The paternal gene of the DDK syndrome maps to the Schlafen gene cluster on mouse chromosome 11

Abstract

The DDK syndrome is an early embryonic lethal phenotype observed in crosses between females of the DDK inbred mouse strain and many non-DDK males. Lethality results from an incompatibility between a maternal DDK factor and a non-DDK paternal gene, both of which have been mapped to the Ovum mutant (Om) locus on mouse chromosome 11. Here we define a 465-kb candidate interval for the paternal gene by recombinant progeny testing. To further refine the candidate interval we determined whether males from 17 classical and wild-derived inbred strains are interfertile with DDK females. We conclude that the incompatible paternal allele arose in the Mus musculus domesticus lineage and that incompatible strains should share a common haplotype spanning the paternal gene. We tested for association between paternal allele compatibility/incompatibility and 167 genetic variants located in the candidate interval. Two diallelic SNPs, located in the Schlafen gene cluster, are completely predictive of the polar-lethal phenotype. These SNPs also predict the compatible or incompatible status of males of five additional strains.

Figure 1.

Mapping by recombinant progeny testing in C57BL/6–DDK background. The reproductive performances of 40 males were used to map the paternal gene in the candidate interval defined previously (Baldacci et al.1992, 1996). The original interval was divided into six smaller intervals based on the presence of five recombinant chromosomes. The markers shown in the bottom of section b convey the complete genotypic information (supplemental Table 2 at http://www.genetics.org/supplemental/). In sections a and b the horizontal axes show distance in Mbp from the centromere of chromosome 11. The vertical axes show the statistical significance of the association findings. Triangles show the results using the entire set of 40 males. Open circles show the results for the 22 males carrying nonrecombinant chromosomes in the D11Mit33–D11Mit35 interval. Filled circles show the results in the 18 males carrying recombinant chromosomes in the D11Mit3–D11Mit35 interval (the inset in the bottom right shows this information visually). (a) The top plot shows the strength of the associations between genotype and litter size using the Fdistribution to assess the statistical significance of the mixed models. (b) The bottom plot shows the strength of the association between genotype and litter size using permutation tests to assess the statistical significance of the mixed models. Empirical results for the 22 nonrecombinant males and for the regions containing markers D11Spn173 and D11Spn178 among the 18 recombinant males were determined exactly. The statistical significance when analyzing all 40 males for the regions containing marker D11Mit33 (P = 0.045) was estimated using a permutation test while the statistical significance for D11Spn173 (P = 1.3 × 10⁻¹⁵) and D11Spn178 (P = 3.4 × 10⁻¹⁶) were calculated exactly (data not shown). It was not feasible to calculate the empirical statistical significance for the other regions (P < 1.0 × 10⁻⁵) using all 40 males. The statistical significance of the findings in these other regions were beyond the resolution of 100,000 random replications of the data and there were too many permutations of the data that would yield a more extreme value than the observed F-statistics to make it possible to determine the empirical significance exactly. (c) Circles represent the average litter size in males with the three possible genotypes in the D11Spn178–D11Spn128. The horizontal bars show the boundaries of the 99% confidence intervals.

Figure 2.

Transmission ratio of paternal haplotypes in the Om region to the progeny of sires with critical recombinant chromosomes. The haplotypes in the vicinity of Om of the two males, 115AA and 735L, that carry recombinant chromosomes between D11Spn173 and D11Spn178, and the number of offspring inheriting each paternal haplotype are shown. The figure also provides the level of significance for each interval using the chi-square test statistics under the null hypotheses of equal transmission of alleles in the progeny of homozygous males for that interval and 66% transmission of the DDK allele in the progeny of heterozygous males for that interval (Pardo-Manuel de Villena et al. 2000b). n.s., not significant.

Figure 3.

Reproductive performance of males from different inbred strains. The vertical axis represents the average litter size observed in crosses between (C57BL/6 × DDK)F₁ females and males from the inbred strain listed in the horizontal axis. Circles denote the strains used for in silico mapping and squares are the strains used to confirm the presence of complete linkage disequilibrium between the phenotype and selected SNPs (see text). The horizontal bars show the boundaries of the 99% confidence intervals adjusted for the correlation between litters from the same sire. Correction factors were applied to determine the reproductive performance of the underlined strains (see materials and methods).

Figure 4.

In silico mapping. The association between the reproductive performance of males from the 17 inbred strains analyzed in Figure 3 and 167 diallelic variants distributed across the candidate interval defined by progeny testing is shown. Variants are shown as triangles and the position along the horizontal axis refers to the distance in megabasepairs from the centromere of chromosome 11. The vertical axes show the statistical significance of the association results while the dashed vertical lines denote the proximal and distal boundaries of the candidate interval. In some cases multiple variants with the same degree of association appear as a single triangle. The top plot shows the strength of the associations between genotype and litter size using the Fdistribution to assess the statistical significance of the nested-mixed models. The bottom plot shows the strength of the association between genotype and litter size using permutation tests to assess the statistical significance of our findings. The empirical significance estimates for the SNPs on the figure with the four most significant findings were determined exactly.

Figure 5.

Rapid evolution of the Schlafen gene cluster in mouse. The three bars shown at the top of the figure represent the candidate intervals defined by recombinant progeny testing (1), in silico mapping (2), and haplotype block in complete linkage disequilibrium with the DDK syndrome phenotype (3). The 26 fragments sequenced are shown as vertical bars directly underneath. Stars denote the four fragments containing the 12 variants most strongly associated with the phenotype. The larger star indicates the fragment containing the two variants that are in complete linkage disequilibrium with the DDK syndrome phenotype. Genes are shown as black arrows. Vertical axes provide distance in Mbp from the centromere in the appropriate chromosome. (a) Dot plot matrix comparing the candidate interval in the mouse against itself. (b) Dot plot matrix comparing the mouse candidate interval (horizontal axis) and the homologous region in rat (vertical axis). Each dot in the matrixes denotes an orthogonal 99 bp region with fewer than 10 mismatches. Consecutive dots form diagonal lines in regions of extended identity/similarity. For any given region on the horizontal or vertical axes the presence of multiple parallel diagonal lines denotes duplicated regions. Short scattered lines are for most part indicative of repetitive elements scattered across the region.

Figure 6.

Phylogenetic relationships of inbred strains in the 128 kb interval defined by in silico mapping. The tree depicted in the figure is a consensus cladogram from three consensus trees obtained by three different phylogenetic methods (materials and methods). Circles denote branches that are consistent among the three trees and the numbers in the circles represent the number of times out of 100 that the branch is observed in each method: top, DNAML; middle, NEIGHBOR; and bottom, DNAPARS. Underlined strains have M. m. domesticus haplotypes in that region. Strains in boldface and italics are derived from other species (SPRET, M. spretus and PANCEVO, M. spicilegus). Asterisks denote strains with incompatible alleles at the paternal gene. All incompatible strains are shown diverging from a single node because the internal branching order within this lineage is not consistent among trees obtained by different methods and the branching order is poorly supported within each method. The length of the branches is arbitrary.