You need a verb which modifies "researches" , so options A and B are out. What are researches doing ? "Employing the same techniques..."
What are researches doing ? "By the same techniques used to...making them.." Does not sign right, does it ?

Option D is out because it is not clear what "which makes them" modifies. The technique or the plants ?
Option E is out for the same reason as D is out - modifying issue.

Kudo me if I was helpful

you need a verb which explains what are you doing " the same technique " - using it, employing it, modifying it or what ? Just mentioning the same technique and not specifying what you are doing with it is not correct. It is understandable of course but it is not grammatically clear.

First question : Whats wrong with A?

A states that "By the same techniques used for genetically enhancing plants, making them disease- or pest-resistant, researchers have been able to increase the amount of protein in potatoes, sweet potatoes, and tobacco."

This is unclear. The correct usage would be "By using the same techniques..." This sentence is saying that because those techniques exist - researchers have been able to increase protein in potatoes, etc. This is not true. The researchers would have to do something with those techniques to increase the protein.

Second questoin : Clarify with...

I'm assuming you mean option B here. B is essentially doing the same thing that A did. Researchers would still have to "use" those techniques. Their existence alone will not increase the protein content of a potato. This option is not saying anything along those lines. Another way to eliminate this option would be the awkward "so that they are disease- and pest-resistant, researchers have been able to increase the amount of protein in potatoes, sweet potatoes, and tobacco." In an awkward way, this sentence is saying that because there are techniques that make plants disease and pest resistant, those resistances enable researchers to increase in protein in potatoes, sweet potatoes and tobacco. But from the way this is worded it sounds like the protein increase is a result of the resistances yet they haven't been unlocked by a researcher even though the same techniques would "unlock" both. This sentence doesn't make sense.

Third question: Used to/Used for/For

Lets take the correct response and use these to make sentences that make sense. Hopefully it makes more sense by example than me explaining (I don't feel that my explaining would be as helpful.)

Employing the same techniques used to genetically enhance plants so that they are disease- or pest-resistant, researchers have been able to increase the amount of protein in potatoes, sweet potatoes, and tobacco. - Correct response.

Employing the same techniques used for genetically enhancing plants to be disease- or pest-resistant, researchers have been able to increase the amount of protein in potatoes, sweet potatoes, and tobacco. - Now I made this one up, it sounds right but I'm hoping if I made an error someone else can jump in and let me know if I made a mistake

I'm not sure what you would use "for" solo in this situation. Anyone else?

Let me know if you have further questions!
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Going to be hitting the books again. Decided that I'd like a 700+ score. Not looking forward to spending the next few months studying, though!