Homologous recombination not only forms the basis for much of the genetic diversity among progeny of common parentage, but it is also essential for correct segregation of homologous chromosome pairs at the first meiotic division. When HR does not occur, homologous chromosomes are not held together and therefore segregate randomly at meiosis I, giving rise to meiotic products that are missing chromosomes or have extra copies of chromosomes. Such grossly aneuploid gametes are not functional. In somatic cells, HR is needed to repair double-strand breaks that arise from exogenous DNA damage sources such as x-rays and from endogenous sources such as defective DNA topoisomerases. Homologous recombination can also be used to repair single-stranded DNA gaps at replication forks. Homologous recombination can restart replication forks that have stalled at a lesion on the template DNA strand or can reinitiate a replication fork that has collapsed at a nick or other single strand interruption on the template DNA strand. Last, HR is needed to maintain telomeres, the specialized ends of chromosomes, when the enzyme telomerase that normally takes care of replicating telomeres is missing.

    In the early days of genetics after the work of Gregor Mendel was rediscovered, two observations led to the concept of linkage the idea that genes can be genetically and physically linked and hence will not segregate randomly from each other during the first division of meiosis.

    Reginald Punnett indicating that two sweet pea traits tended to segregate with each other more often than expected by random segregation. This phenomenon was called coupling. However linkage was not complete, and sometimes nonparental meiotic products or gametes were recovered, These were called nonparental or recombinant gametes and were the product of meiotic crossing over or recombination. The term crossing over was coined by Thomas Hunt Morgan. Morgan was the leader of a Drosopbita laboratory at Columbia University and made some of the most important contributions to genetics. Morgan was awarded the Nobel Prize for his work on genetics using Drosopbia. He suggested that crossing over occurred during meiosis when homologous chromosomes pair, and involves a physical exchange between the chromosomes. Morgan also proposed that the frequency of recombinant meiotic products resulting from exchange would be higher if genes were further apart. Later studies showed that genetic crossing over occurred by a physical exchange between chromosome pairs.