In the current study we explore at the regional level how selection for ethanol preference affects the transcriptome. The regions compared (nucleus accumbens shell [SH], central nucleus of the amygdala [CeA], and prelimbic cortex [PL]) are components of the addiction circuit (Koob and Volkow, 2010, 2016). A previous study (Dhaher et al., 2008) suggested that the CeA but not the SH has a more significant role in preference (2-bottle choice) consumption. The short-term selection of the High and Low ethanol preference lines from heterogeneous stock-collaborative cross (HS-CC) founders has been described elsewhere (Colville et al., 2017). After three generations of bidirectional selection, the difference in the ethanol preference ratio was 0.49 vs. 0.15 in the High and Low lines, respectively. Sixty-five percent of the High females and 37% of the High males had a preference ratio of >0.5 compared with 6.5% of the Low females and 2.3% of the Low males. The HS-CC founders (formed from five laboratory and three wild-derived strains) provide substantially more genetic diversity than would be available in F2 intercrosses or HS animals formed solely from
