A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2
A) Read depth in 100 bp windows, normalized by the genome-wide mean read depth for each strain, for R2d1, a 158 kb region within the 9.3 Mb candidate interval defined in Fig. 1. R2d1 includes a single (non-contiguous) copy of R2d. Strains are represented by the colors shown in the inset. Inbred strains included under the heading “classical” are A/J, 129S1/SvImJ, C57BL/6JN, NOD/ShiLtJ and NZO/HILtJ. The four large gaps represent LINEs that were inserted in the unique copy found in the reference genome after initial duplication. B) R2d copy number estimated by TaqMan assays for Cwc22. Normalized cycle threshold (ΔCt; see Methods) is proportional to absolute copy number on the log scale. Strains are colored as in panel A. The (M16ixL6)F2 samples shown are known to be homozygous for the M16i allele based on genotypes from the MegaMUGA array. C-F) The yellow boxes highlight the 158 kb region depicted in panel A (R2d1) and the 900 kb R2d2 locus mapping interval. Vertical dashed lines indicate the boundaries of the 9.3 Mb candidate interval. C) Locations of Ensembl genes in the NCBI/37 reference genome within the interval. The locations of the Cwc22 gene and of seven Cwc22 pseudogenes (Gm13695), are shown. D) Recombination frequency based on Liu et al. (2014), normalized by physical distance (Mb) and log10-transformed. The red line indicates the mean recombination frequency for Chr 2. E) Frequency distribution measured in 1 kb windows of SNPs with shared alleles among the three strains with TRD (WSB/EiJ, SPRET/EiJ and HR8; gray line), and with alleles perfectly consistent between strains with TRD and strains without TRD (A/J, 129S1/SvImJ, C57BL/6JN, NOD/ShiLtJ, NZO/HILt, CAST/EiJ and PWK/PhJ; red line). Lines are smoothed. Black circles indicate windows in which the strains with TRD share an allele for at least 90% of SNPs. F) Frequency distribution of reported SNPs in the candidate interval. G) The location and the number of copies of R2d that are present in R2d1 and R2d2.