Independent assortment of genes on different chromosomes results from the mechanics of meiosis (Chapter 11), in which different pairs of homologous chromosomes align randomly on the metaphase plate in meiosis I. For some pairs of chromosomes, the maternal chromosome goes toward one pole during anaphase I, and the paternal chromosome goes to the other pole, but for other pairs, just the opposite occurs. Because the alignment is random, gene pairs on different chromosomes assort independently of one another.

Fig. 16.15 illustrates two possible alignments that are equally likely. In one alignment, the B allele (dark red) goes to the same pole as the A allele (dark blue), and, in the other alignment, the b allele (light red) goes in the same direction as the A allele. The first type of alignment results in a 1:1 ratio of AB : ab gametes, and the second type of alignment results in a 1:1 ratio of Ab : aB gametes. Because the two orientations are equally likely, the overall ratio of AB : ab : Ab : aB from a large number of cells undergoing meiosis is expected to be 1:1:1:1. This is the principle of independent assortment for genes located in different chromosomes.

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Not all genes undergo independent assortment. For example, genes that are sufficiently close together in one chromosome do not assort independently of one another. Genes in the same chromosome that fail to show independent assortment are said to be linked and are discussed in Chapter 17.