Option 1 -> "turned down" means rejected or refused, which fits the context of a publisher rejecting a manuscript.
Option 2 -> "turned in" means submitted or handed in, but the manuscript would be turned in TO the publisher, not BY the publisher.
Option 3 -> "turned over" means transferred or handed to someone else, which doesn't match the context of being upset.
Option 4 -> "turned out" means resulted in a particular way, but doesn't work grammatically with "by the publisher" in this context.
Hence, Option 1: turned down -> The phrasal verb "turned down" means rejected or refused. A writer would naturally be upset if their manuscript was rejected by a publisher, making this the most logical and contextually appropriate choice. -> correct