1. Selective Breeding: This is the oldest and most traditional method. It involves choosing organisms with desirable traits and breeding them together. This is how humans have been developing crops and livestock for thousands of years. For example, farmers might choose to breed cows that produce lots of milk, or they might choose to breed corn plants that produce large ears of corn.

2. Genetic Engineering: This method involves directly manipulating an organism's genes. It can be used to introduce new genes, modify existing genes, or delete genes altogether. For example, genetic engineering can be used to create crops that are resistant to pests or diseases, or to create animals that produce more milk or meat.

3. Mutagenesis: This method involves introducing mutations into an organism's DNA. These mutations can be caused by exposure to radiation or chemicals. Sometimes, these mutations will lead to desirable traits that can then be selected for through breeding. This method is often used in research to study the function of genes, but it can also be used to develop new varieties of crops and livestock.

It's important to note that each of these methods has its own advantages and disadvantages. For example, selective breeding is a relatively simple and inexpensive method, but it can be slow and it may not be possible to develop all desired traits. Genetic engineering is a powerful tool, but it can be expensive and it raises ethical concerns about the manipulation of life. Mutagenesis can be used to develop new traits, but it is a random process and there is no guarantee that the desired trait will be produced.