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I've watched a few YouTube videos on the subject of growing chillies. In one of the videos the author is growing several varieties of chillies in the same greenhouse which is what I'm doing.

To prevent cross-pollination they tie mesh "baggies" around the branch/stalk that hasn't yet flowered but has a bud, i.e. before flowering.

My question is, do I need to mesh bag every bud branch/stalk, on every plant, in my crop to keep my four or five chilli different varieties from cross pollinating (these will all reside in the same greenhouse)?

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Yes, but you need to do it only for one or two flowers per variety. And you can repeat this operation few time during the season. A chili contain many seeds.

Cross pollination will not affect the variety of the fruit on a plant, it just affect the DNA in the seed, so the new plants. The hotness on "seeds" it is not due to DNA. And in any case it will no more be a F1 or the same "variety" if the variety were not stabilized.

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