Pepper



Taxonomy of the Pepper (Capsicum annum L.) sec. il Cronquist System
Dominium/Domain: Eucariotae (Eukaryote or Eucarya)
Regnum/Kingdom: Plantae (Plants)
Subregnum/Sub-Kingdom: Tracheobionta (Vascular plants)
Superdivisio/Superdivision: Spermatophyta (Plants with seeds).
Divisio/Division: Magnoliophyta Cronquist, 1996 (Flowering plants).
Subdivisio/Subdivision: Magnoliophytina Frohne & U. Jensen ex Reveal, 1996.
Classis/Class: Rosopsida Batsch, 1788 (Dicotyledons).
Subclassis/Subclass Lamiidae Takht., 1993.
Superordo/Superorder: Solananae R. Dahlgren., 1992.
Ordo/Order: Solanales Dumort., 1829.
Subordo/Suborder: Solanineae Engl. 1898.
Familia/Family: Solanaceae Juss., 1789.
Subfamilia/Subfamily: Solanoideae Kostel, 1834.
Tribus/Tribe: Capsiceae Dumort., 1827.
Subtribus/Subtribe: Capsicinae Kitt. in A. Rich., 1840.
Genus: Capsicum L. (1753).
Specie: Capsicum annuum L. (1753)

Taxonomy of the Pepper (Capsicum annuum Linneo, 1753)sec. the APG SystemII
Regnum/Regno: Plantae (Plants)
Clade: Angiosperm
Clade: Eudicots
Clade: Tricolpate Angiosperms
Clade: Nucleo delle tricolpate
Clade: Asterids
Clade: Euasterids I
Ordine: Solanales
Familia/Family: Solanaceae Juss., 1789
Genere: Capsicum L. (1753)
Specie: Capsicum annuum L. (1753)


Taxonomy of the Pepper (Capsicum annuum L.) sec. the APWebsite System:



The pepper (Capsicum annum L.) is a vegetable from South America which has made ​​its appearance on the European tables in the sixteenth century. According to some researchers the starting center for the dissemination of this plant is the Brazil, according to other Jamaica. The cultivation of numerous varieties of pepper is widely used in worldwide (over 1.26 million of hectares), as Asia, Central and South America, Africa and Europe. The surface dedicated to this plant in Italy is declining and, in recent years, imports exceeded exports.
Pepper we eat the fruit, which is a fleshy berry green, yellow or red. Inside the fruit is the capsaicin, an alkaloid that gives this vegetable its characteristic spicy flavor.
Capsaicin (8-methyl-N-vanillyl-6-nonenamide) is an active component of chili peppers, which are plants belonging to the genus Capsicum. It is an irritant for mammals, including humans, and produces a sensation of burning in any tissue with which it comes into contact. Capsaicin and several related compounds are called capsaicinoids and are produced as secondary metabolites by chili peppers, probably as deterrents against certain mammals and fungi. Pure capsaicin is a volatile, hydrophobic, colorless, odorless, crystalline to waxy compound.


Pedo-climatic requirements
Before cultivating pepper in an area that has never been cultivated before, you must check the vocationality, understood as adaptability to the specific needs of culture to all the pedo-climatic characteristics.
The soil
It 'a good rule to have information on the soil characteristics of the interested area to pepper cultivation. The culture has not special needs of soil but, to avoid soils that are subjected to waterlogging that is not tolerated by the crop. The waterlogging also promote collar disease and tracheomycosis representing adversity parasitic diseases most feared by the pepper. The Table 1 reports the optimal soil parameters for the cultivation of pepper.

Table 1 – Main soil parameters that are optimal for the cultivation of pepper.
Soil parameters Optimal values

Texture

Drainage
Effective soil depth
Limestone total assets
pH
Salinity (CE m S/cm dell’estratto di saturazione)
Franco
Franco-sandy
Franco-clay
must be good
> 60 cm
< 10%
5.5-7.0
< 1.5

You have to remember that effective soil depth (franco di coltivazione in italian) is the distance between the soil surface and the upper limit of a layer which constitutes an obstacle to the growth of the roots of plants. The effective soil depth may also be limited by a rise of the aquifer, following rains.
You have to remember that a franco soil is an equilibrate soil regarding the textural classes, of intermediate composition, where the fractions no prevail with their characteristics on other, ideal for cultivation.
A soil has good drainage when it is able to quickly remove the excess water. The soil water retention curve allows to measure the drainage capacity of a soil. In this curve, the interval corresponding gravitational water has to be very large.
Climate
In climates of Europe, in which the hot season has a limited period, the varieties used of the genus Capsicum are grown as annual, and can not tolerate temperatures below 7 °C and have an optimum development with a temperature comprised between 21 and 28 °C and with a remarkable atmospheric humidity.
Table 2 shows the optimal values ​​for the cultivation of pepper of some climatic parameters.

Table 2 – Optimal values ​​of some climatic parameters for the cultivation of pepper.
Climatic parameters Values
Biologic Minimum Temperatures
Lethal Minimum Temperatures
Growth Optimum temperatures:
 during the day
 during the night
Biologic Maximum Temperatures
Lighting
10-12 °C
0-2 °C

21-28 °C
15-18 °C
30-35 °C flowers fall (anthoptosis)
Not high


Pepper is a tropical plant and cannot tolerate frost. It will not grow where the temperature drops below 7 °C. A moderate winter climate is essential. Pepper plants need about 2,000 mm rain annually. When the rainfall is scarce must be supplemented by irrigation.

Rotation, Crop Succession and Intercropping
Rotation.Vegetable crop rotation is necessary for long term success in commercial vegetable production and farm. Knowledgeable vegetable growers who use correct crop rotation actually increase the productivity of their farms over many years of intensive cultivation. New farmers soon learn that certain vegetables, planted year after year in the same plot, become diseased and decline in productivity.>br> The word "rotation" also describes a planting system in which the vegetable plantings are arranged in a sequence to improve soil health and produce high quality and yield from year to year. Factors which interact to reduce garden potential when rotation is not employed are:
  • increased soilborn diseases, nematodes, and soil insects;
  • lower organic matter,
  • more chance of toxic chemical residues, and
  • imbalance of essential mineral elements.
In a rotation, vegetables are often arranged according to groups so that individual vegetables from the same family do not follow each other in the rotation. The reason for this is that each family of vegetables has unique effects on conditions which reduce field potential. For instance, most vegetables within a given family usually fall prey to the same diseases and insects. Most of the vegetables planted belong to ten distinct families. It is important to know that the pea or legume family includes peas and beans of all kinds.
In a small surface it is often possible to rotate families of vegetables where only a few plants of each kind are planted. For example: tomato, pepper, eggplant, and potato can be treated as a single group in a rotation.
Common vegetable diseases that survive in soil and attack vegetables can be prevented by timely rotation.
Fusarium root rot fungus infection will increase in beans and peas unless there is a span of two to three years between plantings on the same plot of soil. Cabbage disease club root, caused by a fungus, will infect subsequent crops in the mustard family for a period of four to five years. A planting of broccoli, cabbage, or cauliflower which contracts club root fungus disease this year leave behind fungus to infect broccoli, califlower, or cabbage planted there next year. Tomato bacterial canker will persist in a viable state for three years, once it is introduced into the soil. Verticillium wilt fungus that infects a tomato crop one year will probably live in the soil for many years, and will infect subsequent crops of tomato, pepper, eggplant, and potato. There are vegetable varieties which can resist or tolerate infection by certain fungi and bacteria. Today, farmers who know that their soil harbors Verticillium wilt, Fusarium wilt, and root knot nematodes can select tomato varieties that are resistant to all three diseases.
It is wise to precede shallow-rooted crops requiring close cultivation, such as lettuce, beets, and other greens with clean-culture crops such as tomatoes, peppers, summer squash, or melon, which extend roots deeply into the soil and discourage weed growth by shading the soil surface.
Some vegetables leave organic residues in soil that are toxic (allelopathic) to certain crops which may follow. Place crops in compatible sequence so that one which produces a toxic effect will not precede one that is susceptible to that toxin. Consider relationships between sweet corn and some other vegetables. Decomposition of sweet corn stubble liberates organic toxins which inhibit early season root growth of lettuce, beets, and onions. Grain corn and sweet corn are good alternate hosts for the fungus which causes pink root disease of onions. Onions following corn can have severe pink root disease even in soil where onions have never been planted.
Certain vegetables feed heavily on available nutrients, thereby creating a shortage for subsequent kinds which are less efficient feeders.  If celery is planted after heavy feeders like tomatoes, close attention to soil testing and fertilization is required to prevent nutrient deficiencies.
Expert vegetable growers and farmers plan rotations several years.
Think of your field in the square shape and draw it on the paper. Divide the each square into 4 sections. The number of sections you have will be equal to the number of vegetable groups that you intend to plant:
  1. sweet corn (grass family), followed by
  2. blackeye peas and snap beans, followed by
  3. cabbage, broccoli and radishes, followed by
  4. tomato, pepper and potato.
To determine what vegetable group will occupy the four plots next year simply rotate the plan clockwise one section. Next year the blackeye peas will be planted where the corn grew this year, and so on. Other more complicated examples can be worked out using the same procedure. Obviously, you may not want the same size plot of every vegetable that you plant, but a well designed rotation plan will help you.

Crop succession for pepper.Succession cropping is planting two or more different vegetables in sequence in the same field space within one growing season. The same reasoning and rules that were used to explain rotation cropping apply to successions as well. Succession cropping permits several plantings of certain well liked vegetables without causing disease buildup. For example, four or five separate crops of lettuce or two to three separate plantings of beans or squash can be worked into a field inside a single season by an ambitious farmer who plans ahead. One succession that has worked successfully reads like this. In early spring, radishes, kohlrabi and turnip greens are planted. Follow with tomatoes and peppers, and finish out the season with a seeding of beets, spinach and chard.
Another planting plan could include lettuce in spring, squash in early summer and broccoli in fall. Notice that in each case the spring and fall crops are always frost tolerant, cool season vegetables.
Intercropping. When two or more crops are grown together, each must have adequate space to maximize cooperation and minimize competition between the crops. To accomplish this, four things must be considered: 1) spatial arrangement, 2) plant density, 3) maturity dates of the crops, and 4) plant architecture.
Intercropping is considered as the practical application of ecological principles such as diversity, crop interaction and other natural regulation mechanisms. Intercropping is defined as the growth of two or more crops in proximity in the same field during a growing season to promote interaction between them. Available growth resources, such as light, water and nutrients are more completely absorbed and converted to crop biomass by the intercrop as a result of differences in competitive ability for growth factors between intercrop components. The more efficient utilization of growth resources leads to yield advantages and increased stability compared to sole cropping.
Furthermore, the multifunctional profile of intercropping allows it to play many other roles in the agroecosystem, such as resilience to perturbations, protection of plants of individual crop species from their host-specific predators and disease organisms, greater competition towards weeds, improved product quality and reduced negative impact of arable crops on the environment.
Nitrogen fixing legumes can be included to a greater extent in arable cropping systems via intercrops. Legumes contribute to maintaining the soil fertility via nitrogen fixation, which is increased in intercrops due to the more competitive character of the cereal for soil inorganic N. This leads to a complementary and more efficient use of N sources. Intercropping of grain legumes and cereals therefore offers an opportunity to increase the input of fixed nitrogen into agroecosystems without compromising cereal N use, yield level and stability.
Despite all its advantages, the agricultural intensification in terms of plant breeding, mechanisation, fertiliser and pesticide use experienced during the last 50 years has lead intercropping to disappear from many farming systems.
Methodology in intercropping: the agronomic advantages of intercropping are the result of differences in competitive ability for growth factors between intercropped components. In terms of competition, this means that the components are not competing for the same ecological niches and that interspecific competition is weaker than intraspecific competition for a given factor. The fact that the crops involved may have different resource requirements as well as different growth patterns makes it more complicated to define a proper methodology for the study of intercrops compared to studies involving one species – sole cropping. The interpretation of interactive effects between intercrop components activities and soil processes is extremely complex. For example, specific crop growth affects soil shading and light interception and therefore also temperature, plant water uptake changes soil water content in the rhizosphere which effects microbial decomposition rates, decomposition rates affect soil texture, water retention characteristics, rooting profiles and nutrient availability to the crops. Experimentally it is very difficult to disentangle these processes. Thus, to really interpret all these processes at once and under variable and interacting conditions, dynamic simulation models of these systems are valuable.
Extent of intercropping in Europe and worldwide: intercropping was a common practice in Europe before mechanisation, plant breeding and use of synthetic fertilizers and pesticides was implemented in a more intensified the agricultural production starting in the 1950ties. Intercrops of clover and grasses in pastures are still widely used in European agriculture, but arable intercropping (cereals, grain legumes, oil seeds) for feed and human consumption is presently not so common. It has been scheduled that the entire animal feed sources in organic farming should be of organic origin from 2005 in the EU (EU Commission (EC) No. 1804/1999). This will require a major increase in organic cereal and grain legume (protein) crop production, to balance the European organic deficits. As an example, the French deficit for organic feed protein, considering complete organic feed supply, was 9000 tonnes in 1999. In this context, intercropping can be adopted for modern European organic farming systems as a practical alternative to existing mainly sole-cropping strategies. Intercropping perspective in arable systems and the potential area for intercrops in organic farming is large considering the possible economic benefits and future legal requirement in feed and food industry. Re-introducing intercropping in European organic agriculture to a greater extent should not be reversion to old methodology, but rather considering the usefulness of this old and sustainable cropping practice in a modern, innovative and technology-oriented organic agriculture. Furthermore, intercropping constitutes a concrete means to increase the diversification of agricultural ecosystems, for which there is a worldwide appeal.
Agrobiodiversity: the importance of agrobiodiversity encompasses socio-cultural, economic and environmental elements. All domesticated crops and animals result from human management of biological diversity, which is constantly responding to new challenges to maintain and increase productivity. Biodiversity provides not only food and income but also raw materials for clothing and medicines, among others. It also performs other services such as maintenance of soil fertility and biota, and soil and water conservation, all of which are essential to human survival. There is a growing awareness that the variety of landscapes and the related biodiversity shaped by agriculture over centuries could be harmed by the continued intensification. Intercropping is planned biodiversity, and it is thought that planned diversification will increase associated biodiversity, and in this way contribute to conserving biodiversity in the open agricultural land and associated ecosystems.
Organic farming and intercropping: organic farming is a steadily increasing production form in European agriculture. It is environmental friendly, due to low input of nutrients and no use of pesticides, and it contributes to the production of food without pesticides and antibiotic residues. A further expansion of organic farming is needed to meet consumers worldwide having an increasing demand for products, which are healthy, safe, and of high quality and produced with consideration for animal welfare and the environment. European organic farming and research within this area are in the forefront internationally and offers the opportunity of a food production, which could strengthen the competitiveness of EU agriculture. Intercropping is of special relevance and importance in future organic farming systems, because it offers a number of significant enhancements of both the net productivity of organic farming and the ecosystems in farming regions as a result of the increased diversity of the cropping system. Intercropping is a method for simultaneous crop production and soil fertility building and it may also contribute to the prevention of nitrogen leaching risks sometimes observed from sole crops such as grain legumes due to changes in incorporated residue chemical quality involving nutrient turnover. It is also an ecological method to manage pests, diseases and weeds via natural competitive principles that allow for a more efficient resource utilisation. This same competitive principles also contribute to an improved quality of intercrop products. The inclusion of nitrogen fixing crops in an intercrop leads to the utilisation of the renewable resource of atmospheric nitrogen which increases the sustainability of the agroecosystem. Intercropping can also be regarded as a practice to increase the production of less stable crops such as grain legumes and hereby contribute to lowering the protein deficit in EU at lower risk for the farmer. All these potentials strongly comply with the guidelines set up in Agenda 2000 and including ‘the European model of agriculture’, emphasising the production of healthy, safe and high quality food considering animal welfare, and environmentally sound production, especially in relation to reduced nitrate leaching from agricultural land. The project also relate to the Community policy of new preventive methods for improving plant health, since the diverse crop community in an intercrop may prevent the rapid spreading of diseases and pests. Intercropping is also relevant for integrated and conventional agriculture aiming at reducing the input of resources in plant production.
Intercropping involves the simultaneous culture of two or more vegetables or a vegetable with a nonvegetable plant in the same garden space within the same growing season. Many combinations are possible. To keep a rotation sequence in proper order, it is best to intercrop members of the same family whenever possible. Radish can be sown between rows of transplanted cabbage, broccoli and cauliflower.
The radishes will be harvested long before its slower maturing companions take up the space. Bibb lettuce or leaf lettuce can be planted between slower growing endive and escarole. The lettuce will be harvested before the endive needs the room.
The important thing to remember in intercropping is to arrange spacing of different kinds of vegetables in a pattern that will permit each to receive maximum light. When leaves of one plant overlap those of another, the ones which are shaded will grow less vigorously and be less productive. For example, do not interplant marigolds in your summer squash or tomatoes. Either the marigolds or the squash will grow well, but not both. If you wish to rid your plot of nematodes, plant it to sweet corn which nematodes cannot use for food. Always plant a winter cover crop of Elbon Rye where there is no fall vegetable being grown to help control nematodes. Expert vegetable growing is a complex discipline; but rotation, succession and intercropping plans that you make in advance of the season will pay off in your enjoyment of healthy vegetables.

