Sweet Pepper Breeding and Seed Saving Guide - Organic Seed Alliance
Publication date: March 29, 2022
Author: Michael Lordon, Organic Seed Alliance
Funder: USDA SPECIALTY CROP BLOCK GRANT PROGRAM THROUGH THE MINNESOTA DEPARTMENT OF AGRICULTURE
Table of Contents
- Background, Life Cycle, and Basic Biology
- Population Genetics and Breeding
- Seed Harvest, Processing, and Storage
- Seedborne Diseases of Sweet Pepper Seed Crops
- References, Resources, and Citation
Background, Life Cycle, and Basic Biology
Nearly all sweet peppers are classified as Capsicum annuum. The name likely comes from Latin, capsa, meaning satchel or box. Sweet peppers are part of the nightshade family (Solanaceae), along with tomatoes, potatoes, tobacco, eggplant, and more. The genus Capsicum evolved prior to human arrival in the Americas, the seeds spread by birds that are unharmed by the pungency of the fruit.
There is evidence that the species C. annuum was domesticated in modern-day Mexico at least 6,000 years ago. The seeds were spread by humans throughout Europe, Asia, and Africa starting over 500 years ago. The nearly global adoption of peppers in cuisines has led to immense diversity within the genus. Molecular studies are providing a better understanding of how sweet peppers are genetically connected to their many wild and cultivated relatives.
Sweet peppers vary dramatically in their size, shape, color, and flavor. The most common sweet pepper pod types are bell-shaped, heart-shaped, horn-shaped, and round. Immature fruits can be shades of green, yellow, or purple, developing into red, orange, yellow, green, or brown at maturity. A dynamic and complex balance of sugars, antioxidants, vitamins, and other organic compounds give each pepper its distinctive flavor and color.
Field grown sweet peppers require long, warm, frost-free seasons. The lifecycle of sweet peppers is usually over 100 days. Flowers usually start to develop after 8-15 leaves have formed, and stems divide into two branches at each flowering point. Peppers are sensitive to temperature, and plants grow poorly below 60° F. Ideal temperatures for growth are between 60° and 90° F, and plants will not set fruit outside of this range. Seeds germinate optimally in warm soils, with temperatures as high as 86° F.
Sweet peppers are facultative cross-pollinators, which means they are self-compatible, but can mate with another individual if pollen is transferred. Individual pepper flowers have both reproductive parts (pistil and stamen) with the ability to self-fertilize. Sweet peppers should be considered cross compatible with all plants in the genus Capsicum, including hot peppers of all types, though interspecies hybrids may not be viable in all instances. Cross-pollination is typically caused by insects. Recommendations for limiting crossing and encouraging self-pollination are included in the following section.
Population Genetics and Breeding
Two critical factors should be considered in maintaining the genetic health, resiliency, and integrity of a pepper variety during seed production: population size and isolation distance. Maintaining an adequately sized population entails saving seed from enough plants to retain your variety’s genetic variability. Genetic variability refers to genetic differences among plants in the same variety. Although two pepper plants may look the same and produce functionally identical fruit, they may have differences in their genetic makeup that express as varying degrees of tolerance to stressors, such as pests, diseases, drought, and heat. Producing and saving seed from multiple plants will help to ensure that sufficient diversity is preserved for continued reliable and robust future production. Always save seeds from healthy, robust plants to ensure that both the seeds and the progeny are of the highest quality.
Isolation Distances and Population Sizes
To ensure the varietal and genetic integrity of a variety, follow these recommended population sizes and isolation distances for the amount of space to maintain between different varieties and/or different market classes:
An isolation of ¼ mile or more is typically required for commercial production of seed, though isolation of 1 mile or more may be required in some environments or when producing “foundation” quality seed for genetic preservation. In some instances, seed buyers may require 150-600 feet of isolation, if there is a crop barrier between varieties.
Pollinator exclusion cages are also used to prevent unwanted crossing in locations where geographic isolation is not possible. These cages are usually made of synthetic mesh draped over conduit hoops installed over the plants. Lightweight row cover fabric (e.g. Agribon) or insect exclusion netting (e.g.ProtekNet) can be found online in various widths and lengths. These cages can also be purchased from manufacturers such as Redwood Empire Awning.
