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Crossing Chili Peppers

By Julian Livsey
Peppers have two sets of chromosomes. Unlike say pumpkins, which produce male and female flowers, with the female flower needing the pollen from the male flower to create the pumpkin fruit, chilli flowers contain both male and female parts. Being self-fertile, a chilli plant that pollinates itself will produce peppers containing seeds that will grow a very similar replica of the original plant. This is crucial for seed companies who sell packets of seeds with a picture of a known variety on the front. People expect the plant that they spend all summer cultivating, to produce almost uniform pods. The problem arises when you realise that different varieties of pepper plants can pollinate each other - taking one chromosome from the mother plant, and one from a father plant.

Crossing chilli pepper species

F
L
O
W
E
R
Male Parent
Female Parent          
bacca-
tum
praeter-
missum
frutes-
cens
chinense annuum galapa-
goense
chaco-
ense
tovarii pubes-
cens
eximium carde-
nasii

W
H
I
T
E

baccatum  HF PF NG NG  NG NG  —
praeter-
missum
 PF HF IV  IV PF
frutes-
cens
 NG HF PF  NG  — —  
chinense  NG NG PF HF  PF NG —  
annuum  NG IV PF PF  HF IV IV
galapa-
goense
 NG IV  NG HF EC
chaco-
ense
 IV IV NG  NG HF —  
P
U
R
P
L
E
tovarii NG I IV EC IV HF NG
pubes-
cens
IV IV EC IV IV HF HF NG
eximium NG PF NG IV IV IV NG HF HF HF
carde-
nasii
NG IV NG IV IV HF HF HF


NG = F1 hybrids germinate normally
EC = F1 hybrids raised by embryo culture
IV = fruits/seeds set, but F1 seeds inviable
PF = F1 hybrids partially fertile
HF = F1 hybrids highly fertile
— = no data

Genetic Resources of Capsicum, International Board for Plant Genetic Resources, 1983

This can be a problem for seed sellers, who have to be sure they have seed that is going to grow plants that are true to type. But it is also a blessing, because it allows the number of capsicum varieties to continue to expand. There are not a fixed number of varieties and never have been. The capsicum species has come a long way since the early days of its existence, with well over three and a half thousand varieties currently known. But how long before there are four thousand? Technically, there probably already are.

Creating a new variety

Let's go back and take the humble Purple Jalapeno as an example. A stable variety is said to be homozygous. This means that the genes you will find in both sets of chromosomes are the same. Purple dominates the colour part of the gene, the amount of capsaicin is moderate under ideal growing conditions, the fruit shape is like an elongated and slightly bloated bullet. If our Purple Jalapeno keeps self fertilising, or is fertilised by another Purple Jalapeno, then we know for certain we are going to get pods with seeds that will, "come true", that is to say, collected seeds will grow another Purple Jalapeno plant.

But what would happen if we use the Purple Jalapeno as the mother plant (the plant on which the fruit we are interested in will grow), and pollinate one of its flowers with pollen taken from an Orange Habanero? If you are expecting the fruit to look different you will be disappointed, because the resulting pod will look exactly like a Purple Jalapeno. Don't think your cross has not worked; the seeds contained in our crossed pod now have chromosomes from the two different plants. These seeds are known as F1 (first filial generation). If we grow out these seeds, the observable characteristics of the resulting pods will be near identical (for the sake of argument, let's say we get lucky and our cross is orange with purple spots, is Jalapeno shaped and has the heat and flavour of a Habanero – in reality this will never happen. One of the only constants is that the size of your pods will be somewhere between the mother and father plants in shape and size, everything else is less certain, anyway…). You will quite often see seed sellers offering F1 varieties. They are able to cross two varieties and know exactly what the plants and pods will look like.

Stablising the genetics

However! Where the F1 seeds all contain the same dominant genes, allowing identical pods, when you grow the next generation it can get messy. Even if our F1 plant pollinates itself, the seeds for the next generation, the F2 seeds, will not all produce pods that are identical to those you got with the F1 plant. The reason is due to recessive genes. The F1 pods were controlled by dominant genes, but in later generations the less dominant genes can still be present, and utilised. By way of illustration, my wife and I have dark hair and brown eyes, yet our daughter is blonde with blue eyes. While we both made use of the dominant gene for hair and eye pigment, in us somewhere was the recessive genes for blonde and blue. Our daughter chose these recessive genes, and your chilli plants can do exactly the same thing.

Your F2 plants will each have different combinations of genetic material taken from the mother and father plant, meaning ten F2 seeds from our amazing new pod could produce ten completely different plants and pods - some may look like Purple Jalapenos but taste like the Habanero, others may still have the spots but taste like the Jalapeno. This wide variety of traits means that you cannot easily sell seeds saved from F1 plants, because you cannot tell what you are going to get. That said, the super hot Trinidad varieties are being crossed quicker than we can keep up with, and we did find a website offering seeds taken from F1, F2, and F3 plants. If it is unusual, the chilli grower will want it.

If your aim is to produce a completely new variety of pepper, the trick is to keep growing it, year after year, picking the plants and pods that show the characteristics that you want. Some argue that this is why some peppers are pendant while others are erect – years and years of successive breeding where the biggest pods were chosen, created varieties with pods that were too large to grow erect, as most of the wild varieties do. Food for thought. Anyway, the percentage chance the seeds will come true increases with each generation as you filter out the genes that you do not want. Back to our Purple Jalapeno example, you may find most of the F2 plants have purple pods, but a couple may be orange. By selecting the orange pods you can start to shape your new variety. Once you get to about F8 seeds after seven generations of the plant, you have something very likely (99 point something percent) to come true, because the two sets of chromosomes become almost homozygous again. Note the word “almost”. It is quite possible that varieties such as the 7 Pod, which are considered a landrace chilli and therefore stable, occasionally throw up a version with a recessive gene characteristic, which leads to claims of a new variety. Some of the more recent super hot varieties are said to be 'stable' because they have been through this multi-generation selective breeding cycle. Others have not, and a quick look at the discussions on the various pepper forums show people getting different results from what is supposed to be the same variety. The capsicum waters quickly get muddy as more and more people try their hand at crossing.

Even if you go through the cycle of selecting generations of pods, you are still breeding plants that descend from just two original plants. Without a more diverse pool of genes to pull from, your plants are much more likely to fall victim to some inherited disease. Much better would be to start with a hundred plants, fifty of each variety. Then cross all the F1 flowers with each other, and so on. Much more work, but better quality plants.

Selling or trading seeds for a new variety that has not become stable has the effect of releasing myriad variants of that variety into the genetic pool that is capsicum. Does that matter? Some people would rather things were done properly and varieties were made stable before they were made commercially available. Others are happy to take their chances and get their hands on something new and different. Organisations like the CARDI and the Chile Pepper Institute actively cross peppers all the time, with the aim of creating new varieties with traits that will lead to bumper yields, better flavours, or disease tolerance, all of which will that will benefit commercial pepper farmers. But crossing pepper varieties is fun and easy to do in your back garden. Doing it for a year or two, however, does not give you a new variety. Selective breeding for seven generations is definitely time consuming, but necessary if you want to claim a truly new variety of capsicum. If you are working on any of your own crosses, do let us know about them, we'd love to hear your experiences.

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