Overview
C57BL/6J and C57BL/6N are two major substrains of C57BL/6 mice that diverged decades ago through separate breeding programs at Jackson Laboratory and NIH. Although >99% genetically identical, these substrains carry distinct genetic variants that produce measurable phenotypic differences in metabolism, behavior, and other traits. Understanding these differences is essential for experimental design, model selection, and research reproducibility.
Key Genetic Differences
C57BL/6J carries a spontaneous deletion in the Nnt (nicotinamide nucleotide transhydrogenase) gene affecting mitochondrial redox balance and glucose-stimulated insulin secretion. C57BL/6N retains intact Nnt but some colonies carry the rd8 mutation in Crb1 causing retinal degeneration. Additional single nucleotide polymorphisms exist between substrains, detectable by SNP panels.
Metabolic and Behavioral Phenotypes
C57BL/6J shows impaired glucose-stimulated insulin secretion and increased susceptibility to diet-induced obesity and glucose intolerance compared to C57BL/6N. Behavioral studies report subtle differences in anxiety-like behavior and activity levels. These phenotypic differences should be considered when interpreting experimental results or comparing across published studies.
Frequently Asked Questions
Which substrain should I use for metabolic studies?
C57BL/6N is generally preferred for metabolic studies due to intact Nnt and normal glucose-stimulated insulin secretion. The Nnt deletion in C57BL/6J can confound interpretation of metabolic phenotypes, particularly those involving pancreatic beta cell function, mitochondrial metabolism, or oxidative stress responses.
Are Cre driver lines available on both substrains?
Most tissue-specific Cre driver lines were originally generated on C57BL/6J background. However, many have been backcrossed to C57BL/6N or are available on both backgrounds. When crossing conditional alleles with Cre drivers, verify substrain compatibility or plan backcrossing to match backgrounds.
How do I convert my model from one substrain to the other?
Backcross your model to the desired substrain for at least 5 generations (N5) to achieve >97% genetic conversion, or 10 generations (N10) for >99.9% purity. Speed backcrossing using genome-wide SNP marker panels can accelerate this process while ensuring retention of your targeted allele.
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