A chromosome substitution or consomic strain is an inbred strain with one of its chromosomes replaced by the homologous chromosome of another inbred strain. The C57BL/6J and A/J strains in this set were chosen because they differ in their susceptibility to diseases such as arthritis, asthma, atherosclerosis, cancer, several infectious diseases, inflammatory responses, and physiological, behavioral and sensory phenotypes. Chromosome substitution strain nomenclature is designated as Host Strain - Chromosome #<Donor Strain>/Laboratory code. For example, C57BL/6J-Chr1^A/NaJ carries chromosome 1 for strain A/J (A) on a C57BL/6J background, was constructed in the laboratory of Joseph Nadeau (Na) and is maintained at The Jackson Laboratory (J). Chromosome substitution strains or consomic strains can accelerate quantitative trait loci identification and mapping.

Dr. Joseph Nadeau from Case Western Reserve University developed the C57BL/6J-Chr #^A/NaJ strain set by replacing individual chromosomes from the A/J donor strain into the C57BL/6J host strain using a marker-assisted series of backcrosses (Nadeau et al., 2000). The set was donated to The Jackson Laboratory in 2004.