Why does holden have difficulty breathing after only a short run to the main gate?

He is a heavy smoker. Mostly cases of shortness of breath are because of heart or lung conditions. Your heart and lungs are one of the carrier in transporting oxygen to your tissues and taken away carbon dioxide, and problems with either of these processes affect your breathing.

format change of dna.  

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).