Congenic strains are produced by repeated backcrosses to an inbred (background) strain, with selection for a particular marker from the donor strain (Snell 1978, Flaherty 1981).
A strain developed by this method is regarded as congenic when a minimum of 10 backcross generations to the background strain have been made, counting the first hybrid or F1 generation as generation 1. At this point the residual amount of unlinked donor genome in the strain is likely to be less than 0.01.
Marker assisted breeding or marker assisted selection breeding, also known as "speed congenics" permits the production of congenic strains equivalent to 10 backcross generations in as few as five generations (Markel et al., 1997; Wakeland et al., 1997). Provided that the appropriate marker selection has been used, these are termed congenic strains if the donor strain contribution unlinked to the selected locus or chromosomal region is less than 0.01. Ideally, descriptions of speed congenic strains in first publications thereof should include the number and genomic spacing of markers used to define the congenicity of the strain. Because speed congenics depend upon thorough marker analysis and can vary by experimental protocol, the inbred status of speed congenics should be regarded with caution.
Source: Jackson Lab