is located on the stalk. Husk leaves will form at a leaf node, and eventually silks will emerge. Silks are the stigmas and are receptive to the pollen along their entire length. A single kernel or seed is produced from each silk successfully pollinated.

There are a number of techniques for maintaining seed purity in corn. Isolation distance between varieties should be at least 1,000 ft. in arid conditions and increases as humidity increases. Staggered planting times can be very effective. Hand pollination can also be used. We hand-pollinate corn grown at the Conservation Farm because we tend to grow many different accessions at the same time and need to keep each accession from crossing with other accessions, i.e., we’re keeping each accession pure. Home gardeners may want to hand-pollinate because with such small plots (typically), hand-pollinating can increase seed set by ensuring that enough pollen is getting to each ear. Additionally, hand-pollinating can also help ensure that genetic diversity is being maintained.

Once silks have started to appear, the daily ritual of hand-pollinating begins. Anthers begin to shed pollen once the sun is up. After temperatures reach 90-100 degrees, most viable pollen is gone for the day – easily “cooked” by the heat. There are several different strategies for the collection and distribution of pollen when hand-pollinating corn. The easiest is to collect pollen from all tassels shedding pollen that day in a single container and then disperse it equally among all available ears. A large diameter, slick bowl such as glass or enamel works well because the pollen easily slides. Simply bend the tassel over the bowl and gently shake it, being careful not to break the tassel, as it will shed pollen for a few days. The pollen is a bright yellow powder and is an important ceremonial item for several Native American groups.


Cucurbits are a large family of plants that includes squash, cantaloupes, watermelons, and gourds. The plants bear separate male and female flowers and depend on insect pollination for fruit production.

It is important to know the species of squash you plant, as crossing occurs readily between varieties of the same species but is uncommon between species. There are four main species of squash: Cucurbita argyrosperma, C. maxima, C. pepo and C. moschata. Cucurbita argyrosperma is common in the Southwest and is often called cushaw or “calabasa”. Cucurbita maxima includes hubbard, buttercup and banana squashes. Cucurbita moschata is closely related to C. argyrosperma and includes butternuts and calabazas. Cucurbita pepo is a large group that includes zucchini, acorn, crookneck, spaghetti and Halloween pumpkins.

Hand pollination may be necessary to ensure fruit set if adequate pollinators are not available or you are growing more than one variety of the same species and want to save seeds.

Female flowers have a small “baby” squash at the base of the flower and are usually on shorter stems. Male squash flowers are produced on long stems (peduncle) and usually appear well before female flowers. The flowers open in the early morning so it is necessary to get to them before the bees and other insects are active. If you are growing more than one variety of the same species, then taping the flowers shut the evening before they open will help prevent unintentional “pollen mixing”. Tape both male and female flowers shut.The next morning, collect the male flowers and distribute them among the females, using 2-3 male flowers per female. Remove the tape and petals from the male flowers, exposing the anthers and pollen. Quickly open the female flowers without tearing the petals, brush the pollen onto the stigma of the female flower and tape shut again.

A ball of cotton gently placed on top of the pollinated stigma before being taped shut helps prevent pollen-laden insects from burrowing into the flower and crossing it. Label pollinated flowers so that you can save the seed only from those fruits.


Cantaloupes, muskmelons, honeydews and casabas all belong to the same species – Cucumis melo – and will readily cross pollinate. Watermelons also belong to a single species – Citrullus lanatus. For both, hand-pollination will help maintain genetic purity but the flowers on these vines are small and difficult to work with. The plants also have a tenancy to naturally abort 60-70% of the female flowers that bloom. Once fruit has started to set, more flowers will abort. Pollinating the very first female flowers may improve your chances of fruit set. Follow the guidelines for squash pollinating and get out the tweezers!

Though not likely to be something most home gardeners might try, we use isolation cages for our melons and watermelons and rent the services of small hives. Bumble bees are produced in hives small enough to rotate through the 13 ft. X 30 ft. long cages we purchased a few years ago specifically for this purpose. The hives are rotated through all the cages at about 1 week intervals throughout the season. Once the bees take pollen collected from the melon flowers into their hive, it is formed into pollen “balls” and does not leave the hive again. Their careful housekeeping habits prevent cross-pollination between accessions from occurring.



