Independent ortment & linkage?

Law of independent ortment just means that when you have 2 or more genes on the same chromosome--like say one that codes for eye color and one that codes for hair color, then during cellular division, they will segregate separately. And that is what Mendel did. He studied numerous traits and noticed that they "ort independently" from one another. So, in essence, you cannot determine this property usually a monohybrid cross (a cross that just looks at one gene). You would need to do a di- or even tri- hybrid cross. Mendel's explanations were remarkable for his time. Then, it was thought that traits "blended." Meaning that, fore example, if you had a red flower crossed with a white flower, then the progeny would be pink--a blend of the parentals. Mendel discovered with the law of independent ortment, along with other theories, that this was not the case. However, like you mentioned there are exceptions. Sometimes, genes on a chromosome are linked, only if they are in close proximity. This means that gene A will always be with gene B. So if they are undergoing meiosis, then they, of course, will segregate together. There are also various types of linkage, such as epistasis, etc, which dictates the various phenotypes of the progeny of the parentals with linked genes. Such ratios are 9:7, 12: 5, etc.