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breeding Population Mitigation and Variety Isolation for the Small-Scale Seed Saver

The seed starting season is well past and plant-out is complete or nearly so for those of us in the northern hemisphere. In advance of a hopefully busy harvest, my thoughts turn toward my first attempt at seed saving.

I’ll start by saying: if you don’t feel the need to guarantee you’re growing what you intend to, you enjoy a felicitous hybrid every now and then, or you just prefer keeping things simple, there is no need to worry about this at all. Anyone growing from seed, let alone saving it, is already way ahead of the class.

But for those who want to accurately maintain a variety, whether a recent creation like NuMex Trick-or-Treat or a timeless landrace like Jalapeño Zapotec, and be confident that it will remain vigorous and true to type generation after generation, things get a little more complicated.

I think we tend to focus too much on whether seeds were isolated or not. This is insufficient on its own: perfectly isolated seeds from just a few plants will have a genetic bottleneck which is difficult to correct without outside seed sources, whereas open pollinated seeds gathered from the center of a large group would represent healthier diversity and still minimize undesired crosses.

Of course, most of us don’t have space for large groups of one variety. If we want to enjoy peppers widely and also save seed which is reliably true to type, we must rely on some amount of population mitigation and variety isolation. I’ll try to highlight the primary difficulties and their possible remedies.

Population Mitigation

There is no sample population large enough to perfectly represent the full diversity of a variety. In a sense, this is freeing. It also means the big lists you’ll see of minimum populations to maintain a type, such as from the Seed Savers Exchange, are ultimately arbitrary and represent social best practices rather than objective facts. Thus, we should grow as many individuals as possible within the constraints of our garden. If that is fewer than 50 (as a rough guideline, per the SSE above), extra precautions should be taken, such as…

- Extending your population by regularly introducing new seed sources. For instance, you might save and use your own Scotch Bonnet MOA every year, but since you only grow 4 individuals, every so often you plant half your own seeds and half seeds from a friend, seed train, exchange, or vendor. Each time you do that, you’re injecting the genetic diversity of the external population into your own. If you switch up your external sources from time to time, you add even more to your effective population. Yet, you’re still not reliant on anyone for seed in any given year; if sources of a niche cultivar start to dry up, you can take steps to maintain a larger personal population.

- Delaying negative genetic effects by skipping generations. If care is taken in their storage, most pepper seeds are quite viable after 5 years, down to maybe 50% germination after 10 years. (This is from book learning, not experience; take it with a grain of salt.) As such, you needn’t save seeds every generation. If the genetic quality of the population is likely on the decline for any reason (like lack of population), you might regenerate the seed stock only once every 5 years. At that pace, your children and grandchildren could likely enjoy your seed legacy and never notice much genetic decline.

(Seed storage is opinionated, even among experts. In my opinion, one example of good seed storage would be: seed packets kept in an airtight container with self-indicating desiccant which is refreshed when needed, the airtight container then placed within an insulated container (like a styrofoam cooler) which is stored in a refrigerator. The airtight container and desiccant keep things dry, the refrigerator keeps things cool, and the insulated container minimizes temperature variation overall.)

Variety Isolation

“Blessed are those who love one variety, for their seed saving is effortless.”

For the rest of us, maintaining a variety will usually require isolating it from the other sexually compatible varieties we grow. The main problem is that most home isolation methods don’t just isolate varieties, they also isolate the individuals within the varieties.

We want a family tree which looks like lots of Ys and ⅄s, diverging and recombining in myriad ways. Isolating the individuals results in a family tree of parallel lines: a population of non-interbreeding, mostly unchanging clones. This doesn’t allow for the active, recombinant variety and resulting adaptation which provides a properly maintained variety with its broad resilience. A few remedies include…

- Using mesh enclosure over a capacious frame, covering the whole population. I would love to see cheap, collapsible plastic frames with fitted mesh covers sold at ridiculous markup by gardening companies. If they lasted a few years, I bet they’d sell like hotcakes and everyone would be happy. Until then, we’ll have to get handy with bamboo and mosquito netting, or something. For this method, if your area isn’t windy, you will need to schedule sexually compatible varieties to be unmeshed on alternating days (changing before dawn or well after dusk), so every variety you’re maintaining gets rotating access to pollinators. Or, if your population is large enough for it to make sense, you can buy in pollinating insects to release in the enclosures.

- Hand pollinating. This is really only feasible for maintaining a personal seed supply; even producing enough to share in a seed train would become pretty annoying. This would involve carefully pollinating and marking the specific flowers which you will later gather seeds from. The choice of the control freak or the retiree. You could, if desired, ensure a “perfectly diverse” seed population representing every combination of parents, every generation. Time and labor intensive.

- A combination of a lot of common sense measures. I think this is what most casual seed savers arrive at. It looks something like this: these early varieties flowered weeks before anything compatible with them, so selecting their first fruits for seed saving is effective isolation; these few do flower together, but are grouped with incompatible varieties at opposite ends of the garden; this group is my baby and gets the full mesh-and-frame treatment; this group are a breeding playground of hand pollinations; over time one narrows focus on a selection of favorites, reducing all logistics; etc.

