Simply because they are genetically engineered does not make it any more likely for plants to become an invasive or persistent weed, according to a decade-long study published in the journal Nature.
(A) because they are genetically engineered does not make it any more likely for plants to Plural "plants" cannot become singular "weed". Eliminate.
(B) because it is genetically engineered does not make a plant any more likely to We require a noun or a noun idea to function as a subject for the verb "does not make" - "because it is genetically engineered" is a clause beginning with a conjunction and cannot function as a subject. Eliminate.
(C) being genetically engineered does not make it any more likely that plants will Same error as in (A). Eliminate.
(D) being genetically engineered does not make a plant any more likely to Correct answer - "being genetically engineered" is a gerund and functions as a noun idea.
(E) being genetically engineered does not make a plant any more likely that it will Incorrect idiomatic expression "any more likely that" - "any more likely to" is the correct idiomatic expression. Eliminate.