Rotation, Crop Succession and Intercropping Examples
It is showed a rotation consisting of four vegetable groups: 1) Grass (sweet corn and other), 2) Pea (blackeye pea, snap bean, pinto); 3) group formed of cabbage, broccoli, cauliflower); 4) group costitued of tomato, pepper and potato.

First year Second year Third year Fourth year

Peas
Beans

Sweetcorn

Cabbage
Broccoli

Peas
Beans

Tomato
Pepper

Cabbage
Broccoli

Sweetcorn

Tomato
Pepper

Cabbage
Broccoli

Tomato
Pepper


Tomato
Pepper

Sweetcorn

Sweetcorn

Peas
Beans

Peas
Beans

Cabbage
Broccoli


Succession
A succession consisting of three vegetable groups in the same plot, within the same season:
Early Spring
Radish
Kohlrabi
Turnip Greens
Early Summer
Tomato
Pepper
Eggplant
Fall
Beets
Spinach
Chard


Intercropping
Intercropping - the growing of two or more crops simultaneously on the same land - makes efficient use of limited arable land. However, it can complicate chemical pest control as a result of residues and label restrictions, and it is a labor-intensive practice. Traditionally, intercropping has been practiced most widely in developing countries. However, the advantages of intercropping, particularly the potential for increasing sustainability, have stimulated interest in the practice in the United States and other developed countries.
The concept of the land equivalent ratio (LER) was developed by Mead and Willey (1980). The LER is the most common index for measuring the advantages of using intercropping systems on the combined yield of both crops. The LER is calculated as the yield of a crop in an intercrop system relative to the yield of that crop in a monocrop system (that is, intercrop yield/monocrop yield).
Many different species have been intercropped with peppers. The reviewed literature has been organized by botanical family of the primary intercropped species.
  1. Alliaceae family: many different species have been intercropped with peppers. Were compared cropping systems over three successive seasons (monsoon, winter, and summer). In the winter, a pepper–onion (Allium cepa) intercrop increased returns by 59% over sole-crop pepper but decreased returns by 36% over sole-crop onion. The intercropping system was able to accommodate only 30% of the normal population of onion. Was intercropped pepper with onion, garlic (Allium sativu), or coriander (Coriandrum sativum) during the rainy season. The pepper–garlic intercrop receiving recommended fertilization rates produced the highest net return.
  2. Brassicaceae family: interseeded forage brassicas such as kale (Brassica oleracea Acephala group), rape (Brassica napus), and turnip (Brassica rapa Rapifera group)] into standing crops of chile pepper (Caspsicum annuum) at two different times per season. This was an example of relay intercropping; that is, planting a second crop after an initial crop has reached maturity but before harvest is completed on the initial crop. Intercrops reduced pepper yield compared with a sole-cropped control in only 1 of 3 years. Brassica yields were satisfactory and generally were higher with early August seeding than with mid-August seeding into the pepper crop. We concluded that interseeding forage turnip into chile pepper in early August could help support animals that were allowed to graze the pepper fields after the pepper plants had died (late fall) on mixed crop–livestock farms. intercropped cabbage (Brassica oleracea Capitata group) with tomato (Solanum lycopersicum), pepper, muskmelon (Cucumis melo), and cucumber (Cucumis sativus). The LER was highest (5.4) and net returns were best with the cabbage–tomato intercrop, followed by the cabbage–pepper intercrop, which had a LER of 3.7.
  3. Fabaceae family: was planted pepper and soybean (Glycine max) in alternate rows. It found that leaf water potential of pepper plants intercropped with soybean was generally greater than that of monocropped pepper plants. The authors speculated that this was the result of a windbreak effect from the soybean rows. Pepper plant populations differed between the monocrop and intercrop treatments, so pepper yields could not be compared.
    Several experiments were conducted involving interseeding legumes into chile pepper. Pepper yield was unaffected by intersowing with Vicia faba minor, Medicago sativa, or black lentil (Lens culinaris). Vicia faba minor intercropped with pepper and managed as a winter annual increased the yield of a following crop of forage sorghum (Sorghum bicolor) compared with an unfertilized control. However, interseeding snap pea (Pisum sativum) into stands of chile pepper was not economically advantageous compared with monocropped pepper.
    We studied intercrop combinations of bean (Phaseolus vulgaris) and pepper. Intercrop bean yields were lower than sole crop bean yields. However, intercrop pepper yields were greater than sole crop pepper yields, and the LER of the intercrops was greater than 1. We intercropped pepper with bean and amaranth (Amaranthus spp.). Pepper intercropped with bean yielded more than pepper intercropped with amaranth or monocropped pepper.
  4. Rosaceae family: we found no yield differences between strawberry plants relay intercropped with various vegetables, including bell pepper, and those not intercropped. It was possible to plant bell pepper up to 31 d before the end of the strawberry fruit harvest without having a detrimental effect on strawberry fruit yield.
  5. Solanaceae family: we compared monocropped pepper with pepper intercropped with maize (Zea mays) or with eggplant (Solanum melongena). Maize acted as a barrier crop for aphids (Aphis gossypii) and reduced virus infection on pepper in the first part of the cropping season. Eggplant acted as a trap crop for aphids and reduced virus infection on pepper for a longer period than did maize. As a result, yields of pepper plants intercropped with eggplant were the highest in the trial.
Factors such as whether peppers are the primary crop in the system, the timing of the intercrop planting, climatic conditions, pest pressure, and local economics all contribute to the potential success or failure of intercropping with peppers. Positive results are most likely to occur when plant-to-plant competition can be minimized, for example when peppers are used as intercrops in young orchards or in hedgerow crops. Relay intercropping can also increase the likelihood of success. Intercropping may succeed if cultural factors like fertilization and irrigation are adjusted, but some crop combinations may simply be too competitive to produce economic benefits. Although broad recommendations cannot be made, the reviewed studies offer several examples of successful combinations of peppers with other crops.
Follows an intercropping plan for three vegetable groups:

Celery   Celeriac
Parsnip
Carrot
Parsley   Fennel

Broccoli
Cauliflower
Cabbage
Mustard Greens   Kale
Kohlrabi  Radish  Turnip
Cucumber (on trellis)
Bush Buttercup Squash
Bush Butternut Squash
Bush Summer Squash


Cultivation technique
In the examination of the technique for the cultivation of pepper you take into consideration the preparation of the soil, variety choice, planting techniques, fertilization, irrigation, weed control, other techniques such as the use of mulch.
  • Soil preparation
    The main working of the soil is very important for the hydraulic agricultural arrangement of the land. We must pay special emphasis on the implementation of efficient trenching and drainage. Although the roots of the pepper explore mostly a layer of surface soil, equal to about 30-40 cm deep, the culture requires plowing of medium deep (40-50 cm). In case of lands tending to clayey, is preferred replace the plowing with a soil work at two-layer by using a subsoiler plow or by using a 40 cm depth subsoiler before, and then a plow at 30 cm deep.
    The work of the soil complementary for the refinement of the land, work less hard, is performed during the winter and spring recalling the following decreasing order of "intensity" of the use of agricole machines:
    grubber (cultivator) disc harrow rotating harrow spike-tooth harrow.

  • Choice of the varieties
    The choice of varieties is crucial for the success of the pepper cultivation, from a qualitative and quantitative, and must be made in relation to:
    • mercantile aspects: quality required by the market (color, shape, size);
    • adaptation to climatic conditions (good coverage of the berries, foliage well-shaped);
    • tolerance or resistance to the most common pathogens (tracheomycosis, viruses, bacteria).
    It is preferable to focus on F1 hybrids.
    They are set out below some varieties and hybrids of sweet pepper, undergone some to variety trials:
    • F1 hybrid "Ancho Gigante" (Figure 1): fruits, huge, green/reddish 12 x 15 cm, conical, weighing 250 g each, extremely tasty, excellent flavor and great use especially in Mexican cuisine. Vegetative cycle of average guy, with a good resistance to TMV.
    • F1 hybrid "Hytower" (Figure 2): variety intended to culture in greenhouse and open field, good for the precocity of its production cycle for the high quality of the pulp that looks thick and very pleasant and the service life of the fruits. Its vegetative cycle of 78 days after transplantation, the development of the plant is of medium type. Seafood square, 11-17 cm long, with a diameter in the upper part of 8-9 cm; an average weight of 350 g. They are dark green in color when they are immature and turn a brilliant deep red at maturity. Resistant to Tobacco Mosaic virus disease.
    • "California Wonder" (Figure 3): sweet pepper fruit square, sweet, fleshy cm 10 x 10, taken from a plant about 70 cm high, vigorous and compact. Resistant to TMV.
    • "Solero" (Figure 4 and 5): plant height medium-high, with intermediate bearing, good leaf coverage and low susceptibility to lodging. The variety certainly does not appear very early, even if the capacity of fruit (3 fruits per plant) and the commercial production, at the first harvesting, are enough high. The berries, red in color, semi-long, showed a low value of the average weight, even if the size is found to be satisfactory. The junction of the petiole is very hollow. The thickness of the pulp is among the lowest reported. Excellent but the hardiness of the plant and the capacity of production scale, with the plant that maintains good vegetative condition even in advanced harvesting season. In light of the data provided "Solero" confirms the characteristics that make a variety of reference for the production of full-field, be destined for the fresh market, although some measured parameters give rise to several doubts about its industrial purpose.
    • "Pompeo" (Figure 6 and 7): tall plant with erect posture, good leaf coverage, not predisposed to lodging ("allettamento" in italian. "Lodging" can be defined as the state of permanent displacement of plant stems from the upright position). The variety is enough late, the ability to fruit setting was low (2 berries per plant) and lower is the value of commercial production. The data on the average weight and the size of the berries are semi-longs satisfactory results. The junction of the petiole is very hollow. Pompey showed a lower sensitivity to attack by Heliothis armigera than other varieties. Overall, there appears to provide good indications for use in industrial perspective.
    • "Pepola" (figure 8 and 9): plant of medium height, fairly erect posture, poor leaf coverage. The production at the first harvest is quite early, with average capacity of fruit set (2.5 fruits per plant), and satisfactory values also for the weight of the fruits, semi-longs, good and uniform size and color to red. Good data on the thickness of the pulp. It should be further evaluated as it appears, after "Favilla" and "Lido", the red grape variety that has provided the most interesting data in industrial perspective.
    • "Favilla" (Figure 10 and 11): tall plant, with intermediate bearing, quite opaque, with a satisfactory resistance to lodging, tree structure high enough, a total of less balanced than the reference varieties ("Solero"). Red grape variety that comes in very interesting perspective for industrial use; in fact, showed a good precocity, a very good ability to fruit set for the first stage (about 5 fruits per plant) and provided the greatest hits production, among those in the test, in number and in weight, showing a good ability to concentrate the production. Fruit half long, tending to the square, with good value of average weight and size is not high, but very uniform. Highlight a low number of berries attacked by Heliothis armigera. Also the thickness of the pulp was among the highest. Under the conditions of the prov in the plant has shown a tendency to decay fairly quickly after the first harvest, proving to be probably more suited to a concentrated harvesting.
    • "Logos" (Figure 12 and 13): plant very high, with erect posture, good leaf coverage and excellent resistance to lodging. He showed great precocity of production, with a high capacity fruit in the first stage (4 fruits per plant) and commercial production among the best. The berries are semi-long of yellow when ripe, with data on the average weight and size satisfactory, although not very uniform. The thickness of the pulp was among the highest. Very good is also the hardiness of the plant that seems to be able to support large production capacity and scalability for multiple harvests. It is confirmed as one of the yellow-berried variety of reference for the open field, with very interesting features appear in the perspective of an industrial application.
    • "Stellor" (Figure 14 and 15): plant with good posture, adequate leaf coverage but with a high tendency to lodging. The ripening was delayed, with a production level, at the first harvesting, which lies on an average. Good data on the weight and size of the berries, tending to the square-shaped and yellow when ripe. Not particularly high the data on thickness of fruit pulp.
    • F1 hybrid "Mogador" (Figure 16): plant vegetation contained in the production of strong central stem. Fruits regular (over 250 gr.) To 4 lobes yellow at maturity. For greenhouse or tunnel and open field in a mild climate.
    • "Cuneo giallo" (Figure 17): deep yellow sweet pepper fruits, sweets three or four lobes of great weight; exceptional thickness of the pulp. And 'variety is very much appreciated by gourmets.
    • "Corno di toro giallo" (Figure 18): the fruits of conical reach 18-20 cm. in length and a diameter at the petiole of 5-6 cm. Very early is among the first to appear in the markets both green and yellow. Also great for storage in brine or vinegar.
    • "Corno di toro rosso" (Figure 19): sweet pepper fruits conical reaching 18-20 cm in length and a diameter of the petiole 5-6 cm. Very early is among the first to appear in the markets both green and red. Also great for storage in brine or vinegar.
    • "Lungo dolce verde chiarissimo" (Figure 20): sweet pepper, with approximately 70 cm tall plant that produces many fruits 10-12 cm long sweet, thin, pale green to keep even oil or brine, as well as underwater vinegar.
    • Pepper ”Friggitello dolce” (Figure 21): sweet pepper plant compact, medium-sized leaves with dark green, medium-early cycle, suitable for greenhouse and open field. The fruits are 8-10 cm long, are cone-shaped, deep green color that turns bright red in physiological maturity. The flesh is sweet and tasty. They are used both in the green state for the conservation pickled or "skip" in the pan, to the state ripe for the drying and storage in winter.

    Figure 1 - ”Ancho Gigante”, a pepper variety sweet and red.

    Figure 2 - F1 hybrid "Hytower".

    Figure 3 - ”Wonder California”.


    Figure 4 - Plot of ”Solero”.

    Figure 5 - Fruits of ”Solero”.

    Figure 6 - Plot of “Pompeo”.

    Figure 7 - Fruits of ”Pompeo”.

    Figure 8 - Plot of ”Pepola”.

    Figure 9 - Fruits of ”Pepola”.

    Figure 10 - Plot of “Favilla”.

    Figure 11 - Fruits of ”Favilla”.

    Figure 12 - Plot of ”Logos”.

    Figure 13 - Fruits of ”Logos”.

    Figure 14 - Plot of “Stellor”.

    Figure 15 - Fruits of ”Stellor”.


    Figure 16 - F1 hybrid ”Mogador”.

    Figure 17 - ”Cuneo giallo”.

    Figure 18 - ”Corno di toro giallo”.

    Figure 19 - ”Corno di toro rosso”.

    Figure 20 - ”Lungo dolce verde chiarissimo”.

    Figure 21 - Pepper local variety ”Friggitello dolce”.



