A strain is congenic when it differs from a particular inbred
strain at a single locus as a result of backcrossing a particular
allele into the inbred strain. Congenic strains may also differ at
multiple loci that are closely linked to this different locus. Most
congenic strains differ at loci that are immunologically defined,
particularly the H-2 complexes in mice. Harlan produces several
such strains.
Congenic strains are used to investigate the biological
properties of the single different locus without the complications
that arise from differences at other loci. For example, C57BL/10
and DBA/2 mice differ at the H-2 complex and many other loci. A
comparison of strain differences provides little information on the
biology of H-2. However, C57BL/10 and B10.D2/n are two strains that
are identical at about 99% of their genome, but differ at the H-2
complex. Differences in the biological properties of these strains,
such as response to an infection, may be studied by focusing on the
H-2 complex.