Chromosome 1 Sequence Analysis of C57BL/6J-Chr1 KM Mouse Strain

摘要

The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear.In this study, we sequenced the genome of the C57BL/6J-Chr1 KM (B6-Chr1 KM ) strain, the chromosome 1 (Chr 1) of which wasderived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms(SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 ofthem were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functionalvariants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesianconcordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus,M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1 KM was predominantlyderived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysisprovided a detailed description of the genetic variations on Chr 1 of B6-Chr1 KM and a new perspective on the subspecies originof KM mouse which can be used to guide further genetic studies with this mouse strain.