TABLE 2.
SNPs associated with the reproductive performance phenotype
| Strain
|
D11Spn173– D11Spn129
|
Paternal allele
|
SNP
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | Referencea | |||
| BS | domesticus? | I | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | Wakasugi and Morita (1977) |
| NC | domesticus? | I | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | Wakasugi et al. (1967) |
| A | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| DBA/2 | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| BALB/c | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| C57BL6 | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| 129X1 | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| PERA | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| RBA | domesticus | I | C | T | T | A | T | T | G | G | G | A | G | A | This study |
| CBAb | domesticus | I | ND | ND | ND | ND | T | T | ND | G | G | A | G | ND | Mann (1986) |
| C3Hb | domesticus | I | ND | ND | ND | ND | T | T | G | G | G | A | G | A | Buehret al. (1987); Leclercet al. (1994); this study |
| KKb | domesticus | I | ND | ND | ND | ND | A | C | A | A | A | A | G | G | Wakasugi et al. (1967) |
| LEWES | domesticus | I | C | T | T | A | A | C | A | A | A | A | G | G | This study |
| PWKb | musculus | C | C | T | T | A | A | C | A | A | A | G | T | G | Jiri Forejt (personal communication) |
| SKIVE | musculus | C | C | T | T | A | A | C | A | A | A | G | T | G | This study |
| WSBb | domesticus | C | ND | ND | ND | ND | ND | ND | ND | ND | ND | G | T | G | This study |
| DDK | domesticus | C | A | A | C | G | del | del | del | del | del | G | T | G | This study |
| MOLC | castaneus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| PANCEVO | M. spicilegus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| CAST | castaneus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| TIRANO | domesticus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| ZALENDE | domesticus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| JF1 | castaneus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| PERC | domesticus | C | A | A | C | G | A | C | A | A | A | G | T | G | This study |
| MOM | molossinus | C | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | Zhao et al. (2002) |
| CASP | castaneus | C | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | Zhao et al. (2002) |
The table provides the strain name, phylogenetic origin of the haplotype in the candidate interval for the paternal gene defined by progeny testing and whether the allele at the paternal gene is incompatible (I) or compatible (C) with the maternal DDK factor. In addition, the table provides the allele present in each strain at each of the 12 SNPs with the highest level of association with the DDK syndrome phenotype. The alleles at the two SNPs that are most strongly associated with phenotype are underlined. The positions of the SNPs are as follows: 1, 82734817; 2, 82734820; 3, 82735318; 4, 82735343; 5, 82833126; 6, 82833146; 7, 82833386; 8, 82833571; 9, 82833572; 10, 82843176; 11, 82843476; 12, 82857766. The phylogenetic origin of the haplotypes in wild-derived strains is shown as reported previously (http://www.jax.org, Ideraabdullah et al. 2004). The phylogenetic origin of the haplotypes in hybrid strains and classical strains was determined on the basis of the diagnostic alleles shown in supplemental Table 3 at http://www.genetics.org.supplemental/. del, deletion.
References support the assigment of the paternal allele.
Additional strains used to test whether SNP-10 and SNP-11 predict the reproductive performance.