We have examined by fine mapping the S1 nuclease-hypersensitivity of the 5' flanking regions of the human beta-globin and rat preproinsulin II genes and of the SV40 origin/enhancer region. In all cases S1-hypersensitive sites are located in known or presumed promoter/regulatory regions. Though a consensus DNA sequence is not evident, all of these sites reside in predominantly homopurine-homopyrimidine stretches. The alternate (non-B) DNA structure which is revealed by the enzymatic probe is a sequence-dependent feature of a short stretch of DNA, which is retained upon transplantation into a foreign environment. The alternate structure exhibits S1-nicking patterns uniquely different from those associated with the presence of Z-DNA.

Unlike simple Mendelian characteristics, individual differences in complex quantitative phenotypes studied in psychopharmacology are generally distributed continuously and are likely to be influenced by many genes. Recombinant inbred (RI) strains are valuable not only for their traditional use of detecting major gene segregation and linkage but also for identifying associations between quantitative traits and quantitative trait loci (QTL) that account for relatively small amounts of variation in phenotypes as well as loci that account for greater amounts of variation. When applied to published data on genetic markers and on amphetamine, alcohol, and morphine responses in BXD RI strains (RI strains developed from the cross between C57BL/6J and DBA/2J progenitor inbred strains), the RI QTL approach identified several significant associations beyond known major gene effects. Together, significant associations explain more than half of the genetic variance for these measures. The RI QTL approach is especially valuable for investigating the QTL underpinnings of genetic correlations among measures. It is recommended that psychopharmacogenetic research focus on the BXD RI strains. The cumulative and integrative nature of such a program of research is the major benefit of the RI QTL association approach for molecular genetic analysis of psychopharmacological processes, their physiological infrastructure, and their interface with other behavioral and biological systems.

Recombinant inbred (RI) strains are valuable not only for detecting major gene segregation and linkage but also for identifying associations between behavior and quantitative trait loci (QTL) that account for relatively small amounts of variation in behaviors for which strain distribution patterns are not bimodal. When applied to published data on genetic markers and on behavior for BXD RI strains, the RI QTL association approach suggests the presence of QTLs on chromosomes 6 and 12 for open-field activity and on chromosomes 1, 2, and 17 for high-pressure seizure susceptibility. Because the RI QTL approach does not require that the progenitor inbred strains of a particular RI series differ, researchers could focus on the BXD RI series, for which the greatest number of genetic markers are available. Focusing on BXD would capitalize on the cumulative nature of RI research which permits analyses of QTL sources of genetic correlations across studies.

The sac locus, with a major effect on saccharin preference, was discovered by Fuller (1974) in C57BL/6J (B6), DBA/2J (D2), and derived crosses, and is now supported in the BXD/Ty recombinant inbred (RI) series by a marked bimodal distribution in saccharin preference among 20 strains. The B6 allele led to increased saccharin preference compared to the D2 allele. Since the search for bimodal distributions reflecting major gene loci is an essential part of RI strain analysis, a new statistical method is proposed to test for bimodality, and comparisons are made to previously proposed methods. Another new RI method, quantitative trait loci (QTL) analysis, allows provisional detection and mapping of minor as well as major gene loci. Using this method as a screen, significant associations with saccharin preference were suggested with marker loci on portions of six chromosomes. One of these, the D12nyu1 locus on chromosome 12, was independently supported in a panel of standard (non-RI) inbred strains also tested for saccharin preference. It is unclear whether this reflects the sac locus.

The study of genetic influence on behavior has featured two general approaches. The first is to search for a single gene with influence sufficiently great as to be detectable against almost any genetic or environmental background. The second general approach is to apply the statistical models of quantitative genetics that partition variance of a continuously distributed phenotype into various fractions, attributable to the actions of many genes of individually small effect, and to the influence of environment. Recent developments in molecular genetics have provided tools for exploring a middle ground of genetic influence: genes whose effects are not overwhelming, but which account for appreciable proportions of the variance. These quantitative trait loci (QTL) offer attractive prospects of bridging the gap between molecular and quantitative genetic perspectives.