The characteristic traits of an organism are primarily controlled by two: the order that nitrogen bases are arranged in the DNA.
The sequence of nitrogen bases (adenine, thymine, cytosine, and guanine) in the DNA molecule encodes the genetic information necessary for the development, functioning, and reproduction of the organism. The specific arrangement of these bases determines how genes are expressed and ultimately dictates the characteristics of the organism.
While the shape of the DNA molecule (which is typically a double helix) and the number of chromosomes can influence genetic processes and stability, they do not directly determine traits as the sequence of bases does. The reproduction method of its parents can influence traits but is more about inheritance patterns rather than directly controlling characteristics.