International Mammalian Genome Society

17th International Mouse Genome Conference

9-12 November 2003, Braunschweig, Germany


POSTER 23 - CONTRIBUTION OF JAPANESE WILD MICE, MUS MUSCULUS MOLOSSINUS, TO GENOME CONSTITUTION OF C57BL/6 STRAIN

Abe K
RIKEN BRC

Co-Authors: 2) Noguchi H. 3) Tagawa K. 1) Yuzuriha M. 2) Toyoda A. 2) Kojima T. 2) Hattori M. 2) Sakaki Y. 1) Moriwaki K. 2) 4) Shiroishi T
Institutions: 1) RIKEN BRC 2) RIKEN GSC 3) Kumamoto Univ. 4) National Inst. Genet

MSM/Ms is an inbred strain derived from Japanese wild mouse, Mus musculus molossinus, and shows high level of genetic polymorphisms against standard inbred strains. Thus, MSM/Ms represents useful resource for genetic analyses of various biological phenomena. We have constructed an arrayed BAC library from male MSM/Ms genomic DNA partially digested with EcoRI. The library comprised of 2x105 clones with an average insert of 125 kb, covering ~10X genome equivalent. This library can be screened by either colony filter hybridization or PCR of pooled BAC DNA. We have sequenced the ends of the BAC clone inserts and mapped end-sequence pairs onto the C57BL/6J genome (NCBI mouse Build 30). As of July/2003, 41,016 clones were unambiguously mapped, covering 1,977,198 kb or 79.1% of total genome. Comparison of the C57BL/6J and the MSM sequences revealed 253,840 putative SNPs in 28,820,855 bp sequenced (Phred >=30). Average frequency was estimated to be 89 SNPs per 10 kb. Distribution of these SNPs along the C57BL/6J genome is not uniform; long stretches of DNA (up to 12 Mb) are nearly devoid of SNPs, while other parts are highly rich in SNPs. The lower SNPs regions occupy ~5% of the C57BL/6J genome, and are likely to derive from the Asian subspecies, probably M.m. molossinus. The rate of contribution of Asian subspecies in C57BL/6J genome is much lower than the value of 20~30% reported by other group. The BAC library and the derived SNPs information will constitute valuable experimental resources for functional genomic studies including haplotype analysis.


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