While Mendel’s Law of Segregation states that the two alleles for one gene are separated into different gametes, a different question of how different genes are inherited remains. For example, is the gene for tall plants inherited with the gene for green peas? Mendel asked this question by experimenting with a dihybrid cross; a cross in which both parents are homozygous for two distinct traits resulting in an F₁ generation that are heterozygous for both traits.

Let’s think of two homozygous plants, one with round yellow peas (genotype YYRR) and one with wrinkled green peas (yyrr). In the F₁ generation, he found that all the plants exhibited both dominant traits (yellow and round; YyRr).  However, in the F₂ generation, plants had combinations of traits that occurred in a predictable ratio: for every 16 plants, 9 were yellow and round, 3 were yellow and wrinkled, 3 were green and round, and 1 was green and wrinkled. From this result, Mendel proposed that the inclusion of a green allele in a gamete had no impact on whether that gamete would receive the round or wrinkled allele: each combination was equally likely. Mendel’s Law of Independent Assortment states that genes do not impact one another with regard to sorting into gametes.

Scientists now know that Independent Assortment occurs because the chromosomes pair up randomly during meiosis I, along the metaphase plate. As a result, genes on different chromosomes will sort independently. This also means that two genes residing on the same chromosome violate the law of independent assortment, especially when they are very close to one another, as they will nearly always be inherited together. This phenomenon is described as “linkage” on the level of the chromosome. Linked genes do not demonstrate a 9:3:3:1 ratio in the F₂ generation of a dihybrid cross.