  • Techniques of planting
    You have to know with precision when transplant, the planting distances and the investment.
    • Time of transplant. It is recommended the transplant the seedlings with at least 50 days of life, planted with the soil surrounding the roots (in italian con pane di terra), robust and uniformly developed and the first flowers already sketched. It 's very important to the health of the material used. This should be given the necessary guarantees from the dealer. The transplant can be performed approximately from the middle of May, when the soil temperature has stabilized at around 13-15 °C.
      For obtaining the plantlets, pepper seeds should be planted 0,6 cm deep in a fine-textured seed-starting mix or vermiculite to provide good drainage. We recommend using a 20-row tray; the shallow channels in the tray allow you to minimize the amount of growing medium needed while maximizing the number of seeds you can start on a heating mat. The channels also provide a convenient way to grow multiple varieties and keep them separate.
      Bottom heat of 27-32 °C is essential for pepper germination. Seeds will germinate in 7-8 days at that temperature; at lower temps, germination is slower, erratic, and percentage germination is reduced. In about 2 weeks, when the first true leaves begin to form, carefully separate the seedlings and transplant them into cell trays or pots.
      Choosing the correct cell size is another balancing act. On the one hand, you want the pepper plant's roots to fill the cell so that the root ball holds together when you plant it outside. On the other, you don't want the plants to become rootbound, especially if poor weather delays planting. An oversized, rootbound transplant will be significantly stressed and result in a compromised crop. You also have to make the most of your greenhouse space, so you don't want to grow your transplants to an unnecessarily large size. A 50-cell or 72-cell tray is a good choice for peppers that will be grown 8-10 weeks. A good compromise between quality and cost of seedlings is the purchase of containers with 160-196 celles.
      Once the seedlings have been transplanted to the cell trays, grow them at 21 °C days, 16°C nights. Use a well-drained growing medium in the cells, and take care not to overwater seedlings; wait until the soil is dry before watering again. Water once or twice a week with a fertilizer solution diluted to 100 ppm. Plants also can be watered with products plant protecting against root-damaging, soilborne fungal diseases such as Pythium, Verticillium and Fusarium.
      When the seedlings are about 7-8 weeks old, they should be 15-20 cm tall. Ideally, they will have some buds but no open flowers. Harden off the plants by decreasing the day temperature to 16-18 °C for 1 week before transplanting (hardening off).
      Peppers perform best in well-drained, fertile soils with a pH of 6.5.
      When the weather has settled and the threat of frost has passed, the peppers can be planted to the open field or tunnel house. Bury them a bit deeper than the root ball to encourage additional root growth that will make them sturdier. Plastic mulch and row cover may be used to increase warmth and, hence, earliness and yield. You can use hoops to prevent the row cover from rubbing across the plants' growing tips.
      With well-grown transplants, and perhaps a little help from benign summer weather, you may find that peppers are a profitable crop for your farm.
    • Planting distances and Investment. There are two different ways of pepper transpant: single row and twin row. The twin row has the following advantages:
      • minor damage from sunburn;
      • savings of perforated hose for irrigation (only one hose for one twin row);
      • saving of any mulch;
      • easy to passage of the mechanical means.
      By contrast, the adoption of the twin row can give rise to major difficulties for the detection and the detachment of the berries in the inner part to it.
      The planting distances and investments recommended are:
      • Single row. Row spacing: 80-100 cm; investment: 25,000-30,000 plants/ha.
      • Twin row. Distance between the two rows of the twin row: 40-50 cm; distance between the two centres of the twin row: 160-180 cm; investment: 28,000-30,000 plants/ha.
      It is best to use plants equipped with phytosanitary certification and varietal.
    • Fertilization
      The knowledge of the budget in soil nutrients is a prerequisite for the establishment of a proper fertilization plan. it is therefore recommended to have precise analytical data relating to the individual plot, or homogeneous area in which it falls, not older than five years, compared to the following soil parameters:
      • texture;
      • pH;
      • active limestone;
      • organic matter;
      • macronutrients (N, P2O5 assimilating, K2O exchangeable);
      • microelements.
      Even in the absence of analytical data, the calculation of nutrient requirements can be commensurate with the removal as a function of the amount of product expected, the fertility of the soil and loss of fertilizing elements.
      Withdrawals of nutrients per ton of fruits produced, in kg/t, are estimated as follow:
      • Nitrogen 3.9 kg
      • Phosphorus 1.0 kg
      • Potassium 5,0 kg
      • Calcium 2.0 kg
      • Magnesium 0,2 kg
      PHOSPHORUS
      The phosphatic fertilizer promotes plant growth by allowing a good flowering and fruit; should be made ​​with the basic fertilization to the preparation of the soil per hectare at a dose of approximately:
      • 200 units of P2O5 in the case of soils with low endowment;
      • 150 units of P2O5 in the case of soils with high endowment;
      • 100 units of P2O5 in the case of land allocation to very high.
      POTASSIUM
      Promotes tolerance of adversity parasitic and good coloring of the fruits; should be made ​​with the basic fertilization of the preparation to the soil per hectare at a dose of approximately:
      • 200 units of K2O, in the case of soils with low envelope;
      • 150 units of K2O, in the case of land included in the media;
      • 100 units of K2O, in the case of soils with high envelope.
      NITROGEN
      Positively influences the vegetative activity of the plant, flowering and fruit set, and the number and the size of the berries; must be deployed as efficiently as possible fractional part for transplantation (50% of the total dose) and partly in coverage (35% of the total dose one month after transplantation and the remaining 15% after the 1st or 2nd harvestingn). The maximum dose of nitrogen should not exceed the following doses:
      • 300 units/hectare, in the case of land without organic matter supply;
      • 200 units/hectare in the case of soils with organic matter supply.

      Additional information are given following. Soil preparation and fertilization of the pepper crop varies depending on the crop production system used. Regardless of the system used, the field should be fall plowed if erosion is not a problem or plowed in the spring as early as possible to a depth of 20 to 25 cm. Take a soil sample and have it tested for pH, phosphorus, potassium, calcium, and magnesium. Soil tests can be sent off through the local County Extension Office for analysis.
      Potassium and especially phosphorus are likely to accumulate in most soils following several years of heavy applications for vegetable crops.
      Soil pH influences plant growth and availability of nutrients in the soil. Have your soil tested the fall prior to planting so that any needed lime can be applied and will have time to react. Calcium has limited mobility in the soil, so broadcast and incorporate needed lime to a depth of 6 cm in the fall if possible, particularly on sod ground.
      A pH range of 6.5 to 7.0 is best for peppers and liming may be required if soil pH falls below 6.0. Soil test results should show at least 680 Kg of calcium and 45 Kg of magnesium prior to transplanting. If magnesium levels are low (less than 100 Kg/ettato) and lime is needed, use limestone. If the soil pH is satisfactory but the magnesium level is low, Epsom Salts (MgSO4) or magnesium oxide or some other source of magnesium may be used.
      Soils known to be high in residual nitrogen should be avoided to prevent peppers from producing excessive foliage at the expense of fruit. Consider the previous crop when deciding how much nitrogen to apply; there will probably be some residual nitrogen following a crop which received heavy doses of nitrogen fertilizer during the previous season.
      Simple, hand-held electronic meters are now available which growers can use to quickly determine the nitrate nitrogen status of soils and plants. These Cardy meters can be used to determine residual nitrate levels in soils prior to planting as well as to measure nitrate levels in plant sap in order to assess the efficiency of fertigation.
      Nitrate is the form of nitrogen which is most readily available for use by crops.
      Soils also contain varying amounts of ammonium forms of nitrogen which bacteria convert to nitrate forms over time.
      Nitrate ion meters like the Cardy do not measure ammonium nitrogen and therefore may underestimate some of the nitrogen becoming available to plants during the course of the growing season.
      For bare ground plantings on soils known to be relatively poor, apply 50 Kg/Ha of nitrogen preplant. Apply one-half at plowing and one-half just prior to transplanting and disk into the soil. On more fertile soils, apply 12 to 14 Kg/Ha of nitrogen prior to transplanting.
      For processing bell pepper production where plastic mulch is not used, sidedressing or banding additional nitrogen to either side of the plant when the first fruit begin setting is essential for good yields. Apply 30 Kg/Ha of nitrogen at the first sidedressing. A second sidedressing of 30 Kg of nitrogen two weeks later should also be made. Nitrogen fertilizer placed up against the plant stem can burn and injure the plant. Caution should also be exercised that too much nitrogen not be put on before pepper fruits have set on the plant or the plant may grow vegetatively rather than set fruit.
      Pepper plants must, however, obtain sufficient size and foliage before bloom and fruit set in order to prevent sunscald. Fruit set on small plants will stunt plant growth and such plants will fail to develop the size needed to produce a profitable crop.
      For fresh market bell pepper production on most medium-textured soils where raised beds, plastic mulch and drip irrigation are being used, we recommend that all of the phosphorus, all the potassium, and 30 to 50 percent of the nitrogen requirement be applied prior to bedding and laying plastic. The fertigated portion of the total nitrogen requirement can be divided into equal amounts (remaining nitrogen requirement divided by the number of weeks until final harvest) and injected weekly (based on 31,000 plants/Ha).
      Growers with very sandy soils should also consider applying 50 to 60 percent of their potassium requirement in weekly increments through the drip system in addition to nitrogen. For typical nutrient needs of a pepper crop see Table 3.

      Table 3 - Kg of The major nutrients used by a 100 q Pepper Crop.
      Pepper/Nutrient N P K
      Fruit
      Plant
      45
      95
      6
      6
      50
      90
      Total 140 12 140


    • Irrigation
      An uniform soil moisture supply throughout the growing season is essential to produce consistent yields of quality fruit.
      Irrigation increases pepper yields from 20 to 60% and eliminates disastrous crop losses resulting from severe drought.
      Long dry periods will cause plants to abort flowers and produce small fruit. Drought injured plants are usually slow to recover. Moisture stress in peppers also causes fruit drop, sunscalding and blossom end rot.
      Soil moisture should be maintained between 65 and 80% of field capacity. Soil at 100% field capacity is saturated and too wet for prolonged growth of the plants.
      Use tensiometers to determine when to irrigate. Transplanting, flowering and fruit development are the most critical stages where a lack of water will severely reduce production.
      Drip irrigation. With black plastic mulch has become essential for profitable pepper production. One of the major advantages of drip irrigation is its water use efficiency.
      Vegetables always require some irrigation. Using drip irrigation results in water savings of 60% compared to sprinkler irrigation. Weeds are also less of a problem since only the rows are watered and the middles remain dry. Studies have also shown significant yield increases with drip irrigation and plastic mulch when compared with sprinkler irrigated peppers.
      The most dramatic yield increases have been attained by using drip irrigation, plastic mulch and supplementing nutrients by injecting fertilizers into the drip system (fertigation).
      Drip tubing may be installed on the soil surface or buried 6 to 8 cm deep.
      When used in conjunction with plastic mulch, the tubing is installed at the same time the plastic mulch is laid. Usually one line of tubing is installed on each bed. If two rows of peppers are planted on a bed and they are not more than 30 cm apart, then both rows can be watered from the same drip line. A field with beds spaced 150 cm center to center will require 5,000 m of tubing per hectare (one tube per bed).
      The tubing is available in various wall thicknesses ranging from 0.008 mm to 0.6 mm. Most growers use thin wall tubing (0.2-0.25 mm) and replace it every year. Heavier wall tubing can be rolled up at the end of the season and reused; however, take care in removing it from the field and store in a shelter. Labor costs for removing, storing, and reinstalling irrigation tubing are often prohibitive.
      Excellent results have been achieved by injecting at least half of the nitrogen through the drip system. This allos plant nutrients to be supplied to the field as needed. This method also eliminates the need for heavy fertilizer applications early in the season which tend to leach beyond the reach of root systems or cause salt toxicity problems. Only water soluble formulations can be injected through drip systems. Nitrogen formulations tend to be more water soluble and consequently, are easily injected. Nitrogen also tends to leach quicker and needs to be supplemented during the growing season. Drip systems should be thoroughly flushed with fresh water following each fertilizer injection.
      Surface water used in a drip irrigation system should be well filtered to remove any particulate matter which might plug the tubing. The water should be tested for minerals which could precipitate and cause plugging problems.
      Tensiometers or soil moisture blocks to measure soil moisture levels can be purchased and placed in the soil. When using tensiometers, on silt loam soils maintain the soil moisture below 40 centibars at the 30 cm depth. Do not apply too much water, especially beneath black plastic mulch.
      In Italy, especially in central and southern and insular, the profile of climate in the summer months makes it more necessary to integrate water availability of soil with irrigation.
      Irrigation is supplied with the amount of water necessary and sufficient to satisfy, without excess or waste, the requirements of the pepper throughout the development cycle (from transplantation, to harvesting), net of contributions from the soil (water this useful for transplantation any contribution of groundwater) and useful rains (at least 10 mm in 24 hours) falls during the production cycle.
      Studying the irrigation, very important is the water volume. It is the amount of water that is distributed to each irrigation. The irrigation water volume varies, basically, with the soil texture, which affect the hydrological characteristics and the retention of useful water (water retained by the soil and helpful for the plants). It can be estimated empirically through formulas based on the size of soil to be irrigated, which therefore must be known. The volume of irrigation intervals must also take into account the efficiency of the irrigation system chosen (for example, sprinkler irrigation is 0.7-0.8; localized irrigation from 0.9 to 0.95). For the plots to be irrigated, or homogeneous segments of the same, it is essential to have the particle size analysis.
      The water volume can change over time because it depend from the depth of cultivation soil to moisten, as well as from the portion of the reserve water that can be used from the vegetable crop before you make a new irrigation. For pepper the depth of soil to be irrigated is fixed at 0.6 m, while the portion of water used prior to reinstatement is stimated in 50% of the total helpful reserve of the soil. The irrigation interval defines the interval in days between one watering and the next. In practice, it is determined by the following relationship:

      1
      V + Σp - ΣETPc = 0
      n

      Where:

      V
      is the water volume (in mm) distributed with the last watered;

      Σp
      is the sum of the rains "useful" (at least 10 mm in 24 hours) falls between day 1 (the last watering place) and day n (the one in which the relationship becomes = 0);

      1
      ΣETPc
      n
      is the daily consumption amount of evapotranspiration (in mm) of the crop, starting from day 1 up to day n above defined. The day after the n day is done the irrigation and becomes the 1st day of the irrigation next round.


      Per il rilievo delle piogge l’azienda dovrebbe essere dotata di un apposito strumento di misura (pluviometro).
      Per quanto riguarda il calcolo dei valori giornalieri di ETPc si rendono necessarie due determinazioni:
      1. i mm di acqua giornalmente evaporati da un apposito strumento di misura (“evaporimetro”: il tipo più noto e diffuso il Italia è il cosiddetto “Evaporimetro di classe A”), da installare in un sito rappresentativo di un dato comprensorio omogeneo che, moltiplicato per un “coefficiente di vasca” (0,8), ci darà il valore di ETP;
      2. gli stadi di sviluppo del peperone (fenofasi) indicati in table 4, in corrispondenza dei quali varia il valore di Kc. Tale valore, moltiplicato per ETP ci darà il valore di ETPc
      Quindi:
      ETPc = ETP x Kc


      Table 4 - Coefficienti colturali (Kc) in relazione alle fenofasi per la coltura del peperone.
      Fenofasi Date indicative Kc
      Trapianto-Prime fasi di crescita
      Fioritura-Allegagione
      Massima copertura-Raccolta
      Fase finale
      15 maggio-30 giugno
      30 giugno-31 luglio
      1 agosto-30 settembre
      30 settembre-30 ottobre
      0,30
      0,70
      0,95
      0,65


      L’irrigazione può essere effettuata per aspersione a pioggia oppure a goccia, specie nelle coltivazioni pacciamate.
      E’ sicuramente da preferire il metodo a goccia in quanto presenta i seguenti vantaggi:
      • riduce il consumo di acqua;
      • localizza la distribuzione in prossimità delle radici;
      • non crea condizioni favorevoli allo sviluppo di parassiti vegetali e animali;
      • assicura una migliore uniformità di distribuzione;
      • permette di apportare in maniera frazionata ed omogenea nel tempo gli elementi fertilizzanti rispettando cosi i fabbisogni specifici di ogni fase vegetativa;
      Attenzione alle caratteristiche dell’acqua da utilizzare, in maniera particolare per l’irrigazione a goccia in termini di salinità, impurezze.
      Va evidenziato che l’irrigazione a goccia ha dei costi superiori a quella per aspersione dovuti a manichette, filtro, miscelatore, ecc. ma presenta una maggiore efficienza.
      Per quanto riguarda i volumi di adacquamento, nel caso di irrigazione a goccia si consiglia di intervenire reintegrando giornalmente, o al massimo ogni due giorni, l’evapotraspirazione della coltura.
      Per la razionalizzazione della pratica irrigua si auspica comunque l’attivazione di uno specifico servizio agrometeorologico in grado di fornire indicazioni sui sistemi, i turni e i volumi di adacquamento più idonei.
    • Cover Crops
      Winter cover crops help protect the soil from water and wind erosion. When incorporated into the soil as "green manure," cover crops contribute organic matter to the soil.
      Cover crops help protect the soil from water and soil erosion. When incorporated as green manure crops they contribute organic matter to the soil. Organic matter improves soil structure and reduces compaction and crusting. Organic matter also increases water filtration, decreases leaching and releases nutrients to the plants. Cover crops should be plowed under at least one month before transplanting the pepper crop.
      The planting of cover crops and subsequent incorporation of the green manure into the soil enhances pepper production. Pepper growers frequently plant wheat, oats, rye or ryegrass as winter cover crops. If these non-nitrogen fixing cover crops are to be incorporated as green manure, provide them with adequate nitrogen during their growth. This increases the quantity of organic matter produced and provides a carbon : nitrogen (C:N) ratio less likely to "tie up" or immobilize nitrogen during decomposition.
      As a general rule, when non-leguminous organic matter having a C:N ratio exceeding 30 to 1 is incorporated, a supplemental nitrogen application (usually 20 to 28 Kg/Ha of nitrogen) prior to incorporation is recommended. The exact rate required will depend on the C:N ratio, soil type and amount of any residual nitrogen in the soil. Plow green manure crops under as deep as possible with a moldboard plow at least three weeks prior to transplanting peppers.
      The organic matter:
      • improves soil structure (helps to reduce compaction and crusting),
      • increases water infiltration,
      • decreases water and wind erosion,
      • increases the soil's ability to resist leaching of many plant nutrients, and
      • releases plant nutrients during decomposition.

      Controllo delle infestanti
      E’ fortemente consigliato il ricorso alla sarchiatura.
      I prodotti ammessi per il diserbo in pre-trapianto sono il trifluralin alla dose di 0,5-1 l di p.a./ha o pendimetalin alla dose di 0,6-1 l di p.a./ha
      In post-trapianto, nei confronti delle graminacee, è possibile utilizzare:
      • Fluazifop-P-butyl l/ha 1.5-2;
      • Fenoxaprop-P-Ethyl l/ha 1,5-2 (% p.a. 6,6);
      • Sethoxydim l/ha 1,5-2.
      Non sono ammessi principi attivi diversi da quelli precedentemente indicati.

