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.
We can use a diploid (2n) cell with just two pairs of chromosomes to illustrate a genetics concept called independent assortment. We will track the movement during meiosis of the cell's two pairs of homologous chromosomes. Before meiosis begins, the cell synthesizes new DNA and thereby replicates each chromosome.
Early in meiosis, the pairs associate. Note that chromosomes in a pair are not quite identical. In one pair, for example, one chromosome carries a recessive allele of a gene, indicated r, and the other carries a dominant allele, R. The two pairs line up at the cell's midplane during metaphase I, and may adopt one of two alternative alignments. The alignments provide the basis for independent assortment.
The cell may adopt alignment 1, in which the r and Y alleles end up in the same daughter cell; or, the cell may adopt alignment 2, in which the r and Y alleles end up in separate daughter cells. From a large pool of cells that initiate meiosis, on average half of them adopt alignment 1 and the other half adopt alignment 2.
During the second half of meiosis, the two cells from each alignment divide into four haploid (n) cells. The result is an equal number of the possible genotypes: rY, Ry, ry, and RY. Because there are equal numbers of genotypes, we can say that the alleles of the R and Y genes assort independently during meiosis. Note that alleles of different genes always assort independently if the genes reside on different chromosomes, but not necessarily if they reside on the same chromosome.
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.