How plants are harvested depends somewhat on whether you’re trying to maintain a variety ‘as is’ or are selecting for certain traits. If you’re trying to maintain a variety ‘as is’, save seed from as many individual plants as possible, even if only 1 seed per plant. If seed matures over a period of time, save seed from multiple harvests so that seeds from early- and late-maturing plants are included in the sample. This helps ensure that genetic diversity will be maintained in your seed sample. On the other hand, if you’re actually selecting for certain traits, only save seed from those plants that express the desired trait.


When to harvest depends slightly on whether the seeds are produced in ‘dry’ or ‘wet’ fruit. Examples of ‘dry’ fruit include chiles, beans, black-eyed peas, gourds, okra, amaranth, sunflowers, corn, peas, garbanzos, cotton, most greens and herbs, sorghum, tobacco, and wheat. These should be harvested when the fruit/seeds are dry. When the seeds rattle in their pods or have begun to fall from the plant, they are typically ready to harvest. They can be left in the field until completely dry or harvested and placed in a protected area to finish drying.

Examples of ‘wet’ fruit include melons, watermelons, squash, tomatillo and tomato. These should be harvested when the fruit are slightly over-ripe but are not rotten. For vining crops, the fruit are typically mature when the fruit are somewhat whitish on the bottom side and the tendrils on the fruit-bearing stem and two adjacent stems are dry. The fruit are typically split and the seeds are scooped out of the fruit, washed and allowed to dry on cloth towels or pillowcases out of the light and heat.

The following are typically mature, and therefore ready to be harvested, when dry:

  • Amaranth – cut seed head when majority of flowers feel stiff to the touch, continue drying in a paper bag, pillowcase or on a metal tray to collect seeds that drop.
  • Beans/Black-Eyed Peas/Peas/Favas/Lentils/Tepary Beans – pods should be dry and can be picked by hand or by cutting the plant at ground level, letting dry on a tarp out of the rain and threshed.
  • Chiles – allow chiles to dry on the plant, hand harvest.
  • Corn – if temperatures are high, harvest sweet corn when kernels harden just after the milk-stage (milk-stage is the ideal fresh-eating stage, when a finger nail pressed into a kernel produces a white, milky liquid); sweet corn left too long on the plant in high temperatures may begin to ferment in the husk; for other corns, the cobs may dry completely on the plant, unless frost is likely or birds become a problem; remove entire cobs from plant.
  • Gourds – allow to dry on the vine until just before first frost, then continue drying out of the rain; can take several months; gourds are dry when seeds rattle.
  • Okra – let dry on plant but harvest before fruit opens allowing seed to drop.
  • Sunflowers – let dry on plant as long as possible, protect from birds by covering seed heads with netting or pillowcases; cut heads and let dry in a cool, dry place or in paper bags.
  • Melons, watermelons and squash are typically mature and ready to be harvested when the tendrils are dry on the fruit-bearing stem and the two adjacent stems. Some crops require a period of after-ripening in order for the seeds to fully mature. After harvesting, allow squash to after-ripen for 21 days before removing seeds.


Seeds must be cleaned before they can be stored. Different crops require different techniques for cleaning. Overall, seeds should be free of plant material (bits of leaf, stems, etc.) and bad seeds (non-viable, broken, split, etc.).

Download printable instructions for cleaning dry processed seeds here.

Some common techniques for cleaning seed include:

  • Threshing – break up plant material (including fruits or pods) and expose the seeds by stomping, beating, crushing, etc.
  • Winnowing – separate plant material from seed with a gentle fan or light wind, leaving only clean seed.
  • Tarp/fan – slowly pour threshed seeds in front of a fan placed near a tarp, heavy seeds fall onto tarp while the light-weight plant debris is blown farther away.
  • Hand-cleaning – remove plant debris by hand.
  • Blending – some wet processed seeds can be cleaned by blending fruit in a blender; add water and ‘float’ debris off the top as water is poured off slowly; repeat filling and pouring water off until only clean seeds remain (bad seed and plant debris floats to the top and is poured off with water; good seed sinks). This works well for tomatillos, tomotoes, chiltepines, and small chiles.


