Chromosomes (one set inherited from the mother and one from the father) pair up during sperm and egg cell formation. Recombination refers to the breaking and rejoining of paired chromosomes to form new molecules of DNA. This process is known as crossover. Crossovers result in the offspring inheriting a different and totally new combination of genes from those of their parents.
Following the movement of genes during crossovers can be very useful, because the frequency of breakages between two genes is directly related to their physical distance in a chromosome. Genes that are close together are less likely to be separated by recombination than genes further apart. Genes that are commonly inherited together are referred to as being linked.
Plant breeders have to deal with genetic linkage when they try to improve a plant variety. After crossing different plants to improve their performance they repeat many generations of backcrossing because along with the gene for the desired characteristic linked genes will be inherited as well.
The frequency of recombination can be used as an estimate of the distance between genes. Also, one gene in a linked pair can be used as a marker to infer the presence of another gene. This is the basis of the plant breeding technique known as Marker Assisted Selection (MAS).