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Independent assortment hypothesis

The Punnet square protocol

A cross of FF (purple-flowered peas) with ff (white-flowered peas) is shown as an example.

  1. Draw a box with lines bisecting it horizontally and vertically, extending the vertical line above the box and the horizontal line to the left of the box.
  2. Write the segregated alleles of one parent on the cells horizontally above the box. Write the segregated alleles of the other parent vertically to the left of the box. 
  3. Pull the top alleles down into the boxes directly below them. Combine those alleles with the alleles from the other parent (represented on the vertical axis) by pulling the vertical alleles to the boxes to their right.

Punnett square for Mendel’s pea color. 


  • In the case of a heterozygote, always write the dominant allele (represented by a capital letter) in front of the recessive allele (represented by the lower case letter).
  • Each internal box represents the probability (25%) expected of that genotype in the next generation. In the case in which more than one box is represented by the same genotype, the probability increases by 25% for each additional box. 

But wait…there’s more! Mendel’s monohybrid crosses established that inheritance of phenotypes happened by the interactions of discrete ‘particles’ (we now call alleles). Further, he discovered that those alleles segregate during the process of meiosis in the production of gametes, which recombine during fertilization. The result of these two insights can easily be predicted by a technique developed by R. C. Punnett. Once these principles were established, Mendel sought to understand how multiple phenotypes were related to each other during inheritance. He developed two alternate hypotheses: