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Seed Saving and Genetics- Getting It Right

Seed Saving and Genetics- Getting It Right

Seed Saving and Genetics- Getting It Right

From local garden enthusiasts to aficionados in Facebook groups, the topic of seed saving has an air of sacred duty. Individuals engage the ritualistic seed harvest from the crops they grew or purchased, picking through mounds of wet plant goo, smearing seeds on paper towels, and carefully curating them in well-marked recycled jars. Here in Gainesville, FL several organizations pilot the wonderful task of collecting and distributing donated seeds, making them available to everyone from schoolkids to first time planters, to Master Gardeners. All of this is done with the best of intentions– to provide the fundamental resource needed to grow food.

I understand the appeal to be in command of genetics, to be the purveyor of produce, the centerpiece of community commodities, and orchestrating the divorce from pricey seed sources from Johnny’s Select to Syngenta. Stick it to The Man.

But the more you know about genetics, seed physiology, and tree juvenility it becomes apparent that seed saving is not so simple.  In fact, saving and distributing seeds without firm understanding of their genetics can lead to confusion, disappointment and wasted effort. Lately I’ve been reading a lot about weirdo fruits from seedling trees and donated seeds producing a spectrum of products that didn’t match the label on the package. Seed saving has some caveats!

So before you gut that apple core, Ginsu that tomato, or dry those radish pods, please consider the following biological realities:

Many Commercial Varieties are Hybrids

Many elite commercial varieties arise from the well-tested cross pollination of two parental lines and will not breed true from seed. Some of the non-heirloom favorites of home gardeners are hybrids, a marriage of two very different parents. Skilled plant breeders, the inventors of the garden and grove, analyze varieties possessing coveted traits, and then carefully move pollen from one flower to the stigma of the other, transferring genetics in the most fundamental method of genetic modification.

In these cases, planting seeds from a hybrid tomato will give rise to a genetic milieu of variation in subsequent generations. The next generation will produce some plants resembling its one grandparent, some plants resembling its other grandparent, with dozens of combinations in between—with none matching the quality of the desired hybrid.

In contrast, heirloom annual vegetables have been breed to have narrow, self-sustaining genetics. Those can be saved and distributed with confidence– if steps are taken to exclude cross pollination with other varieties.

Nature Fights Genetic Uniformity

Evolution has shaped plant sex into an efficient process. In some cases, microscopic pollen from one plant needs to land on a spot no bigger than a pin head, located a healthy stone’s throw away.  Luckily pollen can surf on the currents of wind and stowaway on the bodies of bees, moths and birds, that vector nectar of another flower, completing pollination. To me, it is magical that it can even happen.

But the seemingly unlikely processes of outcrossing conspire to vex the seed saver. Unless specific efforts are taken to limit cross pollination, the genetic fidelity of the seeds in a fruit cannot be trusted. Planting parental plants/trees far apart, covering flowers in tents of polyester chiffon or silk tulle can prevent insect pollination, and decrease likelihood of unregulated wind-mediated events. Without genetic isolation, you just don’t know the genetic identity of the next generation.

That said, some plants possess reproductive strategies that favor self-pollination. Peas, for instance, undergo pollenization before the flower even opens. You need to know your crop!

Send In the Clones

The lack of true-from-seed production is even more extreme in fruit crops.  Blueberries, strawberries, apples, pears, peaches and many others all arise from a single plant or tree that is then propagated vegetatively. They are genetically identical, clones. The sprawling fields of strawberries that surround Plant City are all clones of one mother plant identified years ago, propagated by its runners. Now if that plant were to self-pollinate, or if it was crossed with random pollen from an adjacent field, the resulting offspring may incorporate the best traits of both parents, but that’s a longshot. When shuffling the genetic deck it takes analysis of thousands of individuals to find a horticultural royal flush. It’s why plant breeders choose parents carefully, cross them, and then plow under thousands of failing candidates before they find one that might produce the next elite Florida tomato, strawberry or juice orange.

But this reality is rarely recognized. A local kid was selling apple saplings on Facebook Marketplace, a post featuring a picture of healthy seedlings outgrowing the confines of red Solo cups. This aspiring John Chapman claimed to be selling Red Delicious, Golden Delicious, Gala, and a dozen other varieties propagated from grocery store fruit. I sent him a private note, kindly letting him know that apples do not breed true from seed, and that his seedlings were likely cross pollinated with a commercial crabapple and would not produce the varieties he claimed to be selling.

And in the spirit of the Internet2023 he told me, “Do Your Research.”

Limits of Time, Space and Stuff

Like humans, fruit and nut trees go through defined life stages.  And like humans, most tree crops are not reproductively competent until they transit a defined period of juvenility.  When seed savers push that pear, peach, or persimmon seed into a pot of moist peat moss, they initiate a relationship that will consume their time, space and dollars for years to come—only to find the fruits are inedible a decade later.  That is, even if the tree lives that long. The odds of growing something exceptional from a random seed are pretty remote.

Because of this reality, commercial tree fruit and nut cultivars are invariably grafted, cut from their original roots and strategically connected onto others. This way that needle-in-a-haystack genetic combination can be propagated for wider production.

Grafting mature plant tissue onto other roots circumvents the years required to reach reproductive competence.  The mature grafted tissue, the scion, has usurped the developmental thresholds of early plant life, and is prepared to produce fruit immediately when conditions and plant size become favorable. The resulting fruit is a dead-on match of the original highly desirable variety.

On the other hand, the planted seedling will limp along on inferior roots, subject to pests, pathogens, and weather stresses. After 4-15 years it might flower and produce a fruit, which probably will be not-so-good.  During that decade it will take water, love, care, tears, protection, and pruning. It will suck up hundreds of dollars of fertilizer and mulch, and will take up significant space on the property. That can be a long and expensive road to disappointment.

If the goal is to raise fruit, not invest in a genetic uncertainty, plant a grafted start on the right roots for your soil and disease pressures.

Seed-Borne Trees Don’t have Improved Roots

It’s hard to believe that half the tree is underground, but that part of the tree is critical for gathering nutrients, collecting water, fighting diseases and nematodes, and building intimate relationships with soil microbes that will propel growth above ground. The roots are a structural foundation, anchoring the tree to the earth, not an easy job.  The random roots of a spurious seedling have not been bred to fight these battles and fill these critical roles. Most folks are surprised that there is an entire discipline in plant breeding devoted to genetic improvement of rootstocks!

Surprisingly, the rootstock can dictate tree size, yield, and disease resistance in the scion. Many studies have shown that root choice also affects the flavor quality of fruit.

 Optimal Seed Saving is a Specialized Discipline

The reason there are seed companies with specialized harvest techniques and storage facilities is because seed saving usually requires specialized harvest techniques and storage facilities. Plants grown for seed are managed differently from plants grown for food. The crop is left on the plant longer, usually fertilized harder, and seeds are allowed to mature fully before harvest. Seeds are harvested under low humidity and stored at cool temperatures. Professional commercial seed operations assess and report genetic fidelity and germination rates, ensuring that when you put commercial seeds in the ground you know exactly what will grow from them.

Inbreeding Depression

Mutts are resilient, they have fewer rare illnesses than pure bred dogs, and that is attributed to onboard genetic diversity. When a plant self fertilizes, its genetics become about 25% less diverse with each generation, at least for a few generations. As genetic diversity narrows, plant vigor decreases, as does fruit size, yield and other favorable traits.

Seed savers need to understand which plants exhibit inbreeding depression, and take steps to not save and distribute self-pollination events. Alternatively, control pollination, and save only the seeds from desirable outcrosses.


  • If your annual vegetables come from hybrid seeds, buy them fresh each season, ensuring the uniformity of production and stable traits across the population.
  • Never save seeds from a hybrid and distribute them as the original variety.
  • If you plan to save seeds from an annual vegetable like an heirloom, make sure you take steps to block potential outcrossing.
  • If propagating fruit trees, learn to graft. It’s easy, satisfying, gets around the juvenility problem, and allows tight control of genetics.
  • If you insist on seed propagation of fruit trees, make sure you at least graft your seedling scions on appropriate roots for your soil, disease/pest pressures and climate.

In Conclusion, Some Hypocrisy

While I just outlined the caveats of seed saving, I’m glad to admit that it’s a common practice under my roof. I can’t resist planting seeds from rogue fruit, especially when I’m certain it is a genetic mess, like a self-pollination event in a diverse genetic background. When that genetic deck is shuffled, what will be the outcome? Digging another hole and running another 20 feet of irrigation line is no big deal for me. Only time will tell how bad it is.

You can save seeds, as long as you know the risks, precisely track the genetics, and never distribute something as a certain variety or cultivar unless you are certain. Find a great fruit you never had before, pick out the seeds and plant them. But understand the pitfalls, the years of commitment to something likely inferior, and the disappointment that time can bring, especially if you have limited space, time or resources. The folks that need to get it right on the first crack shouldn’t play genetic roulette.

But if you don’t mind taking a big risk and rebound well from a decade of failure, it can be a fun pursuit. For me, the potential disappointment is countered by the remote chance to find a rare seedling that laughs at disease and possesses a combination of genes that exists together for the very first time in the history of the universe—maybe giving me a fruit with new flavors and aromas to share with others.

Header photo credit:  K. Folta, one of a gazillion show boxes of seeds in our home.

by Kevin Folta

Source: UF/IFAS Pest Alert

Note: All images and contents are the property of UF/IFAS.

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