Highly polymorphic copy number variation in a segmental duplication in the mouse pseudoautosomal region even within...

Inbred laboratory mice, such as the C57BL/6J strain, are presumed to be genetically uniform and are used in medical and biological research. Here, we report a substantial copy number variation (CNV) in a segmental duplication (SD) in the mouse pseudoautosomal region (PAR), which challenges the widely accepted assumption. The PAR consists of an identical sequence shared by the X and Y chromosomes at their distal ends, enabling proper pairing and recombination during meiosis. The copy number in C57BL/6J mice ranged from 4 to 27 per diploid genome. The mean (± standard deviation) was 12.9 ± 4.8. We found that de novo CNV emerged in nearly every spermatogenesis meiosis. The presence of CNV in the SD has also been detected in other classical inbred mouse strains. Each copy of the SD contains the Erdr1 gene. A correlation was observed between copy number and Erdr1 expression levels in males, and there was a significant negative correlation between expression level and body weight.