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Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.

An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A modifier gene called cream dilution has two alleles: Ccr and C. The Ccr dilutes the coat color from red to yellow when present in the heterozygous state and from red to cream when present in the homozygous state. However, the C allele does not affect coat color. Thus, the horses with genotype eeCC have a reddish-brown coat, tails, and mane, while those with genotype eeCcrC have a gold coat with a white tail and mane.

In contrast, in some organisms like Siamese cats, the coat color is highly sensitive to changes in temperature. These cats show partial albinism due to a mutation in an enzyme involved in the production of melanin. The enzyme is active in colder areas of the skin, which results in a darker color, while it’s inactive in warmer regions of the skin resulting in a lighter color. This results in the breed’s characteristic dark fur on the face and on the extremities.

Similarly, the presence of drugs or chemicals in an organism's immediate environment can also influence gene expression in the organism. For example, C. R. Stockard showed that the Fundulus heteroclitus fish developed just a single eye when the fertilized egg was placed in the magnesium chloride solution.

In conclusion, there is a complex interaction between the genotype and the environmental factors of an organism that can lead to variable phenotypes.

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