Introduction To RQI Genetics. 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. (click here to read more) B6vsC.pbase: a phenotype database C57BL/6J (B6) and BALB/cJ (C), and their various sublines, are among the most often used inbred mouse strains. B6vsC.pbase is an ever growing collection of published complex trait differences between B6, C, and their sublines. The progenitor strains of the quasi-congenic RQI strain set include C57BL/6By and BALB/cJ. RQI.gbase: a genotype database Genome scanning with 400 microsatellite markers provided information about the distribution of BALB/cJ donor chromosome segments on C57BL/6By 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 complex trait difference between B6 and C, phenotypic screening of RQI strains can identify quasi-congenic strains which significantly differ from the background partner. Quasi-congenic strains can give rise to F2 and backcross populations, in which genes segregate on a homogeneous genetic background. The homogeneous genetic background results in lower genetic "noise" in the segregating populations providing a powerful tool for high-resolution mapping and identification of interactions. Also, with marker assisted selection a series of "subcongenics" can be developed for rapid mapping and mechanism oriented work. If a QTL has 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 with the RQI strains, one can quickly proceed towards "positional cloning". SNP and haplotype pattern information on C57BL/6 and BALB/c is available, for example, in dbSNP, www.ncbi.nlm.nih.gov/SNP, Mouse Genome Informatics database, www.jax.org/phenome/, and SNPview, www.gnf.org/SNP. After identifying a QTL harboring chromosome segment in an RQI strain one can initiate high resolution mapping of a QTL. Comparison of SNP distribution patterns with RQI.gbase may identify nonshared regions which underlie phenotypic traits including disease susceptibility. The B6.C RQI strains are of bilineal origin: This design feature eliminates complications in mapping caused by segregation of multiple alleles on heterogeneous genetic background derived from multiple progenitor strains. The RQI approach in combination with the increasing availability of genomic sequence data for C57BL/6 and BALB/c can reduce QTL intervals to sizes amenable to "positional cloning".