We used a set of 55 BXD recombinant inbred strains, 14 conventional inbred strains including C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1s. BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D2). Physical maps in WebQTL incorporate approximately 2 million B6 vs D2 SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.

Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.

BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.

Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 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 (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) have been included in the MDP. Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS.

1. 129S1/SvImJ
       Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
2. A/J
       Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
3. BALB/cByJ
        Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
4. C3H/HeJ
       Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
5. C57BL/6J
       Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
6. CAST/Ei
       Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
7. DBA/2J
       Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
8. KK/HlJ
       Sequenced by Perlegen/NIEHS
9. LG/J
       Paternal parent of the LGXSM panel
10. NOD/LtJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
11. NZO/HlLtJ
        Collaborative Cross strain
12. PWD/PhJ
        Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
13. PWK/PhJ
        Collaborative Cross strain; Phenome Project D list
14. WSB/EiJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
15. B6D2F1 and D2B6F1, aka F1 in some graphs and tables
    F1 hybrids generated by crossing C57BL/6J with DBA/2J. These reciprocal F1 can be used to detect some imprinted genes.