      Altre cure colturali
      Per ridurre l’uso di diserbanti ed avere un prodotto pulito è consigliata la pacciamatura. Allo scopo si consiglia di utilizzare film pacciamanti di colore nero o fumé. La pacciamatura ha anche un importante effetto sulla temperatura del terreno il cui riscaldamento determina un aumento della precocità della coltura. Per le colture non pacciamate e non diserbate si consiglia di effettuare una sarchiatura ogni qualvolta necessario.
      Composizione ed alimentazione
      La caratteristica principale del peperone è il suo elevato contenuto di vitamina C; a parte questo, non presenta altri vantaggi nutrizionali, se non il basso contenuto calorico che lo rende adatto alle diete dimagranti. Le varietà dolci sono ultimamente quelle preferite dai consumatori, per la migliore digeribilità e appetibilità.
      Le varietà piccanti sono sconsigliate a chi soffre di ulcera o iperacidità gastrica e ai bambini.
      INFO ALIMENTARE (giallo) - Carboidrati: 6,32; proteine: 1; grassi: 0,21; acqua: 92,02; colesterolo: 0; sodio: 2; calorie: 27.
      INFO ALIMENTARE (rosso) - Carboidrati: 6,03; proteine: 0,99; grassi: 0,30; acqua: 92,21; colesterolo: 0; sodio: 4; calorie: 26.

      Utilizzazione del peperone da parte dell’industria agroalimentare
      L’industria agroalimentare richiede generalmente frutti:
      a) di elevato residuo ottico, elevato spessore e consistenza della polpa;
      b) facile detorsolatura (con questa operazione si perde in media il 25%);
      c) di ottimo sapore e aroma, non piccanti;
      d) di colore brillante, uniforme (vengono tollerati bacche di colore variegato o “fiammanti” intorno al 15%);
      e) con assenza di lesioni di qualsiasi natura.
      I prodotti che si possono preparare con il peperone sono:
      - All’aceto: si impiegano frutti immaturi, di colore verde, tagliati a falde, oppure frutti di piccolo diametro appuntiti, con polpa sottile, di colore verde giallastro. Il prodotto, posto in vasetti o barattoli di banda stagnata, viene colmato con aceto bollente, con 3-4% di sale, pastorizzato e poi raffreddato.
      - Sott’olio: si usano frutti colorati, tagliati in pezzi di dimensioni diverse, scottati con aceto bollente fino a pH inferiore a 4,5, sgrondati, asciugati, inscatolati e riempiti con olio a temperatura di 80-85°C e, dopo la loro chiusura, pastorizzati.
      - Arrostiti: occorrono frutti con polpa spessa. Dopo lavaggio e detorsolatura, segue l’arrostimento, pelatura, taglio, inscatolamento, aggiunta del liquido di governo, aggraffatura, sterilizzazione, etichettatura e incartonamento. Peperonata e caponata: i frutti, colorati, ridotti in pezzi (costituiscono l’80% del totale), vengono scottati anche al vapore, miscelati con derivati del pomodoro, cipolla, altri ortaggi e aromi.
      - In salamoia: i frutti, tagliati a falde, si conservano in salamoia al 15-22% in fusti con aggiunta di acido citrico o acetico. Per preservare il colore è possibile l’aggiunta di anidride solforosa. Previa desalatura, le falde possono essere impiegate per preparare prodotti all’aceto e sott’olio.
      - Pasta di peperone: si prepara partendo da concentrati di peperone con aggiunta di addensanti ed aggreganti.
      - Crema o purée: si possono utilizzare frutti con dimensioni diverse.
      - Surgelato: i frutti con elevato spessore del mesocarpo e dotati di ottimo sapore si tagliano in pezzi di varie dimensioni e dopo sbollentatura si surgelano.
      - Disidratato: si usano frutti rossi o verdi con mesocarpo spesso ed elevata sostanza secca, si tagliano a cubetti e si essiccano.
      - Essiccati al sole: Il peperone di Senise a denominazione di Indicazione Geografica Protetta oltre che allo stato fresco viene venduto in collane di frutti essiccati al sole (peperoni “cruschi”) di colore rosso vivace, contenuto di acqua non superiore al 12%, oppure in polvere finissima ottenuta dalla macinazione dei frutti secchi, previo trattamento in forno per eliminare il residuo di umidità.
      - Oleoresine: sono dei potenti irritanti, vengono estratti da frutti freschi o secchi di peperone o peperoncino, vengono miscelati con l’olio di soia o di semi di cotone e vengono usati principalmente per insaporire o “colorare” i cibi. Come antiossidante e in erboristeria come carminativo antibatterico, contro dolori di stomaco, lombaggine, nevralgie, ecc. Negli USA sono state usate come spray dai poliziotti per sedare sommosse.

      Cenni storici sul peperoncino
      Quando Cristoforo Colombo scoprì l’America, non solo non si rese conto di avere raggiunto un nuovo continente ma ancor meno poté immaginare che la scoperta di alcune specie vegetali avrebbe così profondamente interagito con gli usi ed i costumi dei popoli del Vecchio Continente. Bisogna infatti ricordare che nell’ambito della famiglia delle solanacee, di cui fa parte il peperoncino, si trovano anche il pomodoro, la melanzana, la patata e il tabacco.
      In realtà le origini del genere Capsicum ( dal latino “capsa” = scatola, per la forma dei frutti) si fanno risalire ad un’epoca abbastanza remota: pare che il peperoncino sia apparso per la prima volta circa 9-10000 anni fa nel Messico centro-meridionale e di lì si sia diffuso in America centrale e nella parte settentrionale dell’America del Sud.
      I nativi americani utilizzavano il peperoncino raccolto da piante selvatiche già nel 5000 A.C. e sembra che la sua coltivazione fosse praticata già a partire dal 3500 A.C.
      Cristoforo Colombo portò in Europa alcuni esemplari di peperoncino al ritorno da un suo viaggio intorno al 1493, e li chiamò "pimentos" in quanto riteneva che, per la loro piccantezza, potessero essere un sostituto del pepe (pimiento in spagnolo), spezia allora assai costosa e di difficile coltivazione.
      All’epoca della sua scoperta, il peperoncino si era già differenziato in circa una dozzina di varietà che venivano coltivate dagli Atzechi per usi alimentari, medicamentosi e rituali.
      In Europa l’accoglienza delle nuove specie vegetali fu abbastanza tiepida in quanto si riteneva che i frutti della famiglia delle solanacee fossero nocivi alla salute, ed in effetti parecchi lo sono, e pertanto queste nuove piante vennero impiegate per anni esclusivamente a scopo ornamentale.
      Solamente verso la metà del 1600 i cuochi europei iniziarono ad utilizzare in cucina patate, pomodori o melanzane, ma con molta cautela.
      Il peperoncino, al contrario, iniziò a diffondersi in Spagna e Portogallo già a poche decine di anni dalla sua scoperta e si propagò ben presto ai paesi costieri del Mediterraneo, portato da commercianti o marinai. Dal Mediterraneo, grazie alle grandi crociere esplorative di quel periodo, il peperoncino si diffuse dapprima in Africa meridionale e successivamente in India ed in estremo oriente entrando rapidamente a far parte integrante delle varie culture gastronomiche di questi Paesi.
      Per un curioso paradosso molte varietà che si erano nel frattempo differenziate in Europa furono reimportate in America durante la colonizzazione del continente da parte di francesi, inglesi, portoghesi e spagnoli, dando origine ad abitudini culinarie “fusion”, si pensi ad esempio alla cucina creola-cajun, o a quella tex-ex o al largo uso del peperoncino nella cucina centro e sudamericana.
      Ai nostri gioni sono conosciute circa 26 specie di peperoncino ma le uniche ad essere coltivate per uso alimentare o industriale sono 5: Capsicum annuum (ad esempio “Jalapeno”, “Caienna”), Capsicum frutescens (ad esempio “Tabasco”), Capsicum chinensis (ad esempio “Habanero”), Capsicum baccatum (ad esempio “Cappello del Vescovo”, “Bishop Crown”) e Capsicum pubescens (ad esempio “Rocoto”).

      Notizie botaniche
      I peperoncini sono originari di ambienti equatoriali o tropicali, in queste condizioni sono arbusti perenni di dimensioni variabili da 30 - 40 cm a circa 2 m e possono vivere alcune decine di anni.
      Nei climi europei, in cui la stagione calda ha una durata limitata, le varietà utilizzate sono coltivate come piante annuali, dal momento che le solanacee del genere Capsicum non tollerano temperature inferiori ai 7 °C ed hanno uno sviluppo ottimale con una temperatura compresa tra i 21 e i 28 °C e con una notevole umidità atmosferica.
      Le varie specie possono impollinarsi reciprocamente dando origine ad ibridi vitali, ad eccezione del “Rocoto” (Capsicum pubescens) che non può essere impollinato che da altri della stessa specie del “Rocoto”.
      Il tempo di maturazione dei frutti è abbastanza variabile, da un minimo di circa 50-60 giorni per Capsicum annuum (ad esempio “Greco Dolce”) ad un massimo di 100-120 giorni per Capsicum chinensis (ad esempio “Habanero”, “Cappello Turco”).
      Il frutto dei peperoncini è una bacca che può svilupparsi nelle dimensioni, forme e colori più vari. Le dimensioni possono variare da quelle giganti di un peperone quadrato a quelle minime di un “chiltepin”, simile ad un piccolo pisello.
      Le forme sono tra le più fantasiose del regno vegetale, a pisello, a ciliegia, a lampioncino, a berretto turco, a sigaro, a cono appuntito o tronco, a disco volante, lisci o grinzosi, diritti o incurvati.
      I colori sono anch’essi variabili, molte varietà maturano da un verde più o meno intenso al rosso o al giallo o all’ arancio o al marrone, ma vi sono cicli di maturazione che partono da un colore bianco per arrivare al rosso scuro passando attraverso il viola e l’arancio. Le varietà più policrome, pur essendo commestibili, vengono abitualmente coltivate a scopo ornamentale.
      All’interno dei frutti vi sono nervature dette placenta su cui si sviluppano i semi solitamente di colore bianco o avorio. Diversamente da tutti gli altri il Capsicum pubescens ha semi di colore nero.

      La piccantezza del peperone
      La sostanza chimica che determina la sensazione definita "piccante" è costituita da una miscela di vari alcaloidi (capsicina e suoi derivati: diidrocapsicina, nordiidrocapsicina,omocapsicina) inodori ed insapori, quasi insolubili in acqua e molto solubili nei grassi.
      Questo gruppo di sostanze stimola selettivamente i recettori dolorifici della lingua e delle mucose e produce vasodilatazione dei capillari superficiali. E’ curioso notare che questo effetto si manifesta esclusivamente nei mammiferi e non, ad esempio, negli uccelli.
      Nel 1912 il chimico statunitense Wilbur Scoville sviluppò un metodo per misurare il grado di piccantezza dei peperoncini (da allora definito "Test Organolettico di Scoville"), basato sulla diluizione in acqua zuccherata di un omogeneizzato ricavato dal peperoncino in esame.
      La misurazione del livello di piccante viene espressa in SU (Scoville Units) che indicano il rapporto di diluizione necessario a rendere impercettibile al gusto la sensazione piccante.
      In base ai risultati del test è stato attribuito, in linea di massima, ad ogni peperoncino un livello di piccantezza:
      • 0-150 SU: peperoni o peperoncini dolci;
      • 150-1.000 SU: peperoncini “New Mexico”;
      • 1.000-2.000 SU: peperoncini “Ancho” o Pasilla”;
      • 2.000-2.500 SU: peperoncini “Aji cristal”, Cascabel
      • 2.500-5.000 SU: peperoncini “Jalapeno”;
      • 5.000-15.000 SU: peperoncini “Serrano”;
      • 15.000-50.000 SU: peperoncini “De Arbol”, “Cayenna”, “Tabasco”;
      • 50.000-100.000 SU: peperoncini Chiltepin”, Pili-Pili”;
      • 100.000-300.000 SU: peperoncini “Scotch bonnet”, “Thai Cayenna”;
      • 350.000 SU: peperoncino “Habanero Red Savin”;
      • 14.000.000 SU: la capsicina pura sotto forma di oleoresina.
      Per fare un esempio 1 cc di “Habanero” ridotto in pasta dà ancora una sensazione piccante dopo essere stato diluito in 300.000 cc di acqua.
      Questa scala è abbastanza approssimativa in quanto dipende in larga misura dalla sensibilità dell’assaggiatore, ma serve a dare un’ idea generale di cosa ci si può aspettare da un particolare peperoncino, anche in base alle sue prospettive di utilizzo.
      La grande variabilità delle Unità Scoville di uno stesso tipo di peperoncino dipende anche da svariati fattori colturali e ambientali: temperatura, umidità, caratteristiche del terreno o momento di raccolta dei frutti influenzano moltissimo la piccantezza.

      I peperoncini e la cucina
      Il peperoncino in cucina svolge due funzioni importantissime che possono essere espletate separatamente o no: conferire al cibo il "piccante" che ne esalta le caratteristiche senza modificarne il gusto oppure conferire al cibo un "sapore" o un "profumo" che si integra con la preparazione modificandola nel risultato. Nei paesi d’origine ed in particolare in Messico l’uso dei peperoncini è assai articolato ed in quasi tutte le ricette vengono indicate specifiche varietà di peperoncino (“Aji panc”, “Serrano”, “Tabasco”, “Habanero”, “Perù giallo”, “Datil”, “Ancho”, “Morita”) che si armonizzano per gusto, aroma o piccantezza con le varie ricette.
      Questa abitudine alimentare, che risale all’epoca pre-colombiana, è stata assorbita dai colonizzatori spagnoli giunti successivamente, ma purtroppo non è stata trasferita alla cultura gastronomica europea o mediterranea. Per motivi legati probabilmente alla facilità di coltivazione e di conservazione, o per ragioni climatiche,in Europa e nei paesi mediterranei si coltivano quasi esclusivamente peperoncini Capsicum annuum e sporadicamente Capsicum baccatum, caratterizzati da notevole piccantezza, ma dall’assenza quasi totale di gusto proprio ( varietà di “Caienna” o “Serran” ).
      In alcuni paesi (Spagna, Ungheria, Bulgaria ) si utilizzano varietà di Capsicum annuum mediamente piccanti ma con uno spiccato profumo di peperone rosso ( Paprika forte, pimenton ).
      Anche in India e nei paesi dell’estremo oriente, nonostante il clima favorevole, si è diffuso prevalentemente iCapsicum annuum in numerose varietà a frutto conico allungato, più o meno sottile e più o meno piccante, spesso utilizzato verde, cioè a maturazione incompleta.
      Nella parte equatoriale dell’Africa si utilizzano varietà di Capsicum chinensis simili ad “Habanero” ma dai frutti più grandi e soprattutto assai meno profumati.

      Specie e varietà di peperoncino
      Cè una grossa confusione nella denominazione delle specie e delle varietà del genere Capsicum. Questo perchè esistono più di 200.000 varietà diverse di peperoncino. Queste varietà sono accomunate da alcune caratteristiche e vengono catalogate in specie. Esiste un discreto numero di specie di peperoncino al mondo, ma queste possono essere suddiviste in poche principali, come già detto:
      • Capsicum annuum;
      • Capsicum frutescens;
      • Capsicum chinense;
      • Capsicum baccatum;
      • Capsicum pubescens.
      Il primo Europeo che scoprì i peperoncini piccanti fu Cristoforo Colombo, intorno al 1493. Tutte le specie di peperoncino infatti sono native del nuovo mondo. Qui quasi tutte le specie possono vivere anche per più di 10 anni, ma può essere coltivata in quasi tutto il mondo, in alcuni casi come pianta annuale.

      Capsicum annuum
      Il nome è stato dato da coltivatori di regioni settentrionali, per indicare che questa pianta è annuale. In alcuni casi può essere fatta vivere più a lungo, sopratutto in ambienti con un clima mite.
      Numerosissimi sono le varietà e gli ibridi coltivati e di cui si è già parlato prima.

      Capsicum frutescens
      Alcuni pensano che questa specie, nella sua forma primitiva, sia l’antenato del Capsicum chinense. Sono piante generalmente perenni. Le varietà più famose di questa specie sono”Tabasco” e “Malagueta”.

      Capsicum chinense
      Anche se il nome indurrebbe a pensare che provenga dalla Cina, non è così. Come tutte le specie di Capsicum proviene dal nuovo mondo. I frutti di questa specie possono variare di molto come dimensioni. Molto spesso i frutti di Capsicum chinense sono fortemente piccanti e profumati e hanno una piccantezza persistente. Le varietà più note di questa specie sono”Habanero” e “Scotch Bonnet”.

      Capsicum baccatum
      E’ una specie proveniente dal Sud America, caratterizzata da fiori colorati. La specie più nota è il famoso “Aji”.

      Capsicum pubescens
      Il fattore che più contraddistingue questa specie è il colore dei semi, che diversamente da tutti gli altri Capsicum sono marroni o neri. Questa specie non può essere impollinata con altre specie di Capsicum. Le specie più note sono il “Rocoto” e il “Manzano”.