Tomato – blend clean, fully ripe fruits in a blender until all the fruits are mashed and the mixture is very thick, add some water to the mashed fruit and stir. Pour into shallow bowl, place in warm spot and allow to ferment for 3-5 days. Stir daily. A thick, white layer of mold, with bubbles, will form on top and produce a strong (bad) smell. If allowed to ferment too long, germination may occur. Be sure to stop the fermentation if this occurs. When fermentation is complete, scrape off mold layer. Add water to bowl, swish and pour into larger container or small bucket. Slowly pour off bits of floating plant and fruit debris, as well as seeds. Good seeds will sink to the bottom. Continue floating off debris and filling with water until only clean seed remains. Rinse seeds and spread on towel or pillowcase to dry. (A slight alternative ‘floating’ method – for use after fermentation – is described below for tomatillo.)

Tomatillo – place in blender with water and blend until mixture is thick and fruits are mashed. Put mixture in small bucket or large bowl and allow seeds to settle to bottom. Let slow stream of water run into one side of container, allowing the pulp to flow over the rim of the container, leaving good seeds at the bottom. “Bad” seeds will float and be removed in this manner as well. Rinse seeds in a strainer, shake to remove excess water and place on a clean cotton cloth or screen to dry.

Chiltepin/Chile – Remove stems and process small-fruited chiles (Coban, Pico de Pajaro, Ordoño, Del Arbol, Pico de Gallo) and chiltepines in the same manner as tomatillos. Be sure to blend in a well ventilated area, taking care not to touch your face, eyes, or mouth after handling chiles. We suggest wearing plastic gloves. Use flotation method as described for tomato or tomatillo.


As with every step until now, it’s important to keep an eye to quality. Below are some basic guidelines to consider when saving seeds:

  • Choose healthy, undamaged seed to save
  • Do NOT keep seed from diseased plants (some viruses are transmitted through seeds)
  • Save seed from as many plants as possible
  • Be sure seeds are clean of unwanted sticks, chaff, seed pods, etc. This will reduce the bulk that is stored as well as the threat of some possible pest and diseases.
  • Keep enough seeds for next year’s planting needs.


Allow seeds to fully dry. Wet processed seeds should be rinsed and placed on a cotton towel (pillowcases work perfect), screens or baskets. Do NOT use newspaper or paper towels as seeds will stick to the paper and the dyes commonly used in both products can transfer to the seeds. Make sure seeds are place in an area with good air circulation and out of direct sunlight. Prolonged exposure to sunlight and high temperatures reduces seed viability. Do NOT try to hasten seed drying by placing them in an oven at low temperature! Seeds take up moisture from the air, equilibrating to relative humidity at the time. In arid areas like Tucson, relative humidity is typically not a problem. Allowing seeds to equilibrate in an air-conditioned room for 7 days is typically fine. They can then be sealed in air-tight jars or ziploc baggies. In other areas, silica gel can be used to dry seeds to low moisture content, a requirement for storing seeds under frozen conditions.


Seeds can last for quite a long time when properly stored. Under frozen conditions, such as in any household freezer, many seeds will last 10 or more years, easily. While seed longevity under any storage condition is primarily dependent on the quality of the seed going in, there are certain conditions that lend themselves to longer seed storage time frames:

  • Storage containers should not allow moisture to enter, nor to build up inside.
  • Use glass jars with lids, metal trash cans, envelopes or bags, plastic ziploc bags (only if freezing).
  • Store seed in a dark, cool, dry place such as a refrigerator or freezer (air-tight containers); paper bags in a closet; do NOT store in outside sheds.
  • Kill insects; freeze seed for 3 days; check for reinfestation periodically and repeat freezing if necessary; watch for bruchid beetles in beans (small white dots appear on outside of seeds, followed by holes; remove damaged seeds and refreeze)
  • Optimal seed storage conditions – 45-55 degrees with ~25% humidity

The International Seed Saving Institute offers online instructions for saving a variety of seeds. They classify techniques into three categories: 1. beginner (bean, lettuce, pea, pepper, tomato), 2. experienced (corn, cucumber, muskmelon, radish, spinach, squash, pumpkin), and 3. expert (beet, swiss chard, cabbage family, carrot, escarole, frisee, onion, radicchio, turnip, Chinese cabbage). The lessons include selection traits, harvesting and processing.