So my parents had two children, me and my sister. Both my parents have blue eyes and so do I, but my sister has hazel. I was just wondering how this could have happened and what that means for the genotype of myself, my parents, and my sister. What are all the posibilities? Also, is eye color one of those complicated traits that get effected by other factors? If so what genetic factors determine eye color? I know there are some traits that are only on one type of chromosome and that usually these are gender based traits, but I was wondering. Is eye color the sort of thing you can do a basic punent square for or is it too complicated?

Recent genetic research has shown that eye-color is determined by a number of genes. As a result, blue and brown eye colours can no longer be viewed as simple recessive/dominant traits. In fact, almost any parent-child combination of eye colours can occur. Nonetheless, one region of the genome plays a more important role than others, so predictions based on the old ‘one gene’ model are correct for most families.

The number of genes that contribute to eye colour is still not known but research over the last 4 years has shown that variations in one small region of chromosome 15, containing the genes OCA2 and HERC2, account for about 75% of the overall variation in human eye colour and are very strongly associated with blue versus brown eye colour.

Interestingly OCA2 has been known for a while to regulate eye colour (see below), whereas HERC2 probably does not directly - it contains a regulatory element that alters OCA2 expression.

http://en.wikipedia.org/wiki/OCA2 

http://www.ncbi.nlm.nih.gov/pubmed/18172690

http://www.ncbi.nlm.nih.gov/pubmed/17952075

http://www.ncbi.nlm.nih.gov/pubmed/18252222