Although it was once thought to be a classic Mendelian trait, eye color is now well known to be subject to polygenic (i.e., multiple genes are involved) inheritance. Our current catalog of genetic variation affecting eye color is incomplete.
However, in a paper published online today in Nature Genetics (abstract here, subscription required for full paper), Dr. Kari Stefansson and colleagues at deCode Genetics report the results of a genome-wide association study focusing on eye color (in addition to hair color and freckling) as a phenotypic trait. This study adds considerably to our knowledge of the genetics of human eye color, in addition to hair color and freckling.
The authors initially studied about 3,000 Icelanders and then performed replication studies in another ~2700 Icelanders and about 1200 Dutch individuals. With respect to eye color, they found the previously reported association with OCA2 gene variants - not big news but providing confidence in the methods. However, the authors also found association of a new gene - SLC24A4 - with both eye and hair color. Additionally, two coding variants in the TYR gene were found to be associated with eye color and freckles.
Interestingly, the SLC24A4 gene is similar to SLC24A5; a SLC24A5 coding single nucleotide polymorphism has previously been shown to be associated with skin color in African-Americans and African-Caribbean populations.
The authors then went on to derive a model in which they attempted to predict eye color based on genotypes. They showed that variants in OCA2 dominate the distinction between brown and blue eyes and that the newly reported variants can contribute significantly to the more subtle distinction between blue and green eyes.
It will be interesting to see what deCode may have in mind with respect to commercialization of this new information.
