In this sentence, the word "fashion" denotes a process, a mode of action. It is the way plants such as tomatoes have been genetically modified.
A word's denotative meaning is what is signified or referred to by the word according to the context. The denotative meaning of the word <em>fashion</em> in this sentence is making use of the term's second definition; the first one being, as you know, a prevailing usage, style, or practice in a specific period.
