A Punnett Square is a tool to visualize the genotype*s possible from mating a pair of individuals. It is set up by subdividing a square into enough spaces to contain every allele* combination for the gene(s) of interest given the parents genotypes.
It is most useful when looking at one or two loci because the number of possible genotypes increases rapidly as the number of loci observed increases. A single locus Punnett square contains four allele combinations. A two-locus Punnett Square contains 16 combinations, and a three locus square contains 64.
A pairing where two traits are observed is called a dihybrid cross.
Multi-locus Punnett Squares can be hard to draw and are difficult to interpret. The large number of genotypes possible with multi-locus crosses makes it easier to avoid drawing the square. Instead, the probability of specific genotypes arising are calculated using equations.
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