This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).

The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.

The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.

Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:

• genetic and phenotypic diversity, including use by the Phenome Project
• their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
• their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
• genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
• availability from The Jackson Laboratory

All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.

1. 129S1/SvImJ
       Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
2. A/J
       Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
3. AKR/J
       Sequenced by NIEHS; Phenome Project B list
4. BALB/cByJ
       STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
5. BALB/cJ
       Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
6. C3H/HeJ
       Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
7. C57BL/6J
       Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
8. C57BL/6ByJ
       Paternal substrain of B6 used to generate the CXB panel
9. CAST/Ei
       Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
10. DBA/2J
        Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
11. KK/HIJ
        Sequenced by Perlegen/NIEHS
12. LG/J
        Paternal parent of the LGXSM panel
13. NOD/LtJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
14. NZO/HILtJ
        Collaborative Cross strain
15. PWD/PhJ
        Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
16. PWK/PhJ
        Collaborative Cross strain; Phenome Project D list
17. WSB/EiJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
18. B6D2F1 and D2B6F1
    F1 hybrids generated by crossing C57BL/6J with DBA/2J

We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.

These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.