Learn English – Come in or come into or both

As this ELU answer indicates, the correct version of this phrasal verb is actually to home in (to head directly towards a target). But OP shouldn't let that bother him; quite possibly most native speakers use the "wrong" version.

So the combination isn't really in + on - it's home in + on. It occurs with other phrasal verbs of the general type [verb] in, such as...

I'll look in on you this afternoon (to look in = visit briefly)
We'll check in in the afternoon (to check in = confirm arrival - at a hotel, for instance)
The burglar broke in in the night (to break in = enter illegally by breaking a lock or window, etc.)

As those last two examples show, although it might look a little odd to some, there's nothing "incorrect" about repeating even the same preposition. The first occurence is part of the phrasal verb, the second is just a normal preposition indicating the relationship between verb and object.

EDIT: Per comments below, I've just changed "sound a little odd" to "look a little odd" in the above text. The stress patterns of normal speech mean you'd barely notice the same preposition occurring twice (one would normally stressed, the other not, so they'd sound very different). But in the written form it's distracting/off-putting for the reader. Suppose, as per @J.R.'s example, your first thought was to write...

I didn't understand what she was getting at at first.

In that particular case, you could just insert a comma between the two at's to help the reader along, but it's only a partial solution which won't always work. Unless you're committed to accurately reporting actual speech, a little rewording is probably better...

At first I didn't understand what she was getting at.

To put virus-resistance genes in the sweet potato.

To put virus-resistance genes into the sweet potato.

From above sentences, second sentence is correct. To know the reason we must aware about the difference.

In general, the word "in" emphasizes the situation of something or someone being inside of something. For example: I am in the library. The cheese is in the refrigerator. There is a mouse in my house.

"Into" emphasizes the action of a thing or a person entering or being put inside something. For example: I am walking into the library. He put the cheese into the refrigerator. I saw the mouse creeping into my house.

In your examples we are going to put virus resistance genes into sweet potato because virus resistance genes don't exist in sweet potato and we are going to put/insert in it. If it is already exist we can use 'in'.

One approach that works very well is to segment the market into three different areas.

Above example is about 'Segmenting', means we are going to separate/divide market in 3 different areas, that's why 'into' could not be replaced by 'in'.