For myself, this is my first serious season and I’m growing small amounts of lots of varieties to sample the waters. I haven’t fully decided what to do… likely a mix of things, as in the last option listed. I think with as much compatible stuff crammed together as I have this year, it will be best not to worry about it too much. Next year or soon after, I’ll have standby varieties that I can focus on more seriously maintaining starting from a fresh pool of seed from multiple quality sources.

Did I miss anything? Any thoughts?
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I've come around to agreeing with most of your conclusions. If you take a single plant, cover it with painters cloth to isolate, and keep doing that year over year, your seeds will very likely lose important parts of the essence of the original pepper.

As a hobbyist pepper gardener, I've just had to become comfortable with the realities of saving seeds from only a handful of examples.

But I often wonder how many of our seed vendors isolate just a single plant, and consider that good-enough. Especially for many of the more obscure niche peppers.
Good info! Been thinking a lot about this and haven't found the best strategy so far.
In my backyard i'm growing sixteen "experimental" varieties on a few square meters and can see the bees going from plant to plant all day long. So isolating here is an absolute must. I do choose the plants that i cover on characteristics i like. Mainly vigor and stature wich is probably the same as choosing the plant that adapted the best to the climate and growing conditions offered by me. This year i have some varieties i liked last year growing in bigger numbers and in tight rows on open ground. Hoping to find more selection criteria here like fruitshape, taste, fruitquantity and whatever turns up in the group. Diversity is greater in those tight large groups i guess but they all descent from the same motherplant.
I don't know for sure but doubt that it is necessary to introduce genes from other isolated lines. A variety that adapted to a dessert climate like Arizona for example won't bring me much in the northern hemisphere. I rather keep pulling seeds from plants that adapt the best to the growing conditions in my climate. Even when i can get some genes from another grower in my own climate there are still lots of variables. Grower x might be growing in potting soil or hydro while i try to grow in clay on open ground. My garden is within a few miles of the coast and plants endure a lot of wind and salty sand dispersion in the area, the ground is heavy and wet clay around here. 50 miles to the east there are sandy and dry soils and to the northeast there are peatsoils and so on. I do see advantages in growing big groups in isolation but with the ammount of varieties i want to grow i will be needing a lot of acreage... Might resort to the handpollinating option you mentioned, that will keep me busy! 😀
This is insufficient on its own: perfectly isolated seeds from just a few plants will have a genetic bottleneck which is difficult to correct without outside seed sources, whereas open pollinated seeds gathered from the center of a large group would represent healthier diversity and still minimize undesired crosses.
Pepper varieties are always inbred and have already gone through that bottleneck during creation of said variety and all plants of your large group will be genetically identical. The only problem would be the accumulation of deleterious spontaneous mutations and the hybridization with other varieties. The only strategy against that is selection, i.e. planting enough plants and only use seeds from those that are true to type and are healthy. Theoretically, you could even run a maintenance breeding program that involves controlled cross-pollination, phenotyping, and selection, perhaps even crossbreeding with other varieties, followed by backcrossing.
Pepper varieties are always inbred and have already gone through that bottleneck during creation of said variety and all plants of your large group will be genetically identical.

This isn’t true. Landraces are defined by their diversity and are not created by bottleneck. And a large group of pepper plants grown from seed cannot be genetically identical; it’s impossible.
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I’m sorry for that early morning response; looking back, it reads more harshly than I intended. We’re probably just using slightly different definitions of the same terms…
In terms of variety maintenance, which is my primary goal, I’ve been thinking about the necessity to actually moderate selection pressure, even what we would consider positive pressure.

I think it’s probably a mistake to apply more selection than roguing for crosses and some level of basic vigor. Any more than that, and one is effectively working on an “improved” seedline of the original variety.

Where’s the harm, everyone benefits from the improved genetics right? Not necessarily. Suppose I maintain NuMex Heritage Big Jim for a decade or so here in western Kentucky. If I apply more selection pressure than the minimum, the variety will adapt to my local climate and my horticultural practices.

To me, “my” Big Jim performs better than the original, while apparently maintaining its proper phenotype. Why shouldn’t I confidently spread this seed as originally labeled? Because it’s not actually Big Jim anymore. For all I know it lost the diversity which allowed it to thrive in ground, say, or maybe now it performs worse in dry climates, making it inappropriate in its intended growing region. Anyone relying on known traits of Big Jim are in fact getting a subset which is useful to me, but may be deleterious to them.
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Genetics (mitochondrial) can be environmentally effected along the breeding line, as well. An outdoor control grow has many variables to consider/contend to have success creating true to type offspring. Technically, unless gene splicing is an option genetics can be different from fruit to plant and plant to plant, regardless. Genetics are constantly being realigned due too many factors. Even cloning won‘t guarantee genetic order for the long haul. One person’s preference differing from another’s can effect the outcome when it gets down to genetics/phenotype, as well. Unless, you’re growing laboratory controls you’re going to have variations in genetics. Seeds respond to their environment. When it’s fit for the seed to respond it will but, replicating the seeds genetic response outdoors is a pipedream. Lab results will always differ from outdoor results and vise versa. GMO is in play for genetic control and that isn’t going to maintain genetics regrowing from their saved seeds either. Diversity is the key to genetic order meaning that order is constantly being realigned to suit it’s needs. An exact replica won’t happen outdoors, but an improved replica can be had.
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