As one of his many breeding experiments with pea plants, Gregor Mendel crossed plants that differed at two different gene loci. These experiments led him to the concept called Mendel's second law. According to this law, the alleles of two (or more) different gene pairs—for example, Rr and Yy—assort independently of each other during meiosis, such that a random combination of the genes from each pair winds up in the gametes.
Independent assortment occurs because chromosomes may be aligned in various ways in metaphase I of meiosis. However, keep in mind as you watch the animation that for two genes to assort independently they must reside on different chromosomes; or if they reside on the same chromosome, they must be located relatively far from each other along the chromosome's arms.
Independent assortment has its basis in the mechanics of meiosis. In meiosis I, homologous chromosomes pair up and align at the midplane of the cell, such that each chromosome in a pair is equally likely to be found on one side of the midplane as the other. All the homologous pairs along the plane line up randomly. The two chromosomes of each pair migrate to opposite poles of the dividing cell, providing each new daughter cell with a random assortment of chromosomes and alleles.
Mendel's second law does not apply to all genes. When genes lie close together on the same chromosome, they are "linked" and are more likely to travel together during meiosis. Therefore, linked genes do not independently assort. If the genes are located on different chromosomes, they do independently assort. For two genes located far apart on the same chromosome, crossing over essentially unlinks the genes, and the genes assort independently.
Textbook Reference: Concept 8.1 Genes Are Particulate and Are Inherited According to Mendel’s Laws