Alcohol "sensitivity" has been proposed as a predictive factor for development of alcohol dependence (Schuckit et al., 2005). Most measures of alcohol sensitivity in humans and animals include a component that can be ascribed to acute functional tolerance (AFT). AFT is a form of tolerance that develops within a single period of alcohol exposure and has a genetic component. We used microarray technology as well as quantitative trait locus analysis of phenotypic and gene expression data across 30 BXD recombinant inbred strains of mice, 20 inbred strains of mice, and two replicate lines of mice selectively bred for differences in AFT, to identify differentially expressed candidate genes that contribute to predisposition to AFT. Eight candidate genes were identified by our statistical and filtering methods. The location of brain expression of these genes was mapped using the Allen Brain Atlas (http://www.brainmap.org), and the transcript location and molecular pathway analysis indicated that brain structures and biochemical pathways implicated in long-term potentiation and memory might also participate in the generation of acute functional alcohol tolerance.The term ethanol (alcohol) tolerance refers to a decreased behavioral response to a given dose of alcohol after prior experience with alcohol or the need for a greater dose of ethanol to produce a given level of effect. Alcohol tolerance is an important diagnostic criterion for alcohol dependence in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) (American Psychiatric Association, 1994).Functional (pharmacodynamic) alcohol tolerance manifests itself in three different forms: chronic (Tabakoff et al., 1986), rapid (Khanna et al., 2002), or acute (Mellanby, 1919. Acute functional tolerance (AFT) refers to the tolerance that is manifested during a single session of alcohol drinking (Mellanby, 1919), and it can start to develop within minutes after an individual starts to imbibe alcohol. The phenomenon of AFT was initially described by Mellanby (1919) through experiments that showed that humans display a greater degree of intoxication at a given blood alcohol concentration on the rising phase of the blood alcohol curve than at the same alcohol concentration on the falling phase of the blood alcohol curve. Acute functional alcohol tolerance is a neuronal resistance to alcohol effects (Tabakoff et al., 1986); however, its molecular mechanism is still not well characterized.Sons of alcoholics (SOA) are three to five times more likely to develop alcohol dependence than sons of nonalcoholics (Cotton, 1979). SOA also display less alcohol intoxication when measurements are made at least 1 h after drinking alcohol. The low level of response to alcohol has been found to predict future alcohol dependence (Schuckit et al., 2005), and both men and women with no prior history of alcohol dependence, but with a positive family history of alcohol dependence, display a lower response to alcohol than those with no family history of alcohol dependence (Schuck...