Genetic mutations are harmful.

the darker peppered moth species were favored due to the fact that the industrial revolution had made all the nearby trees a darker color instead of white.

the last one: artificial selection/genetic engineering

plant breeding is modifying the genetic composition of the plant - but this isn't cloning (which is specifically introducing a gene into a genome). but you are artificially selecting for the phenotype that you want.

the second one is literally genetic engineering - the gene would have been cloned first and then inserted or genetically engineered into the new plant cell (the cotton).