Most biological traits of adaptive significance, and the most common diseases, from a genetic point of view, are complex, quantitative phenotypes. In spite of intensive efforts, the genetic control of complex traits are not well understood because traditional human genetic studies could not overcome the difficulties presented by genetic heterogeneity, polygenic effects and interactions, uncontrollable developmental-environmental variability, etc.
The striking genomic similarity between humans and laboratory animal species (99% of the genes in humans have their counterparts in the mouse) is encouraging for using animal models to analyze complex traits. The Recombinant Quantitative Trait Locus Introgression (RQI) strain system was established to circumvent some of the above described difficulties, to facilitate mapping of Quantitative Trait Loci (QTLs), and to generate advanced quasi-congenic animal models.


B6vsC.pbase: a phenotype database
C57BL/6 and BALB/c are among the most often used inbred mouse strains. B6vsC.pbase is an ever growing collection of published complex trait differences between the two progenitor strains of the RQI strain set.

RQI.gbase: a genotype database
Genome scanning with about 350 microsatellite markers provided information about the distribution of BALB/c donor chromosome segments on C57BL/6 background in 100+ RQI strains. Genotyping to further increase the resolution of the genome scan is still in progress.

How to use the databases
The B6vsC.pbase and RQI.gbase datasets can be used in an interactive manner or individually. The possible uses include the following.

• If there is a B6vsC complex trait difference, phenotypic screening of RQI strains may identify quasi-congenic strains which significantly differ from the background partner C57BL/6 strain.
• If a QTL have been mapped in a C57BL/6 X BALB/c cross derived population, a search can identify a quasi-congenic strain with a BALB/c chromosome segment which harbors the mapped QTL. If the mapping results can be verified one can quickly proceed towards “positional cloning”.
• Haplotype pattern information on C57BL/6 and BALB/c is available in a haplotype pattern database, SNPview (www.gnf.org/SNP). After identifying a QTL harboring chromosome segment in an RQI strain it may no longer be necessary to initiate difficult high resolution mapping of a QTL. Comparison of SNPview with RQI.gbase can identify nonshared haplotypes which underlie phenotypic traits including disease susceptibility. This approach can reduce QTL intervals to sizes amenable to “positional cloning”.