Strain Selection
Strains used for SNP discovery
To maximize the amount of useful information generated by this study, we chose 15 strains based on the following criteria:- Maximization of genetic and phenotypic diversity
- Ease of breeding, to enable follow-up studies
- Inclusion in the Mouse Phenome Project, an international program which aims to make a comprehensive database of inbred mouse strain phenotypes available to the public
- Widespread use in the research community
- Availability of considerable background information
The strains selected fall into three groups:
- Common inbred lines
- Strains chosen to further maximize genetic diversity
- Inbred lines derived from the major taxonomic groups that gave rise to the common laboratory mouse lines
| Common Strains1 | Strains maximizing genetic diversity |
Strains derived from the major taxonomic groups |
|---|---|---|
| 129S1/SvImJ | BTBR T+ tf/J2 | CAST/EiJ (M. m. castaneus) |
| A/J | KK/HlJ3 | MOLF/EiJ (M. m. molossinus) |
| AKR/J | NZW/LacJ4 | PWD/PhJ (M. m. musculus) |
| BALB/cByJ | WSB/EiJ (M. m. domesticus) | |
| C3H/HeJ | ||
| DBA/2J | ||
| FVB/NJ | ||
| NOD/LtJ |
publicly available, account for over 85% of all inbred strain usage in research.
2 BTBR T+ tf/J is a genetically diverse strain of special interest to those
detecting and studying behavioral abnormalities.
3 KK/HlJ was chosen for its distant relationship to other inbred strains.
4 NZW/LacJ was chosen for its importance in understanding immune
phenomena underlying multiple pathologies.
These 15 mouse strains were resequenced using the array-based resequencing technology. Multiple individual mice, all of which were males, were used for each strain. By coordinating with Dr. Molly Bogue, Director of the Mouse Phenome Project at the Jackson Laboratories, we used DNA from pedigreed foundation stock animals, which have detailed breeding records available.
Strains used for Genotype Imputation
For an additional 40 strains we used empirically-derived genotypes for approximately 150,000 SNPs to impute genotypes for the additional ~ 8.27 million SNPs analyzed in this study. The 40 strains are listed below, along with their Jackson Laboratories (JAX) stock numbers.
|
STRAIN |
JAX STOCK # |
|
129T2/SvEms
|
2065 |
|
129X1/SvJ |
691 |
|
BPH/2J |
3005 |
|
BPL/1J |
3006 |
|
BPN/3J
|
3004 |
|
BUB/BnJ |
653 |
|
C57BLKS/J |
662 |
|
C57BR/cdJ |
667 |
|
C57L/J |
668 |
|
C58/J |
669 |
|
CBA/J |
656 |
|
CE/J |
657 |
|
CZECHII/EiJ |
1144 |
|
DBA/1J |
670 |
|
DDY/JclSidSeyFrkJ |
2243 |
|
I/LnJ |
674 |
|
JF1/Ms |
3720 |
|
LG/J |
675 |
|
LP/J |
676 |
|
MA/MyJ |
677 |
|
MOLG/DnJ
|
555 |
|
MRL/MpJ |
486 |
|
MSM/Ms |
3719 |
|
NON/ShiLtJ |
2423 |
|
NZB/BlNJ |
684 |
|
NZL/LtJ |
5067 |
|
NZO/HlLtJ |
2105 |
|
PERA/EiJ |
930 |
|
PERC/EiJ |
1307 |
|
PL/J |
680 |
|
PWK/PhJ |
3715 |
|
RBA/DnJ |
874 |
|
RIIIS/J |
683 |
|
SEA/GnJ se/se |
644 |
|
SJL/J |
686 |
|
SM/J |
687 |
|
SOD1/EiJ |
1224 |
|
SPRET/EiJ |
1146 |
|
SWR/J |
689 |
|
TALLYHO/JngJ |
5314 |