The International Complex Trait Consortium

Analysis of a tenth generation advanced intercross and a new set of ~45 derivative BXD recombinant inbred strains

Lu Lu1, Jing Gu1, Shuhua Qi1, David C. Airey2, Glenn D. Rosen3, Jeremy Peirce4, Robert W. Williams1, Guomin Zhou5

1Center for Neuroscience and Department of Anatomy and Neurobiology, University of Tennessee, Memphis, TN 38163
2Center of Genomics and Bioinformatics, University of Tennessee
3Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA 02215
4Department of Molecular Biology, Princeton University, Princeton, NJ 08544
5Medical Center of Fudan University, Shanghai, P.R.China

ABSTRACT
 
We have generated a set of 1500 tenth-generation advanced intercross progeny from reciprocal F1 crosses between C57BL/6J and DBA/2J. Animals were bred so as to minimize inbreeding in each generation using the Silver-Peirce modification of the original breeding scheme advanced by Ariel Darvasi. Approximately 20 to 30 cages were maintained per generation. Multiple litters were generated from single breeding pairs to produce the generation of G10 animals. Genomic DNA from all cases (n = 1547) was typed at ~340 markers by the Mammalian Genotyping Service. Complex trait analysis exploiting this mapping panel has very high power and approximately 3-4X the positional precision of a standard B6D2F2 intercross. For example, the genetic map of Chr 1 is approximately 390 cM long as compared to ~110 cM in an F2 intercross.

The majority of animals (n = 1300) were sacrificed at about 60 ▒ 10 days. The remaining 240+ cases were aged through to 600 to 750 days prior to sacrifice. Animals were perfused transcardially with 4% paraformaldehyde or with mixed aldehydes for electron microscopy. Brains and eyes were dissected, weighed, and processed as part of the Mouse Brain Library project. Histological images of over 400 of these cases are currently available online at www.mbl.org. The remainder of all bodies of these mice have been archived in 50 ml conical tubes at 4 íC. Tissue are available upon request and we encourage investigators to make use of this G10 tissue bank.

We initially have mapped coat color loci segregating in this cross to confirm the alignment of genotype assignment and case number using Map Manager QT and QTX. When coat color is scored as a "quantitative" trait, the LOD score at the Tyrp1 coat color on Chr 4 locus reaches a high of 210. The corresponding LOD score at Myo7a (dilute locus) is ~45. Analysis of conventional polymorphic quantitative traits such as brain and eye weight also give high LOD scores and excellent precision. Three brain weight QTLs on chromosomes 2, 5, and 9 have LOD scores between 20 and 30. 2-LOD confidence intervals are approximately 2-5 cM normalized to an F2 map. For example, the brain size control locus, Bsc9a, maps between D9Mit192 (26 cM) and D9Mit229 (28 cM).

To extend the utility of this advanced intercross and to make it a more permanent resource, we have generated a large set of recombinant inbred strains from the G8 through G14 offspring. Twenty lines were generated by Jeremy Peirce and Lee Silver (Princeton University). These lines have been red rived into a pathogen-free colony and are now at the 15th generation of inbreeding. An additional ~25 lines were generated at UTHSC (Lu et al.) from the same G10 animals described above. These lines are now at the 8th to the 12th generations of inbreeding.

[Please contact Dr. Lu at lulu@nb.utmem.edu regarding use of the tissue collection. We thank the Mammalian Genotyping Service and NHLBI for providing us with ~500,000 genotypes. The Mouse Brain Library and the Informatics Center for Mouse Neurogenetics is supported by the Human Brain Project (NIMH MH62009)]