Rats have 42 chromosomes in the nucleus of each cell in their body (except for the sex cells - eggs and sperm - which have 21). Each complete set of chromosomes contains all the information needed to make that particular rat. All along the chromosomes are genetic loci or genes, each one containing information about a particular trait (eye color, fur texture, ear shape, etc.). When rats mate, the eggs and sperm, which have exactly half the number of chromosomes as a complete cell, pair up and share their information. So each chromosome ends up with a partner, with corresponding genetic loci (these loci are called alleles). If the alleles are the same, they are called homozygous. If they have different information, they are called heterozygous. In most cases, if the alleles are not the same, one will be dominant over the other. This means that a rat can carry a hidden trait that can not be seen from its appearance, health, etc. - called a recessive trait. Genotype (genetic make-up) does not usually equal phenotype (what you see).
Lesson 1: Pink Eye Color
Eye color is controlled by several different genes, but this one's the easiest to understand (I hope!). The information to make black eyes is dominant over the information to make pink eyes. As an example, we'll mate two virtual rats named Blacky and Pinky. Blacky has the homozygous allele for black eyes, which we'll write as PP. He got the information for black eyes from both mom and dad. The P's are traditionally written in capitals, because the black eye allele is dominant over the pink eye one. Pinky has the homozygous allele for pink eyes, which we'll write pp, meaning she got the information for pink eyes from both her mom and dad. If we mate these two, Blacky will give all the babies information for making black eyes, and Pinky will give all the babies the information to make pink eyes. The babies will all have a mixture of the two, Pp. Since P is dominant over p, the babies will all have black eyes, but will carry the information to make pink eyes as a recessive trait.
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