      Varietà di peperoncino piccante
      • Habanero Dolce (Capsicum chinense). Matura dal verde al rosso-arancio ed ha le stesse caratteristiche del cugino piccante per quanto riguarda profumo, forma e dimensioni. Originario del Venezuela è chiamato “Aji Dulce”.
      • Paprika (Capsicum annuum). Frutto conico lungo 6-7 cm largo alla base 4 cm., matura dal giallo-verde al rosso, ha buccia sottile, polpa spessa, con profumo erbaceo e di peperone. Esistono varietà dolci e piccanti. Coltivato in Europa centrale.
      • Cayenna Turco (Capsicum annuum) Frutto conico lungo circa 15 cm, diametro circa 2-3 cm, incurvato. Matura dal verde al rosso acceso o al giallo. Buccia e polpa sottili, ottimo da essiccare. Nessun profumo, vago sentore di peperone.
      • Cayenna Indiani tipo Achar (Capsicum annuum).Frutti conici lunghi circa 8 cm, leggermente incurvati. Matura da verde a rosso intenso. Buccia sottile, polpa abbastanza spessa, profumata di peperone. Poco piccante. Usato in salamoia o sottaceto.
      • Cayenna Indiani tipo Assam (Capsicum annuum) Come sopra ma piccantissimi. Si utilizzano spesso a maturazione incompleta.
      • Poblano (Capsicum annuum). Moltissime varietà. Tutte a forma conica di lunghezza massima 18-20 cm, diametro alla base 7 cm, ce ne sono altre più piccole. Maturano dal verde al rosso, all’arancio o al marrone. Buccia sottile, polpa di spessore medio. Poco piccante. Profumo di peperone con sfumature di cuoio da fresco. Da essicato si chiama ANCHO ed ha netto profumo di cuoio e tabacco. Usato ripieno cotto al forno (chile relleno) o essicato in preparazioni messicane (è un ingrediente delle salse ‘Mole’).
      • Cappello turco (Capsicum chinense). Frutto conico abbastanza tozzo (a ‘trottola’) a superfice irregolare. Lunghezza max circa 7-8 cm diametro max circa 3 cm. Matura dal verde pallido all’arancione brillante. Buccia sottilissima, polpa di medio spessore, molto consistente. Spiccato profumo analogo all’habanero. Usato in Piemonte conservato sott’olio dopo farcitura con acciughe e capperi (ricetta Guazzotti a richiesta).
      • Carota Bulgara (Capsicum annuum). Frutto conico lungo circa 8 cm, diametro circa 3 cm. Matura velocemente dal verde pallido all’arancione. Buccia sottile, polpa di medio spessore. Molto piccante. Sentore di peperone. Utilizzato per salse piccanti fresche o conservato sottaceto.
      • Anahaim (Capsicum annuum).Frutto conico tozzo, lunghezza circa 15 cm, diametro circa 4 cm. Matura dal verde al rosso pallido. Buccia sottile, polpa spessa. Profumo di peperone. Poco piccante. Molto coltivato in Nuovo Messico. Ottimo per l’essicazione. Viene anche usato fresco(ripieno o arrostito) o conservato in salamoia o sottaceto.
      • Jalapeno (Capsicum annuum) ha forma di cono abbastanza tozzo, ad apice arrotondato con caratteristiche screpolature della buccia. Non molto piccante. Matura dal verde scuro al rosso acceso. Dimensioni variabili, mediamente diametro circa 3 cm, lunghezza circa 7-10 cm. Polpa abbastanza spessa e soda. Da fresco ha intenso profumo di peperone con sfumature di erba e cuoio. E’ forse il peperoncino più diffuso nella cucina messicana e texana. Si utilizza fresco nelle Salsas messicane o nei vari ‘chili con carne’ oppure conservato in salamoia o sottaceto. Negli Stati Uniti si utilizza per insaporire i pomodori in scatola (ad es. quelli della marca Ro-Tel). In Messico viene sottoposto ad un lungo procedimento di essicazione-affumicatura – che viene fatto risalire alle civiltà precolombiane- dando origine al ‘Chipotle’ dall’inconfondibile e penetrante aroma affumicato. I “Chipotle” servono per la preparazione di marinate (ricetta a richiesta) per arrosti o carni alla griglia ma sono impossibili da trovare in Italia.
      • Serrano (Capsicum annuum) Frutto conico a punta smussa, leggermente incurvato, mediamente piccante. Dimensioni circa 2,5 cm di diametro, 6-8 cm di lunghezza. Matura dal verde al rosso. Ha buccia non molto sottile e polpa morbida. Usato fresco in varie salse messicane e nel ‘mole’.
      • Peruviano Giallo (Capsicum baccatum) frutto a sezione piramidale a 3 o, raramente, 4 spigoli smussati e punta arrotondata. Molto piccante. Dimensioni circa 1,5 cm di diametro, circa 7-8 cm di lunghezza. Matura dal verde pallido al giallo tenue. Ha buccia sottile e polpa spessa e soda. Ha un caratteristico profumo di limone con sottofondo di peperone e resina. E’ ottimo nella preparazione di salse alla frutta per il pesce.
      • Cappello del Vescovo o Bishop Crown (Capsicum baccatum) frutto dalla caratteristica forma a campana con 3 protuberanze laterali situate in prossimità dell’apice (in Piemonte è chiamato anche ‘disco volante’), poco piccante. Dimensioni circa 6-8 cm di diametro, circa 5-7 cm di lunghezza. Matura passando dal verde all’arancio e poi al rosso. Buccia sottile, polpa non molto spessa ma soda. Profumo di peperone. La pianta forma un grosso cespuglio e può arrivare a produrre 10 Kg di peperoncini in una stagione. Io lo utilizzo fresco ( alla ‘pizzaiola’ : dopo averlo svuotato dei semi viene riempito con passata di pomodoro, origano, sale, un cubetto di mozzarella ed un filo d’olio e cotto al forno per 15-20 minuti a 180 °C), oppure conservato sott’olio farcito con acciughe e capperi (dopo essere stato pulito dei semi e sbollentato in aceto speziato).
      • Rocoto (Capsicum pubescens) il frutto è rotondeggiante ed assomiglia ad una mela del diametro di circa 5-6 cm , da cui il nome “chile manzano” con cui è conosciuto in Messico. E’ il peperoncino più comune delle regioni andine. È caratterizzato da fiori viola e da semi neri. Matura dal verde al rosso o al giallo. Ha buccia sottile e polpa spessa e soda dal netto profumo di peperone con sottofondo di zucchero di canna. E’ estremamente piccante ( in particolare la varietà gialla) ma è delizioso. Nei paesi d’origine viene consumato fresco nelle “salsas” oppure ripieno di carne o formaggio e cotto al forno. Non si presta ad essere essicato per l’eccessivo spessore della polpa. Si possono utilizzare come i “Bishop Crown” (alla pizzaiola o sott’olio), ma bisogna essere molto abituati al piccante.
      • Tabasco (Capsicum frutescens) frutto conico del diametro di circa 8-10 mm della lunghezza di circa 3-4 cm. Matura dal verde pallido al rosso oppure al giallo. Discretamente piccante. Si può essiccare facilmente. Ha profumo di peperone verde con una sfumatura aromatica indefinibile (buccia di limone). E’ conosciuto in Europa per l’omonima salsa. In Messico viene utilizzato prevalentemente secco ed ogni commensale sbriciola direttamente nel piatto la quantità di peperoncino che desidera.
      • Pasilla- Chilaca (Capsicum annuum) grandi frutti conici lunghi fino a 25 cm. Nella maturazione passa dal verde chiaro al verde scuro al marrone scuro. Ha buccia sottile rugosa e polpa non molto spessa, soda. Ha profumo di peperone e cuoio, simile al poblano, ma più intenso. Viene utilizzato fresco ( e allora viene detto Chilaca) o essicato nella preparazione di ‘salsas’ o mole.
      • Pomodorino (Capsicum baccatum) frutti di forma rotondeggiante appiattita con costolature esterne. Dimensioni: diametro circa 3-4 cm, lunghezza circa 1,5-2,5 cm. Matura dal verde scuro al rosso brillante. Buccia molto sottile, polpa spessa e croccante. Profumo di peperone maturo con sfumature erbacee. Poco piccante. Facile da coltivare ed assai produttivo. Utilizzabile come il Bishop Crown.
      Seguono alcune varietà ed ibridi coltivati di peperoncino piccante:
      • Peperoncino ibrido F1 “Coccinella” (figura 22): questa nuova varietà ha la duplice attitudine per colture in vaso ed in pieno campo. Pianta relativamente compatta di medio sviluppo, con fogliame coprente. I frutti sono a forma di ciliegia, uniformi, del diametro di circa 3 cm, di colore verde scuro e rosso vivo alla maturazione, al palato sono piccanti.
      • Peperoncino ciliegia piccante “Bacio di satana” (figura 23): peperoncino piccante con frutti a forma di trottola, simili a ciliege, alla maturazione sono di colore rosso scarlatto, sono lisci e la polpa è relativamente spessa; messi ad essiccare e ridotti in polvere costituiscono una grossa risorsa, in cucina, nella preparazione di cibi particolarmente piccanti. I frutti possono anche essere utilizzati allo stato fresco come nella famosa “peperonata” di tipo dolce piccante e nelle insalate miste. Il ciclo colturale è di tipo medio come di tipo medio è pure lo sviluppo vegetativo della pianta.
      • Peperoncino “Adorno” (figura 24): varietà di peperoncino piccante della specie Capsicum frutescens, con pianta compatta, con foglie color verde violaceo, idonea per colture sia in vaso sia per bordure. La produzione di frutti assai piccanti, conici, lunghi cm 1-1,5 è alquanto elevata. I peperoncini sono di colore verde, viola scuro, rosso alla maturazione. Di bella presentazione, questa varietà è anche valido ornamento nei giardini come macchia di colore.
      • Peperoncino “Fuoco della prateria” (figura 25): varietà di peperoncino piccante appartenente alla specie Capsicum chinense con pianta molto compatta dalle foglie piccole adatta per colture in vaso e per bordure. Produce un numero elevato di piccoli frutti conici, a portamento eretto, lunghi cm 2-3, di colore variabile dal verde al giallo, all’ arancio, al rosso, al viola a seconda dello stadio di maturazione. I peperoncini sono molto piccanti tanto che raggiungono le 95.000 unità Scoville.
      • Peperoncino ”abanero-orange” (figura 26): peperoncino piccante appartenente alla specie Capsicum chinense pianta vigorosa, tardiva che produce frutti a forma di lanterna, larghi cm 2,5 e lunghi cm 5 di colore verde chiaro all’ inizio e arancio salmone alla maturazione. è in assoluto una delle varietà di peperoncino più piccante al mondo.
      • Peperoncino ”Abanero red caribbean” (figura 27): peperoncino piccante appartenente alla specie Capsicum chinense pianta vigorosa, tardiva che produce frutti a forma di lanterna, larghi cm. 2,5 e lunghi cm. 5 di colore rosso vivo alla maturazione, molto piccante.
      • Peperoncino ”Piccante di Caienna” (figura 28): Peperoncino piccante lungo circa cm 11-13, sottile, forte, abbastanza piccante. Si usa essiccato in vari condimenti e nei classici spaghetti all'aglio, olio e peperoncino.
      • Peperoncino piccante “Fuoco giallo” (figura 29): Peperoncino piccante con frutto lungo cm 14-15, a maturazione di color giallo arancio, particolarmente carnoso, quindi con polpa di buon spessore, saporita, gustosa ed assai piccante. La pianta si presenta di buon sviluppo con abbondante produzione; questa varietà, poi, offre una certa resistenza alle varie patologie fungine alle quali, di solito la specie è frequentemente soggetta. Si raccomanda a tutti coloro che amano la piccantezza del peperoncino.
      • Peperoncino piccante”Jaladuro” (figura 30): varietà creata per il mercato dell’industria conserviera viene utilizzata, in maniera altrettanto ottimale, anche per il mercato fresco. La produzione è così straordinariamente abbondante da rimanere alquanto impressionati alla vista di tanti frutti. La pianta ha un portamento relativamente compatto; il ciclo è di tipo medio offrendo una buona resistenza al CMV e TMV. Tutte queste caratteristiche fanno sì che sia considerato un vero campione fra tutti i peperoncini ibridi.


      Figura 22 - Peperoncino ibrido F1 “Coccinella”.

      Figura 23 - Peperoncino ciliegia piccante “Bacio di satana”.

      Figura 24 - Peperoncino “Adorno”.

      Figura 25 - Peperoncino “Fuoco della prateria”.

      Figura 26 - Peperoncino ”abanero-orange”.

      Figura 27 - Peperoncino ”Abanero red caribbean”.

      Figura 28 - Peperoncino ”Piccante di Caienna”.

      Figura 29 - Peperoncino piccante “Fuoco giallo”.

      Figura 30 - Peperoncino piccante”Jaladuro”.



      Semina del peperoncino piccante
      Il peperoncino può essere coltivato con successo in tutta Italia (e in buona parte del mondo) con qualche piccola accortezza relativa al clima tipico della zona uin cui vivi. Per quanto riguarda l’italia, può essere seminato in casa nei mesi di Gennaio/Febbraio nel sud Italia, mentre è consigliabile aspettare Marzo nell’Italia settentrionale. In generale è consigliato seminare un mese e mezzo prima dell’ultima gelata prevista, per travasare la piantina dopo circa due mesi e portarla gradualmente all’esterno.

      Germinazione
      La germinazione del peperoncino avviene facilmente, con tempi variabili in base alla specie e alla varietà della pianta. Per far germinare un seme è sufficente metterlo in terra, in vaso o in semenzaio, inizialmente non sotto il sole diretto, e innaffiare di tanto in tanto.
      E’ richiesta una temperatura almeno superiore ai 15 °C perchè la germinazione avvenga, ma la temperatura di 20 °C rappresenta un valore ottimale. Come terreno una torba abbastanza fine sarebbe l’ideale, ma a un terriccio standard può svolgere il suo compito.
      Se si dispone della vermiculite (fine) , mettetene uno strato sopra la torba dopo aver seminato, e innaffiate. E’ un accorgimento utile per evitare che la torba diventi idrofoba (non assorbe più l’acqua ma la lascia scorrere). La vermiculite comunque non è indispensabile.
      Un altro metodo, che permette al seme di germinare un poco più velocemente, consiste nell’utilizzare un po’ di cotone bagnato e mettervi sopra il seme. Questa pratica però è leggermente più scomoda perché dopo che il seme è germinato deve essere messo a dimora nella torba, in un vasetto o in semenzaio, e nel farlo si rischia di rovinare irreparabilmente la neo piantina.
      Dopo la germinazione è consigliabile la maggior luce possibile, quindi mettete il semenzaio il più vicino possibile alla finestra o a una fonte di luce. Questo permetterà alle piantine di non crescere troppo in altezza nelle prime fasi per cercare la luce, cosa che porterà alla morte della pianta non appena sarà esposta alla luce solare.
      Durante i primi due mesi di vita la pianta di peperoncino deve stare in ambiente protetto (sempre che non abbiate seminato molto tardi, in questo caso se il tempo lo permette potete tenerlo all’aperto). E’ consigliabile tenere le piantine appena nate alla luce, vicino a una finestra o in una zona luminosa. Questo permetterà alle piantine di non crescere troppo in altezza nelle prime fasi per cercare la luce perchè in questo modo lo stelo si indebolisce e risulta sottilissimo, cosa che purtroppo porterà alla morte della pianta se portata sotto la luce troppo tardi. E’ consigliato concimare anche dopo qualche settimana dalla nascita delle pianta, ma in dose ridotte e senza mai esagerare. Un eventuale ingiallimento delle foglie può essere un sintomo di scarsa concimazione, ma è molto piu facile uccidere la pianta per un eccessivo zelo nel versare concime.

      Conservazione del peperoncino piccante
      Quando si maneggiano i peperoncini per almeno 1 giorno bisogna lavarsi spesso le mani e non toccarsi gli occhi (oppure lavorare con i guanti) Nella conservazione dei peperoncini conviene seguire le seguenti fasi:
      • tagliare i peperoncini a metà per il lungo e disponetene uno strato su un piatto piano con i semi verso l’alto;
      • cospargere con una buona presa di sale fino;
      • disporre un nuovo strato di peperoncini sezionati ad angolo retto rispetto ai precedenti, quindi cospargere anche questi di sale; continuare fino ad esaurimento, quindi coprite con un altro piatto e porre sopra un peso di almeno 3-4 Kg.
      • dopo 2-3 ore sgocciolare, capovolgere il tutto, rimettere il peso e lasciate ancora un paio d’ore.
      Trascorso questo tempo sgocciolare nuovamente e con uno spazzolino togliere l’eventuale eccesso di sale dai peperoncini, asciugarli il più possibile con un tovagliolo, facendo attenzione a non perdere i semi e metteteli sott’olio (extra vergine).
      Il sale priva i peperoncini dell’acqua lasciando inalterato tutto il loro sapore; dopo 15-20 giorni si avranno, oltre all’olio meravigliosamente aromatizzato, i peperoncini addirittura più saporiti di quando erano freschi.
      -Si possono conservare sott’olio come i precedenti facendoli essiccare in modo che rimangano un po’ morbidi. Purtroppo l’essicazione toglie gran parte del sapore ma se a forza di aspettare a mettere via i peperoncini nel frattempo si sono essiccati rimane uno dei metodi migliori.

