How do alteration of genes affect the trait or characteristics ??

It is said that genes control the characteristic or trait but the question arises how ?  The genes control the characteristic by making a specific protein. Genes are the segment of DNA that contains information to form RNA which ultimately forms protein. Each gene contains two alleles and this instructs the cell to make protein for expression of traits. 

If the plant has gene for green seeds then it will make protein which will give green colour to seeds.