A recommended population size of at least 50 individuals is recommended for variety maintenance and commercial production, though sometimes only 5-20 plants are used.
To “rogue” is to remove inferior or atypical plants from a population to prevent the perpetuation of unwanted traits. Essentially, roguing involves walking through your planting and pulling out the plants that you do not want to reproduce. Roguing helps eliminate the ill effects of accidental crosses that may have occurred in a previous generation, accidental mixing of home-saved seeds, or genetic mutations. If you do not rogue, your variety will become more variable and may “deteriorate,” showing more and more undesirable traits season after season.
Rogue more than once. Roguing varieties at more than one point in the season is often the best strategy. For example, at the beginning of the season, you may remove seedlings that were the slowest to grow. Later in the season, you may remove plants that have off-type fruit. Still later, you may remove plants that appear to be the most affected by disease.
Consider variable conditions in the field. Plants that are in a poorer part of your field may perform poorly in comparison to their neighbors not due to inferior genetics but because they have had proportionately less sun, water, soil nutrients, et cetera. When considering how many plants to rogue, be sure to keep enough plants to maintain genetic variability, stability, and health of the variety.
New and improved sweet pepper cultivars can be developed by selective seed saving and cross-pollination. Breeders have countless techniques available, though most methods focus on traits related to fruit quality, growth habit, and resistance to diseases and environmental stressors. Historically, mass selection has been the most common means to breed peppers. Starting with a diverse population or with a controlled crossing of multiple varieties, breeders begin selectively saving seed from plants with desirable traits, continuing the process for several generations until the new variety is stabilized. Fruits are evaluated for their color, flavor, size, shape, earliness of maturation, and yield. Plants can express differently sized leaves, as well as varying amounts of branching and fruit set. There are numerous pests, pathogens and environmental conditions that harm sweet peppers, and the level of resistance to these stressors varies between cultivars, and between individual pepper plants.
Seed Harvest, Processing, and Storage
Fruit color is often used to assess seed maturity, and only fully mature fruit should be used for seed saving. Harvest begins once fruits have fully changed color on the plant but before they start to rot. Harvested fruits can be held around room temperature to increase seed maturity, though rotting may occur and care must be taken to isolate clean fruit before processing.
Removing the seeds from sweet peppers can easily be done by hand, though larger quantities can be processed more quickly with machine assistance. Seeds are detached from the core, rinsed with water, and dried for preservation. To detach seeds, simply cut off the fleshy walls with a knife, and scrape off the core by hand or with a utensil. For large batches, unscraped cores or small whole fruits can be covered with water and broken up with a strong, dull mixing blade (e.g. paint stirrer attachment on an electric drill).
The mature seeds will sink to the bottom, while the pulp and immature seeds float to the top and can be poured (decanted) off. Wet threshing machines, such as the Millett Wet Vegetable Seed Separator, have also been developed for extracting seeds from large batches of fruit. Once mature seeds are separated, they should be rinsed in fresh water and quickly set out to dry.
Ideally, seeds are set in a warm, dry spot with good air circulation, away from direct sunlight. Seeds can be spread into a thin or single layer on window screens, sheet pans, ceramic plates, coffee filters, or other non-stick surfaces, and should be stirred occasionally to ensure even drying. Mature seeds can be extracted from dried fruits, though this is only commonly done with thin-walled pods grown in hot, arid environments.
Yield can vary significantly between different varieties of peppers and with management practices. Some reports suggest roughly 1 lb of sweet pepper seed can be produced in 1,000 square feet of commercial growing space, or about 43 lbs per acre. The weight of harvested fruit can be anywhere from 0.5% to 10% seed by weight, in other words, 10 lbs of pepper fruit may have between 0.05 – 1 lb of seed. Hot peppers generally have more seeds than sweet peppers, often yielding 3 to 5 times more seeds per plant than sweet pepper varieties.