      Peperoncini sotto aceto
      Lavare ed asciugare i peperoncini freschi, poi bisogna stiparli in un vaso con tappo ermetico (di quelli usati per conservare frutta, funghi marmellata) colmare con aceto non troppo forte ed una discreta quantità di sale, avvitare il tappo, mettere a bagnomaria e far bollire per 5-6 minuti togliendo dall’acqua quando è quasi fredda. La sterilizzazione si può evitare ma dopo qualche settimana i peperoncini si rammoliscono notevolmente (la cosa avviene anche a quelli sterilizzati una volta aperti, quindi evitare i vasi troppo grandi). Anche questi sono ottimi in mezzo al pane, sono fantastici con il lesso, nelle salse ed ovunque l’odore dell’aceto non infastidisca.

      Preparazione del Tabasco
      Calcolare per ogni chilo di peperoncini mezzo litro di aceto ed un buon cucchiaio di sale o anche più se piace. Dopo aver lavato i peperoncini togliere i gambi, spezzettarli, metterli nel frullatore con il sale, metà dell’aceto e frullate per 5-10 minuti, eventualmente in più riprese per non fondere il motore, in modo che anche i semi risultino completamente frantumati, aggiungere il resto dell’aceto e frullare per un paio di minuti, lasciare riposare per 2-3 giorni mescolando di tanto in tanto e ritornare a frullare il tutto per poi passare al setaccio.
      Il tabasco e’ comodissimo in quanto si amalgama immediatamente ai piatti a cui viene aggiunto, se si usano peperoncini molto piccanti ed aceto non troppo forte si avrà il sapore del peperone quasi intatto. E’ migliore se consumato dopo almeno un paio di settimane.

      Genetic of the Pepper
      Following, we report a very interesting research, published on Plos one, February 08, 2013, carried out by
      • Theresa A. Hill, Seed Biotechnology Center, University of California Davis, Davis, California, United States of America, Department of Plant Sciences, University of California Davis, Davis, California, United States of America.
      • Hamid Ashrafi, Seed Biotechnology Center, University of California Davis, Davis, California, United States of America, Department of Plant Sciences, University of California Davis, Davis, California, United States of America.
      • Sebastian Reyes-Chin-Wo, Seed Biotechnology Center, University of California Davis, Davis, California, United States of America, Genome Center, University of California Davis, Davis, California, United States of America.
      • JiQiang Yao, Seed Biotechnology Center, University of California Davis, Davis, California, United States of America. Current address: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America.
      • Kevin Stoffel, Affiliations: Seed Biotechnology Center, University of California Davis, Davis, California, United States of America, Department of Plant Sciences, University of California Davis, Davis, California, United States of America.
      • Maria-Jose Truco, Affiliation: Genome Center, University of California Davis, Davis, California, United States of America.
      • Alexander Kozik, Genome Center, University of California Davis, Davis, California, United States of America.
      • Richard W. Michelmore, Genome Center, University of California Davis, Davis, California, United States of America, Department of Plant Sciences, University of California Davis, Davis, California, United States of America.
      • Allen Van Deynze, Seed Biotechnology Center, University of California Davis, Davis, California, United States of America, Department of Plant Sciences, University of California Davis, Davis, California, United States of America.
      Thank you all for allowing me to enrich, spraying the results of their researches, this webpage regarding the pepper.

      Peppers, Capsicum spp, are grown worldwide for vegetable, spice, ornamental, medicinal and lachrymator uses and are a significant source of vitamins A and C. Peppers have been found along with other food fossils from as early as 6,000 years ago and are considered the first spice to have been used by humans. The genus Capsicum lays within the Solanoideae sub-family of the Solanacea family and is believed to have its ancestral origins in the tropical South American region centered in what is now. Currently, 38 species of Capsicum are reported. Of these, five (Capsicum annuum, Capsicum frutescens, Capsicum chinense, Capsicum. pubescens, and Capsicum baccatum) are thought to have been domesticated through at least five independent. These domesticates are believed to be derived from three distinct genetic lineages, with Capsicum pubescens and Capsicum baccatum each representing independent lineages while the domesticated taxa Capsicum annuum, Capsicum frutescens and Capsicum chinense are considered members of a species complex that were each independently derived from wild progenitors that may or may not be independent species. This is supported by the ability to make interspecific hybrids between these three Capsicum species. The most commonly cultivated species worldwide, Capsicum annuum, was domesticated in Mexico from the wild bird pepper. Its predominance among cultivated species globally has been attributed to it being the first Capsicum introduced to Europe, by Columbus and other early new world explorers, rather than superior agronomic or consumer traits. Capsicum annuum has subsequently become one of the most important spice commodities as well as an important vegetable crop globally.
      The wild progenitor of cultivated Capsicum annuum has erect, small fruit (about 1 cm in length) that are pungent, red colored, deciduous and soft-fleshed. These traits promote consumption and seed dispersal by birds rather than mammals as birds do not have receptors for capsaicin, the source of pungency. Through domestication and subsequent commercialization several domestication-related traits have been selected for, including compact architecture, increased efficiency of self-pollination and fruit set, early flowering and non-deciduous, pendant fruits. The diversity of uses for peppers has led to the development of individual Capsicum annuum lines that have been selected for specific sets of consumer-driven fruit traits such as degree of pungency, flavor, color, shape, fruit wall thickness and drying ability. It has been proposed that, in general, continued selection during domestication has led to lines with larger, non-pungent fruit with greater shape variation and tremendous increases in fruit mass. These large-fruited non-pungent Bell or blocky type peppers were found in pre-Columbian Mexico and were first described approximately 500 years ago. The putative acyletransferase AT3, encoded by Pun1, is the primary determinant of pungency and non-pungent Capsicum annuum share a common deletion in Pun1.
      Even though the pungent pepper lines are considered the most important spice crop worldwide the large, non-pungent Bell peppers, also consumed worldwide, are the most economically important pepper type.
      Breeding programs for crop improvement are enabled by the availability and detailed characterization of genetically diverse germplasm. A limited horticultural classification of pepper types with 7 main catagories and a total of 13 groups by fruit type, was developed to distinguish commercially significant varieties by Smith in 1987.
      This scheme is still relevant today as the only major change has been the division of the Small hot group into multiple categories by Bosland. Standardized definitions of Capsicum descriptors were developed by the International Plant Genetic Resources Institute (IPGRI) and the United States Department of Agriculture, Germplasm Resources Information Network (GRIN).
      The IPGRI descriptors include 79 phenotypic traits divided into 25 vegetative, 16 inflorescence, 22 fruit, 6 seed and 10 yield and quality characters. However, the IPGRI descriptor for overall fruit shape is broadly defined by only 6 categories:
      1. Elongate,
      2. Almost round,
      3. Triangular,
      4. Campanulate,
      5. Blocky and
      6. Other.

      The USDA GRIN evaluation of peppers includes 55 descriptors including 5 growth, 38 morphology, 1 phenology, 3 chemical and 8 production traits. The 7 GRIN fruit shape descriptors:
      1. Elongate,
      2. Oblate,
      3. Round,
      4. Conic,
      5. Campanulate,
      6. Bell and
      7. Mixed
      are similar to those of IPGRI.
      GRIN includes as an additional trait 13 commercial categories that differ considerably from Smith's original groupings. Substantial Capsicum germplasm collections are held in several countries with over 53,000 total accessions held worldwide reported by the UN-FAO. Some gene bank accessions have been characterized phenotypically with subsets of the IPGRI or GRIN descriptors. The challenge in developing a practical phenotypic classification scheme underscores the added value of molecular characterization for understanding diversity. The diploid Capsicum genome consists of n = 12 chromosomes with an estimated haploid genome size of 3.3–3.6 Gb. Molecular studies assessing the overall diversity of Capsicum annuum breeding germplasm have been carried out using tens to a small number (<200) of low throughput, mostly anonymous markers such as RFLPs, AFLPs and SSRs.
      Genome-wide molecular characterization of available germplasm enables
      • identification of novel alleles and subsequent introgression via molecular breeding;
      • differentiation of cultivars and classifying inbred lines into heterotic groups;
      • development of core collections by identifying gaps and redundancy in germplasm collections;
      • and monitoring genetic shifts that have occurred during domestication, breeding, regeneration and germplasm conservation.
      With recent advances in sequencing technologies, cost-effective means for developing genome-wide functional markers have become available. Single nucleotide polymorphisms (SNPs) have become the marker of choice due to their abundance and uniform distribution throughout the genome. Characterization of genomes and populations via the application of high-throughput SNP marker technologies have broadened the possibilities for breeding strategies from simply inherited trait integration using marker assisted selection (MAS) to genome-wide association studies (GWAS) and multi-locus trait integration using genomic selection (GS). These advances are expected to improve breeding strategies for complex traits such as the improvement of crop yield and resistance to biotic and abiotic stress.
      A requirement for GWAS and GS-directed breeding strategies is the determination of genetic relatedness, the presence of population structure and linkage disequilibrium. The widely used methods for determining population structure, the Bayesian cluster estimation of population structure and LD implemented in the program Structure and principle components analysis (PCA), each analyze single mutations individually. Although it has been suggested that the accuracy of these methods may be compromised when analyzing large numbers of genome-wide markers in which there will inevitably be linkage, the addition of the admixture and linkage models to the Structure package have been useful for resolving complex populations and large datasets with linked markers.
      Recent studies in tomato and potato have shown that these methods are complementary and biologically informative DNA microarrays, initially used for expression analysis, have been used widely for both marker discovery and assays for known SNP polymorphisms.
      Microarrays designed specifically for polymorphism detection have short, 25-nucleotide, probes (also known as features or oligos) and are able to detect sequence polymorphisms, termed single feature polymorphisms or single position polymorphisms (SFPs or SPPs), with good specificity.
      Recently, this technology has been refined for use in the more complex genome of lettuce (Lactuca sativa) where a comprehensive analysis of lettuce diversity was defined across 5 species.
      To more thoroughly understand Capsicum annuum genomic diversity and improve breeding resources, a high-throughput marker discovery platform was designed for Capsicum (Stoffel K et al.,2012). A large collection of EST sequences (Kim HJ et al.,2008), Capsicum GenBank sequences and conserved orthologous sequences (Wu FN et al.,2006; VanDeynze A et al., 2007) were assembled into 30,815 unigenes that were used to design the Pepper GeneChip. In this paper we describe simultaneous detection of polymorphism in DNA using the Pepper GeneChip from a diversity panel of 43 pepper lines including 40 Capsicum annuum lines and one line each of Capsicum frutescens, Capsicum chinense and Capsicum pubescens. With this approach, over 30,000 robust markers were identified among the diversity panel including highly informative markers within both the 21 pungent and 19 non-pungent capsicum annuum lines. The dataset provided sufficient markers for assessing differences in allele frequencies around the Pun1 locus between pungent and non-pungent lines. We also report the first high density genome-wide analysis of molecular diversity among capsicum annuum lines using gene based markers which identified genetic classes that were clearly and consistently defined.

      Methods
      Pepper GeneChip design. As described by Stoffel et al., 2012, an array design which utilizes an Affymetrix GeneChip array format 49 with a 5 µm feature size and a maximum capacity ~6.5 M features of 25 nt was used. Sequences submitted to Affymetrix for probe design included 31,196 unigenes consisting of 30,500 pepper unigenes assembled from EST sequences, 54 pepper promoter sequences and 642 COSII genes, which will be referred to here as the Pepper Chip assembly (Figure S1 dataset s1). Features were subdivided as follows:
      • 6,473,556 genomic tiling probes,
      • 24,336 control probes including 16,900 Capsicum probes in 13×13 blocks and B2 Affymetrix control probes surrounding each control block,
      • 33,886 anti-genomic probes for detecting background hybridization.
      Anti-genomic (AG) probes represent probes selected by Affymetrix that do not match any sequence in GenBank (in 2006) with G/C content (the number of guanines and/or cytosines) ranging from 5 to 18 per 25 nt probe (Figure S2B).
      Probes were arranged to assay a 2 bp tiling path where possible. An Affymetrix quality score >0.25 and redundancy ≤3 were required, resulting in over 90% of probes having a G/C content between 7 and 14 (Figure S2A). Final probe reduction to 6,473,556 tiling probes was achieved by requiring unigenes to be covered by 10 or more probes and trimming 19.92% of probes for each unigene covered by 500 to 1000 probes, 8.96% from both the 5′ and 3' ends. A total of 30,815 unigenes were represented on the chip.

      Germplasm and DNA extraction. A set of 43 Capsicum lines representing four cultivated species (40 Capsicum annuum, 1 Capsicum frutescens, 1 Capsicum chinense, 1 Capsicum pubescens) were provided by:
      • I. Paran, The Volcani Center, Bet Dagan, Israel;
      • P. Bosland, New Mexico State University, Las Cruces, N.M., USA;
      • J. Prince, California State University Fresno, Fresno, CA, USA;
      • Molly Jahn, Cornell University, Ithaca, NY, USA;
      • Deruiter Seeds, Enza Zaden;
      • Monsanto;
      • Nunhems;
      • Rijk Zwaan;
      • Syngenta and Vilmorin.
      Seeds were germinated in a glasshouse under standard conditions for Capsicum. DNA was extracted from 2.0 grams of developing leaves, up to 3.0 cm in length. Leaves were collected from 2 to 6 individuals for each line, flash frozen in liquid nitrogen and stored at −80 °C. A modified CTAB procedure was used for genomic DNA extraction. Genomic DNA was quantified by agarose gel electrophoresis with a lambda DNA standard.

      Chip hybridization. For each hybridization, 30 ug total genomic DNA was fragmented to 50–250 bp and visualized by agarose gel electrophoresis. Following fragmentation, DNA was end-labeled and hybridized to the Pepper GeneChip as described. Three replicate hybridizations were carried out for each line. Hybridization levels were adjusted by correcting for background followed by quantile normalization across all chips. To test for consistency of replicate hybridizations, a cluster analysis was performed in R on normalized hybridization values across all chips using 5,431 probes covering known polymorphisms. Close clustering of all three replicate chips for each variety was required prior to SPP analysis Figure S3). The effect of G/C content on hybridization efficiency was determined Figure S2C). There was no difference in the percentage of probes above background between lines. Of tiling probes, 76% were hybridized at levels above background with probes having between 9 and 13 Gs and Cs having the best performance.

      SPP detection. Samples were analyzed based on SPPdev values using an algorithm designed for polymorphism detection across multiple genotypes simultaneously (RIL algorithm) as described by Stoffel et al., 2012. Probe hybridization values were weighted using an empirically-determined weighting factor for pepper based on sensitivity of bases within an oligo to the position of sequence polymorphisms Figure S2D). The SPPdev ratio is a measure of the hybridization difference between modes of a bimodal distribution of SPPdev values for a given position across all chips. For each polymorphic position, an allele call (A, B or –) was assigned for each chip. When there was a difference in the allele assignment between the 3 replicate chips of a given line, the summarized allele assignment was designated as inconsistent (I). Thus, the 3 replicates were summarized as A, B, C, D, I or “–” as follows:
      • A/A/A = A; B/B/B = B; B/B/– = C (not A);
      • A/A/– = D (not B);
      • –/–/– = “-“
      • and A/A/B, B/B/A, A/B/–, –/ – /A or –/ – /B = I.
      The pepper SPP detection software package and its manual can be downloaded at the following web address: https://pepper.ucdavis.edu/public/data.php.
      The RIL algorithm allows the stringency for calling SPPs to be increased by increasing minimum SPPdev ratio, and minimum number of probes above background (informative probes) required for SPP detection. The dataset can be further filtered by requirements for minimum number of bases spanned by an SPP, minimum and maximum allele frequencies allowed and maximum inconsistent (I) and missing (–) calls allowed across all genotypes. A schematic summarizing the collection and processing of data is presented in Figure S4.

      Validation. Using BWA and SAMtools a set of high quality SNPs, heterozygous positions, and InDels were identified in Illumina GA2 (IGA) transcriptome sequence assemblies derived from root, leaf, flower and several fruit tissues of Early Jalapeño, CM334 and Maor.
      Custom Perl scripts were used to identify false positive SPPs by comparison to the IGA assemblies and SPP markers mapped in two pepper mapping populations. A SPP was considered a true positive if SNPs were within 8 bp of the SPP ranges. An 8 bp range on either side of detected SPPs was chosen to account for detection of SPPs with the overlapping 25 nt oligo design and empirically determined sensitivity of oligos Figure S2D). SPPs that were not represented by IGA sequence were excluded from the validation as we were not able to verify if they were true or false SPPs. In order to determine the effect of adjusting detection stringency and filtering parameters on data quality, SPP detection rates and false discovery rates (FDR) were compared between resulting datasets Figure S5). Datasets generated at SPPdev ratio settings of 1.2, 1.5 and 2.0 are available in Datasets S3, S4 and S5 respectively.
      In order to determine if sequences surrounding an apparent SPP were present in multiple unigenes (multi-copy sequences), each SPP plus and minus 8 bases on either side of the SPP range was queried using BLASTn against two separate search sets of sequences: the pepper whole IGA assembly and the EST assembly that was used for the array design. To maintain confidence in the BLAST hits a minimum of 95% of the subject in the query with no more than two mismatches was required.

      Accuracy of calls. Since most of the sequences used for the Pepper Chip assembly were derived from a F1 hybrid pepper variety (Bukang), we were able to design and run SNP assays (Kbiosciences, Hoddesdon, UK) from our assembly for all lines. We determined the correlation between calls made by the SNP assay and SPPs spanning the SNP nucleotide for 27 polymorphisms across the 43 lines for a total of 1,161 allele calls.

