In each of the examples discussed in the dihybrid crosses portion of this lecture, the genes looked at were on different chromosomes. A chromosome, however, contains numerous genes. It is possible that one might decide to follow the segregation of to genes only to discover that they were on the same chromosome. Crossing experiments rather than generating offspring according to the Mendelian predicted ratios, would show these traits moving as one or would indicating their separating at a much lower than predicted ratio.
Linked genes do sometimes separate.
Remember that in the first prophase of meiosis the homologous chromosomes synapse. During this period of close association and intertwining, breaks in the chromatid backbones may occur. The repair mechanism will activate to reattach the breaks. Since, however, maternal and fraternal like chromatids are so intertwined, the reattachment may accidentally involve reattaching a break point in the maternal chromatid to the corresponding break point in the fraternal chromatid. This recombining of the alleles introduces more variety into the offspring possibilities without risking introducing untried information.