For storage and preservation after drying, transfer seeds to a cool, dark, and non-humid location. Sweet pepper seeds that are properly dried for storage should not be flexible, and should snap instead of bend when folded.
For short-term preservation (1–2 years) or if moisture content is unknown, transfer seeds to a permeable container, like a paper envelope or cloth bag, and keep away from light, moisture, and heat. Permeable containers can help mitigate losses to some fungi and bacteria, but do not prevent insects or rodents from eating the seeds.
For long-term storage, ensure seed moisture content is adequately low before using sealed containers and cold storage. Refrigerators can extend seed viability for years, and freezers can be even better, but precaution must be taken to ensure seed moisture is maintained within proper range at these low temperatures and that seed containers are acclimated to room temperature before being opened.
Seedborne Diseases of Sweet Pepper Seed Crops
Many pathogens affect sweet peppers, with varying prevalence and severity across growing areas and throughout the seasons. Bacterial, fungal, and viral infections can cause abnormal growth or reduced fruit yield. Growing practices are critical in preventing disease, especially with soil-borne and air-borne infections.
Some diseases are seed-borne and can be transmitted to seedlings from the surface of the seed. Treating sweet peppers seeds in a hot water bath or with a dilute bleach solution prior to planting can prevent the spread of some seed-borne diseases. Check with your organic certifier or contracted buyer to determine whether or not seed treatment is necessary. For more details on hot water treatment, see PennState Extension’s online publication here.
Identifying diseases based on their symptoms is possible in many cases, though sometimes disorders can appear similar to other abiotic stressors. There are resources available to help identify symptoms and take action to prevent damage, including local extension agents, testing services, or published guides. Saving seed from disease free plants reduces the chances that future generations will be affected. For resources and photos of plants affected by these pathogens, see extension resources from Cornell University or University of California.
These pathogens, nearly all of which can be seed-borne, have been associated with sweet peppers:
- Bacterial spot (Xanthomonas campestris pv. vesicatoria)
- Bacterial wilt (Pseudomonas solanacearum)
- Bacterial canker (Corynebacterium michiganense)
- Bacterial soft rot (Erwinia carotovora pv. carotovora)
- Anthracnose (Colletotrichum spp.)
- Early blight (Alternaria solani)
- Cercospora leaf spot (Cercospora capsici)
- Water molds (Phytophthora spp.)
- Damping-off (Pythium, Rhizoctonia, and Fusarium)
- Gray mold (Botrytis cinerea)
- Stemphylium leaf spot (Stemphylium botryosum f. sp. capsicum)
- Verticillium wilt (Verticillium dahliae)
- White mold (Sclerotinia)
- Alfalfa mosaic virus
- Beet curly top virus
- Cucumber mosaic virus
- Gemini viruses, pepper mottle virus
- Potato virus Y
- Tobacco etch virus
- Tobacco mosaic virus
- Tomato mosaic virus
- Tomato spotted wilt virus
Seed Saving and Breeding
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The Organic Seed Grower: A Farmer’s Guide to Vegetable Seed Production. John Navazio. 2012. Chelsea Green Publishing.
Organic Seed Production and Saving: The Wisdom of Plant Heritage. Bryan Connolly. 2011. Edited by C.R. Lawn. Chelsea Green Publishing.
Pepper Seed Production. Version 1.2. Jeff McCormack. 2006. Available at:
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Breeding Vegetable Crops. 1986. Mark J. Basset. AVI Publishing Company.
Chapter 3: Pepper Breeding. Walter H. Greenleaf
Vegetable Seed Production. 2nd edition. Raymond A. T. George. 1999. CABI.
Pepper Specific Books
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Peppers: The domesticated capsicums. 2nd edition. Jean Andrews 1995 University of Texas Press.
Chile Peppers: A global history. Dave Dewitt 2020. University of New Mexico Press.
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Parry C., Wang Y-W., Lin S-W., Barchenger D. W. 2021 Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes. PLoS ONE 16(3): e0243689.
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Citation: Lordon, M. 2022. Sweet Pepper Breeding and Seed Saving Guide. Organic Seed Alliance, Port Townsend, WA. 8 pp.
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