      Analysis of Capsicum annuum diversity. The dataset used for diversity analysis was generated with minimums of SPPdev ratio 1.2, two informative probes and four bases spanned. With these parameters, 104,470 SPPs were identified within 23,724 unigenes. This dataset was filtered by removing SPPs within multi-copy sequences (homology to multiple assembled sequences). C and D calls were converted to B and A, respectively. Then requirements of minimum A or B allele frequency greater than or equal to 0.02 (1 of the 43 genotypes in the panel), zero inconsistent calls and no missing values were applied resulting in a final dataset of 33,401 SPPs/13,323 unigenes with an estimated SPP FDR of 6.8% (Figure S5E).
      A phylogeny of the Capsicum annuum lines was inferred using the PHYLIP 3.69 package. SPPs polymorphic among the 40 Capsicum annuum, the Capsicum frutescens and capsicum chinense lines (leaving out capsicum pubescens–specific SPPs) were selected. Unique SPP allele profiles (haplotypes) across the panel for each unigene were selected to reduce linked markers showing no recombination across the panel. The SPP markers were treated as restriction site markers, converted from A and B to 1 and 0. The seqboot module was used to create 7,500 re-sampled data sets for bootstrapping. The restdist package using the modified Nei and Li method was used to generate distance matrices for input into the Fitch module for tree building. The Fitch–Margoliash distance method with global rearrangement and randomized input order of species with 5 jumbles was used to generate each of 7,500 replicate trees. The consensus tree with bootstrap values was calculated and visualized using MEGA4 with Capsicum frutescens & Capsicum chinense used as the outgroup root.

      Population structure analysis. The Bayesian cluster estimation of population structure was carried out using the software Structure (Pritchard et al., 2000). SPPs polymorphic within the Capsicum annuum lines identified within unigenes that were also mapped in a Capsicum frutescens × Capsicum annuum (FA) RIL population were selected and map positions based on the FA map were assigned to each SPP. Among the resulting set of SPPs with associated map positions, unique allele profiles across Capsicum annuum lines for each genetic bin were selected to eliminate markers completely linked across the panel. Ten replicates were performed for each defined value of K number of clusters assumed from K = 1 to K = 10 using the linkage model and independent allele frequencies model. A constant value of lambda (allele frequencies parameter) was defined at K = 1 to be 0.5397 and this value was used for all subsequent runs at values of K = 2 to 10. Each run used an admixture burn-in period 35,000 iterations then 35,000 burn-in iterations followed by 30,000 Markov Chain Monte Carlo (MCMC) iterations. The replicate producing an output with the highest probability for each K value was selected.

      Principal component analysis. For principle component analysis, 6,426 SPP markers polymorphic among the 40 Capsicum annuum lines were used. These SPPs were found within 3,818 unigenes and converted to unigene haplotype frequencies using custom Perl scripts. Frequencies were calculated as the number of times the haplotype occurs in the panel divided by the total number of genotypes in the panel. Haplotype frequencies were used as input for principle component analysis using the SAS/STAT® software's PRINCOMP procedure (Version 9.1.3, SAS Institute, Cary, USA). Eigenvalues for each of the first three principal components were extracted for each genotype, visualized by 3-dimentional graphs and used to cluster lines using the Ward method. Each of the first three Eigenvalues were tested for separation of groups defined by either breeding class or Structure clusters using an analysis of variance (ANOVA) and pairwise Student's T-tests for means separation. Graphical and statistical analyses were performed using JMP (JMP, Version 7. SAS Institute InCapsicum, Cary, USA).

      Genetic diversity estimates. Genetic diversity (He) was estimated from the 6,426 Capsicum annuum polymorphic SPP markers using PowerMarker. He is defined as the probability that two randomly chosen alleles from a population are different.

      Results
      Affymetrix Pepper GeneChip design. A high-density pepper genotyping array was created based on the design of the Lettuce Affymetrix GeneChip. The pepper array includes 33,886 features for anti-genomic (AG) background probes and 6,473,556 features for genomic tiling probes. Probe selection resulted in 30,815 unigenes represented. Coverage ranged from 11 to 1,597 probes per unigene with 80% of the unigenes covered by 70 to 375 probes Figure S1B).

      SPP detection, false discovery and accuracy. Forty-three Capsicum lines were hybridized to the Affymetrix Pepper GeneChip for simultaneous polymorphism detection (Table 5). Large changes in the number of SPPs identified and a significant effect on FDR was observed with changing the parameters minimum SPPdev ratio, minimum bases spanned and inconsistent calls allowed. To determine accuracy of calls, allele calls between SPP and SNP assays were compared. A high correlation of allele calls was observed, with an exact match between the SNP and SPP assays for 95% of all alleles called and 99.9% of all unambiguous calls made by both assays. The SNP assay detected a heterozygosity rate of 3.5% across the 43 lines.

      Effect of copy number variation on SPP calls at the Pun1 locus.To investigate further the source of false positives, the potential effects of copy number variation and paralogs on SPP calling was examined. Pun1, formerly known as C, is the primary determinant of pungency in Capsicum and encodes the putative acyltransferase AT3 that is required for the synthesis of capsaicin. Pun1 corresponded to oligonucleotides derived from CAPS_CONTIG.2339 on the Pepper Chip. Capsicum annuum lines carrying the null pun11 allele, which has a deletion of the 5' coding region, are non-pungent. Lines were classified by the presence of the Pun1, pungent, versus pun11, non-pungent, alleles (Table 4). For a large deletion such as in pun11, there should be no informative probes for SPP detection in non-pungent lines. However, SPPs were detected across the deleted region, likely due to hybridization of paralogous acyl-transferases with shared sequence identity to CAPS_CONTIG.2339 probes (Figure 31). A pseudogene, AT3-2, present in Capsicum genomes is annotated in GeneBank and has 84% DNA sequence identity to a portion of the Pun1coding region. In addition, nine unigenes with significant identity to CAPS_CONTIG.2339 were identified in the Pepper Chip assembly. Two unigenes shared 100% identity with AT3-2 leaving 7 additional unigenes with significant similarity to Pun1 Figure 1). Sequences for Pun1, pun11, AT3-2 and Pepper Chip assembly putative acyltransferase unigenes were aligned with CAPS_CONTIG.2339 revealing common regions that were highly conserved (87–98% identity) or moderately conserved (75–85% identity) (Figure 31). Six SPPs were detected in the deleted region of pun11, of which five had allele calls specific to pungent (A, high hybridization) and non-pungent (B, low hybridization) lines. Five SPPs overlapped with regions less conserved between Pun1 and the putative acyltransferase unigenes. At the 3' end of the pun11 deletion, GenBank sequences indicate several SNPs between pungent lines. This region had lower conservation between acyltransferase unigenes and CAPS_CONTIG.2339. SPPs detected in this region had marker profiles among the pungent lines similar to profiles 3' of the pun11 deletion suggesting that these calls are accurate and there is an additional Pun1 allele with multiple 3' polymorphisms in four of the 21 pungent lines.

      Table 5 - Pepper lines.
      Classificationa Fruit Shapeb Name Pungencyc Unique
      SPP allelesd SPP allelese
      C. annuum var. annuum
      Bell













      Long Wax



      Other







      Cayenne
      Anaheim chili

      Jalapeňo

      Ancho
      Small hot







      C. chinense
      C. frutescens
      C. pubescens
      Total Unique SPPs

      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Blocky
      Triangular
      Triangular
      Triangular
      Triangular
      Triangular
      Triangular
      Other
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Triangular
      Triangular
      Elongate
      Elongate
      Triangular
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Elongate
      Almost Round
      Almost Round


      Yolo Wonder
      Rumba
      Violetta
      Bruinsma Wonder
      Maor
      Ariane
      Charleston Belle
      Jupiter
      King of the North
      Dempsey
      Infante
      Grande de Reus
      Grosso di Nocera
      Dolmalik
      Midal
      Sweet Banana
      Long Yellow Marconi
      Corno di Toro
      Doux des Landes
      Quadrato d’Asti
      Lange Westlandse Rode
      Sivri Biber
      Erjintiao
      Jeju
      Cheongsong
      Milyang
      Carolina Cayenne
      NuMex R Naky
      NuMex Joe E Parker
      Jalapeňo
      Early Jalapeňo
      Ancho 101
      CM 334
      PI 201234
      Charleston
      Perennial
      Pusa Jwala
      G-4
      PSP-11
      Thai Bird
      PI 159234
      2814-6
      Rocoto


      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      np
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p
      p


      0
      1
      2
      7
      9
      7
      1
      0
      3
      3
      17
      11
      3
      2
      30
      6
      46
      12
      19
      15
      69
      19
      121
      19
      76
      123
      115
      30
      15
      19
      13
      119
      205
      110
      21
      53
      121
      87
      53
      85
      4,960
      3,859
      13,643
      24,129

      0
      1
      2
      14
      10
      8
      2
      0
      3
      3
      20
      13
      3
      2
      44
      9
      58
      16
      29
      16
      87
      25
      162
      29
      111
      159
      210
      49
      19
      22
      23
      144
      330
      163
      33
      73
      170
      126
      69
      129



      2,386
      aClassification of Capsicum annuum lines assigned according to Smith.
      bFruit Shape of glasshouse grown fruit as defined by IPGRI, AVRDC and CATIE.
      cPungency is indicated by np (non-pungent) and p (pungent).
      dUnique SPP alleles among all 43 lines (33,401 total SPPs).
      aUnique SPP alleles among 40 C. annuum lines (6,426 total SPPs).



      Figure 31 - SPPs identified in the Pun1 locus (Pepper GeneChip CAPS_Contig.2339). At the top, the diagram represents an alignment of CAPS_Contig.2339 with GenBank sequences for Pun1 (FJ755173.1, GU300812.1, AY819028.1, AY819029.1, AY819032.1, AB206919.1), pun11 which has a large 5’ deletion (gb AY819031.1), AT3-2 (FJ687524.1) and Pepper Chip assembly unigenes with significant similarity (>80% identity, >50 nucleotides aligned). The number of SNPs per 50 bp window between CAPS_Contig.2339 and aligned sequences are indicated by color boxes with key shown above. Regions not aligning are indicated by black lines. Below are the (40, option1 or 43 option 2) Capsicum annuum lines with SPP calls (red = A, blue = B) along the length of the CAPS_CONTIG.2339 from 5’ to 3’ shown left to right with positions shown above the allele calls. Black lines link the positions of the SPP calls to the alignment cartoon. SPPs at positions with no additional sequence information are indicated (ns).SPP positions, indicated in the top row of SPP calls, highlighted in blue were identified as duplicated sequences among the pepper assemblies and thus were removed prior to subsequent analyses.



      Figure 32 - Polymorphism among pungent and non-pungent lines on chromosome P2. Minor allele frequency by cM position across (A) non-pungent and (B) pungent lines. An 8.75 cM region of P2 containing pun11 (↓) is monomorphic among the non-pungent lines.


      Several SPPs identified within the pun11 deletion are detecting polymorphisms between paralogs and therefore could be considered false positives as they indicate SNPs or Indels not a large deletion. To verify the influence of duplicated sequences on false positive rates, BLAST searches were carried out with SPPs and surrounding nucleotides against pepper transcriptome assemblies to identify SPPs found in sequences represented multiple times in the transcriptome. The removal of SPPs with multiple significant BLAST hits caused a reduction in the false positive rate of 1% to 1.4% across datasets. Taken together, this indicates that there is meaningful information in SPP calls within multi-copy sequences. However, the information is complex, difficult to interpret and may be observed as false positives without the benefit of sequence data. Therefore, SPPs identified within multi-copy sequences were removed from further analyses.

      Allele sharing around Pun11. The 43 Capsicum lines in this study included 40 Capsicum annuum lines and a representative from each of three additional cultivated species Capsicum frutescens, Capsicum chinense, and Capsium pubescens (Table 4). The 40 Capsicum annuum lines, 21 pungent and 19 non-pungent, were selected by breeders specifically to represent a broad range of germplasm currently used in commercial breeding programs. A total of 33,401 polymorphic SPP markers within 13,323 unigenes were identified across the 43 lines (Dataset S2). Within this set, 6,426 SPPs covering 3,818 unigenes were polymorphic among the 40 Capsicum annuum lines.
      A total of 276 Capsicum annum SPP markers have been mapped to linkage group P2, including Pun1 (CAPS_CONTIG.2339) at position 65.7 cM (Figure 32A). Among the 19 non-pungent lines in this study, there were 42 monomorphic SPPs within 34 unigenes around pun11 that extended over 8.74 cM of P2. All but one of these SPP markers were polymorphic among the 21 pungent lines with varying allele frequencies (Figure 32B). Of the nine unigenes with significant similarity to Pun1, seven mapped to the same position as Pun1 while the remaining two were not mapped. A search against the tomato genome shows that there are 3 acyltransferases highly similar to Pun1 (< e-115) present in tandem on T2 and a total of 5 sequences annotated as acyltransferase sequences between positions 40,149,035 and 40,193,345 of T2.

      Distribution of allele frequencies and polymorphism within and between groups. Of the 33,401 polymorphic markers among the 43 lines, the overall distribution of SPPs with unique alleles was highest in the non-annuum lines (Table 4), with the largest number of unique alleles identified in Capsicum pubescens followed by Capsicum chinense and Capsicum frutescens at 13,643, 4,960 and 3,859 SPPs respectively. The increase in SPPs with the inclusion of non-annuum lines was largely but not solely due to these unique alleles with over 3,000 SPPs having alleles specific to two of the three non-annuum lines and over 1,400 having alleles specific to all three non-annuum lines (Figure 33A).

      Figure 33 - Polymorphisms among 19 non-pungent, 21 pungent Capsicum annuum and 3 non-annuum lines. (A) Venn diagram depicting the number of SPPs and unigenes (shown in parentheses) polymorphic within each group out of 9,272 SPPs within 5,712 unigenes having >2 minor alleles across the 43 lines. (B) Allele frequency matrix for 1729 informative SPPs among pungent and non-pungent Capsicum annuum lines. Numbers indicate SPPs found at each minor allele frequency pair. At the corners are shown the total number of SPPs for minor allele frequencies pairs divided by 0<0.25 and 0.25<0.5. At left and bottom are shown total SPPs at each minor allele frequency for pungent and non-pungent lines respectively.


      Capsicum annuum diversity and population structure. Phylogenetic trees were constructed using 13,621 SPP markers found to have unique allele profiles within each unigene among lines. Using the Capsicum frutescens and Capsicum chinense lines as an outgroup to the Capsicum annuum, the bootstrap consensus cladogram showed a general clustering of horticultural classes (Figure 34). Clades representing several pungent types including Small hot, Other-East Asian, "Jalapeño" and "Anaheim" plus "Ancho" were well supported, at 96% to100%. "Carolina Cayenne" and the Phytophthora-resistant Mexican land races CM334 and PI 201234 were each found on independent branches among the pungent clades. The relationships between the pungent clades were unresolved. The remaining lines form a well-supported (98%) monophyletic grade sister with 96% support to the pungent "Anaheim"/"Ancho" clade. The non-pungent "Bell" types were found in the most derived positions (Figure 35A).


      Figure 34 - Consensus tree and population substructure estimated from SPP markers. At the top, a Fitch & Margoliash tree of 40 Capsicum annuum lines, rooted with Capsicum frutescens and Capsicum chinense. The majority-rule consensus cladogram (overall equal branch lengths) was generated from 13,621 SPP markers. Numbers associated with branches indicate percent support based on 7,500 bootstrap replicates. Branches with less than 50% support have been collapsed. At the bottom is shown Capsicum annuum population substructure determined using Structure with 2,712 mapped SPP markers for K = 2 to K = 6. Each genotype is represented by a vertical column and genotypes are ordered according to the cladogram. Each color bar represents a different subpopulation and the proportion of a given variety's color bar represents the proportion that variety belongs to the corresponding subpopulation. The branches of the cladogram are colored according to the highest proportion subpopulation assignment when K = 6 with grey branches indicating highly admixed individuals, having no more than a 0.60 fraction assigned to any subpopulation. Grouping by common structure subpopulation constitution is indicated by colored border with assigned names shown below. "Long Yellow Marconi" and "Lange Westlandse Rode" are abbreviated "L. Yellow Marconi" and "L. W. Rode", respectively.


      Figure 35 - Principle component analysis & phylogram derived from SPP markers. (A) A representative Fitch and Margoliash phylogram with branch lengths reflecting phylogenetic distances based on Nei and Li genetic distances. Boxed clades and labels correspond to clusters based on Structure simulation at K = 6. "Long Yellow Marconi" and "Lange Westlandse Rode" are abbreviated "L. Yellow Marconi" and "L. W. Rode", respectively. (B) Graph showing the coordinates of the first 3 principle components for each variety. Clusters are circled and labeled. Non-clustered lines PI 201234 and CM334 are labeled separately. In this view the "Anaheim"/"Ancho", "Mixed" and "Bell" clusters, boxed in black, are difficult discriminate, therefore, this area was expanded in (C) which shows the arrangement of these clusters. Symbols correspond to those representing horticultural classifications in Figure 34.


      A model-based clustering algorithm, implemented in the software Structure, was used as a second means of identifying subgroups among the Capsicum annuum lines (Figure 34). The algorithm identifies a predetermined number of clusters, K, that have distinct allele frequencies. A genome can have membership in multiple clusters with genomic membership coefficients summing to 1. The Structure algorithm was run using 2,712 mapped SPP markers with K values set at K = 2 to K = 10. At K = 2 there is a varying degree of admixture across the lines. The Structure output was arranged by line according to the phylogenetic tree. At K = 2, the two clusters are anchored by the pungent Small hot and the non-pungent Bell types with a clear transition in membership coefficients seen where the Anaheim/Ancho clade branches off from the rest of the pungent groups in the phylogeny, at the base of the monophyletic grade leading to the Bells. The Bell cluster contributes to the genome of all individuals across all values of K with the exception of Milyang at K = 6. Each increase in K up to K = 6 splits one of the clusters obtained with the previous value with at least one individual having >0.60 membership to the new cluster. At K = 7 and greater no individuals were assigned to any additional cluster at >0.50 membership. Therefore, K = 6 was chosen as the appropriate K value for clustering of subpopulations. Of the resulting 6 clusters, 5 correlated with clades in the phylogeny with 96% or greater bootstrap support. The sixth cluster which only included one variety, the Mexican land race CM334, was found on an independent branch in the cladogram. There are seven pungent and non-pungent lines, while having less than 0.60 membership in any given cluster, share similar membership coefficients for both the Bell and Anaheim/Ancho clusters indicating a seventh cluster by common overall genomic constitution and will be referred to as the Mixed cluster. These are present in the phylogeny at the basal portion of the monophyletic grade leading to the derived Bell types. There were two additional lines, the Phytophthora resistant accession PI201234, and Carolina Cayenne, that showed a high degree of unique admixture, consistent with their positions in the phylogenetic tree.
      A third method employed to examine genetic diversity and substructure within the Capsicum annuum lines was a Principal Components Analysis (PCA) of allele frequencies across the 40 lines for 3,818 polymorphic unigene haplotypes. Cumulatively, the first three principal components (PCs) explained 27% of the variation in the data with 12%, 8% and 7% by PC1, PC2 and PC3 respectively. A 3-dimentional graphical representation of the first three Eigenvalues for each line indicates clusters that correspond to the clusters identified by structure and phylogenetic analyses (Figures 35B and 35C). The only exception is that the PCA placed Carolina Cayenne with a cluster including the East Asian cluster while this line is unique in the Structure and phylogenetic analyses.<
      Analysis of variance indicated that the groups defined by the Structure clusters shown in (Figure 34) were significantly different for all three PCs (P<0.0001). T-tests for mean separations between clusters showed that PC1 (P<0.05) and PC3 (P<0.0005) separated all groups. PC2 separated the Small Hot and East Asian clusters from all others (P<0.01).

      Hybridization efficiency of Solanum spp. To determine the potential utility of the Pepper GeneChip across Solanum spp., DNA hybridization efficiency for representative Solanum crops including eggplant (Solanum melongena), tomato (Solanum pennellii and Solanum lycopersicum) and potato (Solanum tuberosum) was determined.
      Hybridization efficiencies, measure as the number of probes above background (the 90th percentile of anti-genomic probes) were ~50% lower for each of the Solanum lines than for Capsicum (Table S4). However, greater than 99.9% of all unigenes were represented by probes above background for all of the Solanum lines tested, indicating the degree of homology between transcriptomes in Solanum species.

      Discussion
      Pepper GeneChip design. High throughput marker discovery and analysis of genetic diversity among crop species has become essential for modern breeding programs. In order to improve genomic and genetic resources for pepper breeding we have developed a method for high-throughput parallel detection of polymorphisms in pepper. Taking advantage of recent Capsicum EST sequencing efforts along with a custom genotyping array design, hybridization methods and algorithms (Stoffel et al, 2012) an Affymetrix Pepper GeneChip was designed based on 30,815 pepper unigenes with an average of 210 probes per unigene. The utility of the array was demonstrated by its application in the identification and analysis of polymorphism across a diversity panel of 43 Capsicum lines and Solanaceae species.

      SPP detection and data filtering. The efficacy of the chip and custom algorithms for polymorphism detection were tested using a panel of 43 Capsicum lines. Replicate hybridizations of genomic DNA from each line were completely reproducible by cluster analysis. Filtering parameters for SPPs identified relevant criteria for filtering SPPdev ratios, number of informative probes, number of bases spanned missing calls, inconsistent calls and allele frequencies. Adjustment of these parameters resulted in datasets ranging from 20,000 to over 80,000 SPP markers identified within 10,000 to 20,000 unigenes across the 43 Capsicum lines at false positive rates ranging from 6.2% to 10.3%. The lowest FDR among the datasets analyzed was observed with a SPPdev ratio ≥1.5, bases spanned ≥4, zero inconsistent and zero missing calls allowed with multi-copy sequences removed with accuracy of calls at known SNPs of 99.9%. Similar results were observed in the lettuce diversity study, although FDR was ~5% lower for lettuce, likely due to a more comprehensive set of mapped SPPs used for validation in lettuce. This study defined genetic diversity in Capsicum using a set of reliable gene-based SPP markers with greater than 40 fold resolution than previously reported.
      Presenting the results of adjusting filtering parameters enables users to choose an appropriate dataset based on the intended application. For analysis of diversity and population structure, a stringent dataset with maximum coverage is desirable. We chose minimum detection requirements of 1.2 SPPdev ratio, 2 informative probes and 4 bases spanned and eliminated inconsistent calls and SPPs within multi-copy sequences for analysis of lines in this study. A SPPdev ratio of 1.2 was selected since it provides 30% more SPPs, 13% more contigs, with a minimal increase, 0.6%, in FDR compared with a SPPdev ratio of 1.5. Allowing I calls can overestimate diversity by defining new haplotypes. Eliminating SPPs covering multi-copy sequences reduces potential ambiguity, as shown with (Pun1). For more line-specific applications, such as attempting to identify SPPs between two closely related lines, it may be more advantageous to use the low stringency (2 bases spanned) dataset at an SPPdev ratio of 1.5 and 0 I calls with over 83,000 SPPs in 21,000 unigenes and an estimated FDR of 9.7%.
      The quality of the data observed for polymorphism detection with the Pepper GeneChip was comparable to the most current sequencing technologies. The custom design and analysis of array data produce 6 to 10% FDR while current FDR estimates for SNPs derived from sequencing data can range from 5 to 50%. Similar to sequencing, several filters need be applied at the expense of eliminating true positives with microarray data. SNPs derived from sequenced populations have been filtered to remove rare alleles particularly unique alleles. We found the rare alleles identified by our method to make biological sense and did not observe a difference in FDR with the inclusion of unique alleles (data not shown). Sequence depth requirements for SNP discovery are analogous to our replicate chips and multiple probes per position requirements. Until recently, high-throughput transcriptome sequencing and subsequent data analysis was cost prohibitive for parallel high-throughput SNP discovery. Microarray based polymorphism discovery was an attractive alternative even though a small region surrounding a polymorphism rather than the precise nucleotide position of a polymorphism is identified. Very recent advances in sequencing technologies leading to next generation sequencing and beyond have led to more cost effective methods for high-throughput sequencing providing even larger and more detailed marker datasets. At the current time, the cost effectiveness of sequencing has surpassed microarray based methods for both polymorphism discovery and expression analyses. However, arrays (eg, Illumina Infinium and Affymetrix Axiom Arrays) remain an affordable method for SNP assays designed based on known SNPs.

      Polymorphism detection across 43 Capsicum lines. The capacity for polymorphism detection using the Pepper GeneChip was assessed using a diversity panel of 43 Capsicum lines. With 33,401 robust SPPs detected, 24,129 represented a unique allele across the panel. The three non-annuum lines had the largest number of unique alleles with diversity estimates congruent with other molecular studies that have shown Capsicum annuum is most closely related to Capsicum frutescens followed by Capsicum chinense as a three-species complex, and more distantly related to Capsicum pubescens (Jeong H-J et al., 2010; Pickersg B, 1971). Among the 40 Capsicum annuum lines, we identified 6,426 high quality SPP markers. As a whole, these markers indicate a 3-fold reduction in genetic diversity within non-pungent vs. pungent lines. Consistent with the derivation of the non-pungent lines from pungent precursors, >90% (1,729) of the non-pungent group polymorphic markers were also polymorphic within the pungent group. Among these, 251 markers were highly informative (>0.25 allele frequency) within both groups allowing for effective use for breeding. Inspection of allele frequencies between pungent and non-pungent lines across pepper chromosome P2 confirmed lower diversity in non-pungent lines. Additionally, allele distortion around pun11 is a dramatic 100% over >8 cM, indicating a common conserved region/introgression shared among these non-pungent lines. Thus, high-throughput marker discovery using the Pepper GeneChip has produced robust SPP markers providing high resolution diversity estimates, highly informative markers sets and new information regarding the genomic constitution of non-pungent Capsicum annuum.

      Capsicum diversity and population structure among Capsicum annuum. The use of a genome-wide set of markers specifically tailored for each of three independent methods; distance based phylogeny calculated using Fitch; a Bayesian analysis of population structure (Structure) and a principle components analysis (PCA) resolved a clear description of genomic contribution and relatedness between 40 Capsicum annuum lines into six clusters. These were statistically supported by phylogenetic bootstrapping and t-tests on PCA principle components 1 and 3. All three analyses consistently identified six clusters of related genotypes and show a grade of reduced diversity in the non-pungent Capsicum annuum. However, the phylogenetic relationships between the identified pungent clusters were unresolved and the genomic constitution of three pungent accessions found to be unique within the panel could be misinterpreted using only one or two of these methods, the results of these three analyses taken together provided a clearer understanding of the population substructure and relationships between lines.
      The PCA results for PI201234 and Carolina Cayenne are difficult to interpret alone. PCA places PI201234 between the Anaheim/Ancho and Mixed groups and Carolina Cayenne with the Japanese/Korean types. However, relationships become clear with the benefit of the Structure and phylogenetic analyses. PI201234 and Carolina Cayenne, were each found to be highly admixed and genetically independent from the six identified Structure clusters with admixture components that resolve the PCA results. PI201234, while on a solitary branch in the phylogeny, has substantial contributions from the CM334, Anaheim/Ancho, Small hot and Bell clusters in the Structure analysis is in agreement with its position in the PCA. Similarly, the Structure analysis showed Carolina Cayenne having substantial contributions from the Mexican Hot, Small hot, and Anaheim/Ancho clusters and the PCA coordinates for Carolina Cayenne lay between these same clusters. Both cases suggest inclusion in a PCA cluster can be a coincidence of a line's relationships to other groups and PCA alone in these cases can be misleading.
      Instances where specific information regarding pedigree or geographical origin was available, we found our analyses to be congruent with that information. The two Jalapeño and two Anaheim lines each form well supported clusters in all three analyses. The Bell line Jupiter was used as a recurrent backcross parent to generate Dempsey (Pickersg B iet al., 1997). The phylogeny clusters these two lines with 90% support and the two lines were present in the Bell cluster by both PCA and Structure analysis. The Phytophthora resistant lines CM334 and PI201234 were each found to be genetically unique by these analyses. These lines are each derived from accessions collected in the states of Morelos in South-Central and Oaxaca in Southwestern Mexico, respectively. Even though their fruit shape is similar and both lines are sources of Phytophthora resistance, the genetic basis of resistance differs between these two lines. This along with their distinct geographical origins is consistent with the distinct genetic makeup identified in this analysis
      The phylogeny shows a general clustering of lines across the panel but the relationships between the pungent lines was unresolved. This was not due solely to long branch attraction and/or the unresolved positions of CM334, PI201234 and Carolina Cayenne as the removal of these the lines from the analysis did not resolve the tree. The Structure analysis at K = 2 indicates that the ancestral population has a small contribution from the Bell cluster and large contribution from the Small hot cluster. This Small hot genomic contribution has been gradually lost during the selection for larger, fleshy, non-pungent fruits. This is in agreement with the overall trend during domestication and selection that has been previously observed (Paran I et al., 2007; Paran I et al., 1968). This transition is clearly supported for the Anaheim/Ancho through Bell groups by Structure through K = 6, the phylogeny and the PCA with both the Structure and phylogenetic analyses indicating a grade of reduced diversity from the moderately fleshy, pungent Anaheim/Ancho types to the fleshy, non-pungent Bell types. Additionally, both the Structure and phylogenetic analyses indicate that the Bell types are derived from an ancestor in common with the Anaheim/Ancho types. This relationship was not apparent from previous studies (Tam SM et al., 2009). The phylogenetic relationships among the remaining pungent types were unresolved and there was no clear ancestral type. This coincides with the Structure results at K = 6 where each of these pungent groups have distinct genomic contributions from different sets of clusters. A clear resolution of the relationships between these groups may require additional pungent types including semi-domesticated and wild Capsicum annuum.
      Only a few studies attempting to characterize a broad selection cultivated Capsicum annuum genetic diversity using molecular markers have been reported. Each of these studies uses a small number (<150) of mostly anonymous markers (Adetula OA, 2006; Tam SM et al., 2009). The most comprehensive of these studies used retrotransposon LTRs to characterized 64 diverse Capsicum annuum lines Tam SM et al., 2009). A Neighbor-Joining tree based on 107 polymorphic LTRs indicated four clusters among the Capsicum annuum lines. Unlike our analyses, the pungent lines Jalapeño, CM334 and Perennial in the LTR-based analyses clustered together in the Neighbor-Joining tree and by Structure membership coefficients. This indicates that the high density of SPP markers provided higher resolution for analysis of population diversity and structure.
      The growing affordability of high-throughput marker discovery has led to investigations into the most appropriate method for detecting population structure from large marker datasets (Smith PG et al., 1951). Bayesian clustering and PCA are common methods and have been applied in several SNP studies of population structure in humans, livestock and crops (Hamilton1 JP et al., 2011; Robbins MD et al., 2011; Riztyan et al., 2011). These methods having been developed for relatively small marker sets have limitations in their application using high density genome-wide markers (Helyar SJ et al., 2011). The number of clusters estimated by Bayesian methods may be influenced by the inclusion of markers in linkage disequilibrium, an inevitability with large marker datasets. PCA methods are sensitive to missing data and sampling effects for populations with continuous distributions. Both methods can be affected by ascertainment bias, particularly when using SNP markers, due to unequal sampling across minor allele frequencies. The SPP markers analyzed using Structure and PCA were detected de novo across the entire panel. This approach eliminates analytical issues associated with ascertainment bias. In addition, all markers with missing data were removed and, for the Structure analysis, the number of markers in linkage disequilibrium were reduced by removing SPPs with redundant allele profiles across the panel within each genetic bin. We found it critical to use the linkage model, applied to markers within mapped contigs. Without the benefit of map data, these analyses were more difficult to interpret (data not shown). An additional difficulty with Structure was in the estimation of K (the number of populations) since there was little difference in the posterior probabilities of each K (Pritchard JK et al., 2000; Falush D et al., 2003). In this case it is suggested that the value of K that makes the most biological sense be used (Pritchard JK et al., 2000) At each added K population, a high proportion of that population was assigned to an individual(s) that made biological sense up to K = 6, beyond which no large proportion was assigned any individual. Ultimately, this approach produced a high congruence of results between both the Structure and PCA analyses. The results of the Structure analysis appear most comprehensive, informative and in complete agreement with the phylogenetic analysis.
      This work demonstrates that genome-wide SPP markers analyzed using three methods provided a clear description of diversity and relatedness among Capsicum breeding lines. A core collection of Capsicum has been established using clustering analysis of phenotypic characters (Zewdie Y et al., 2004). A genome-wide marker analysis of this collection would extend our knowledge of the relatedness and diversity among its members. In addition to gene bank collections and modern cultivated lines, important sources of genetic diversity include the wild and semi-domesticated (land race) lines. A large number of wild and semi-domesticated land race populations of both Capsicum annuum and Capsicum frutescens are found growing in various environments from southern United States throughout Mexico (Votava EJ et al, 2005; Aguilar-Melendez A et al., 2009 Kraft KH et al., 2009). It is clear that Capsicum annuum was domesticated in Mexico, however the number and geographical centers of domestication events remain unclear. The application of the analyses implemented in study using a genome-wide set of SNP based markers to semi-domesticated and wild annuums may unravel the mysteries of Capsicum annuum domestication. Understanding the populations derived from ancestors which have and have not contributed to modern breeding lines will aid in the selection of lines for future breeding programs. Additionally, identifying Capsicum annuum populations that have contributed to modern domesticates may be required to more thoroughly dissect the genomes of and relationships between the cultivated pungent annuums.
      Many of the traits of interest for current Capsicum breeding programs include complex, multi-genic traits that are not easily integrated through traditional breeding strategies. This is the first gene-based, genome-wide marker assessment of molecular diversity and population substructure among a broad collection of Capsicum annuum lines. This work will complement our development of an ultra-high density pepper map and conversion to SNPs using the same chip technology enabling MAS for the introgression of complex traits, such as disease resistance, into the available breeding germplasm while retaining the integrity consumer driven traits.



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