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We have been using the Inbred Long- and Short-Sleep mouse strains (ILS, ISS) and a recombinant inbred panel derived from them, the LXS, to investigate the genetic underpinnings of acute ethanol tolerance which is considered to be a risk factor for alcohol use disorders (AUDs). Here, we have used RNA-seq to examine the transcriptome of whole brain in 40 of the LXS strains 8 hours after a saline or ethanol "pretreatment" as in previous behavioral studies. Approximately 1/3 of the 14,184 expressed genes were significantly heritable and many were unique to the pretreatment. Several thousand cis- and trans-eQTLs were mapped; a portion of these also were unique to pretreatment. Ethanol pretreatment caused differential expression (DE) of 1,230 genes. Gene Ontology (GO) enrichment analysis suggested involvement in numerous biological processes including astrocyte differentiation, histone acetylation, mRNA splicing, and neuron projection development. Genetic correlation analysis identified hundreds of genes that were correlated to the behaviors. GO analysis indicated that these genes are involved in gene expression, chromosome organization, and protein transport, among others. The expression profiles of the DE genes and genes correlated to AFT in the ethanol pretreatment group (AFT-Et) were found to be similar to profiles of HDAC inhibitors. Hdac1, a cis-regulated gene that is located at the peak of a previously mapped QTL for AFT-Et, was correlated to 437 genes, most of which were also correlated to AFT-Et. GO analysis of these genes identified several enriched biological process terms including neuron-neuron synaptic transmission and potassium transport. In summary, the results suggest widespread genetic effects on gene expression, including effects that are pretreatment-specific. A number of candidate genes and biological functions were identified that could be mediating the behavioral responses. The most prominent of these was Hdac1 which may be regulating genes associated with glutamatergic signaling and potassium conductance.

This study evaluated the use of short-scrotum castration to create sterile ram lambs. East Friesian x Lacaune male lambs born in February on a commercial sheep dairy were left intact (n = 19; IN) or rendered short-scrotum (n = 17; SS) within 10 d of birth. At 3 mo of age lambs were transferred to the study site and grazed as one group, while being supplemented with a grain mixture at 0.7 kg/d. Lambs were harvested at 6 mo of age, and reproductive tract of 5 IN and 5 SS lambs collected at random and shipped cold overnight for processing. Testis and epididymis were weighed. Segments of the left testis and epididymis were processed for histology, while a subsample of testicular parenchyma and epididymal segments of the right side were used to determine sperm reserves by tissue homogenization. Differences between testis types were determined using GLM of SAS. Testes and epididymal weights were reduced (P < 0.001) in SS (115 and 22 g) compared to IN (364 and 50 g) lambs. Seminiferous tubule diameter was also smaller (P < 0.001) in SS (142 µm) than IN (234 µm) lambs. Daily sperm production per gram testicular parenchyma (DSPG) was not different between types (3.8 vs. 2.3 million sperm/g; P = 0.06), but total daily sperm production was lower (P < 0.01) in SS (0.23 billion) than IN (1.34 billion) ram lambs. Considerable variation was noted in DSPG in IN lambs suggesting still incomplete development at this age, and accounting for the lack of a significant difference. Epididymal sperm reserves were markedly reduced (P < 0.001) in SS (0.1 billion) compared to IN (10.5 billion), and decreased along the epididymis, supported by evidence of phagocytic action by the epididymal epithelium. Data suggest that ram lambs rendered short-scrotum shortly after birth develop smaller testes with reduced sperm production, making them effectively infertile.

Short-scrotum (induced cryptorchid) rams can retain growth and performance characteristics of intact-rams while making them sterile and facilitating co-grazing with ewe-lambs. East Friesian x Lacaune male lambs left intact (n = 19; IN), rendered short-scrotum (n = 17; SS) or neutered (n = 25; WE) by 10 d of age, were used to evaluate libido and semen quality at 7-mo old. Lambs were managed as one group on a forage-based diet supplemented with a grain mixture (barley and soybean meal at 0.7 kg/d). Four CIDR-treated estrus-induced ewes were placed two/pen in adjacent 2.5x2.5 m pens for libido testing. Males were introduced individually to ewe pens for 5 min and reproductive behaviors recorded (anogenital sniffs, foreleg kicks, flehmen, false mounts, and service). Semen was collected from 6 random IN and SS lambs via artificial vaginas using estrus-induced ewes as teasers. Volume was recorded, and ejaculate extended in milk/egg yolk, packaged into straws, and stored at 5°C for analysis with a CASA system the following day. Behavior measurements were compared between types using PROC GLM. Ejaculate characteristics are presented as mean±SD due to insufficient sperm concentrations of SS ejaculates. Anogential sniffs, foreleg kicks, and mounts were similar in IN and SS, and higher (P < 0.05) than in WE (7.44 and 6.34 vs. 4.76; 1.72 and 1.60 vs. 0.17; 1.78 and 2.05 vs. 0.22; respectively). Number of services were higher (P < 0.001) in IN than SS (1.11 vs. 0.53), but time to service (112 sec) was not different. Ejaculate volume was similar in IN and SS (0.51 mL), but SS ejaculates were essentially devoid of sperm. Ejaculates from IN lambs had 0.69x109±0.48 x109 sperm, with 68.9±12.5% progressive motility, 81.8±6.1% viability and 87.1±6.1% morphologic normality. Ram lambs rendered short-scrotum by 10 d of age had reproductive behavior similar to intact post-pubertal rams, but ejaculate characteristics showed them to be sterile

This was the second year of a study comparing the growth and carcass characteristics of (intact) ram, wether, and short-scrotum lambs from a commercial sheep dairy in Maryland. East Friesian x Lacaune lambs were left intact (RAM, n = 21), castrated (WETHER, n = 25), or made short-scrotum (SS, n = 18). All banding of WETHER and SS lambs was done by d 10. When the lambs averaged 65±17 d and 44.5±10.6 lbs., they were transported to the Western Maryland Research & Education Center, where they grazed cool season pastures and were supplemented with grain (3 lb/d) for 107 d, before being harvested to collect carcass data. Data were analyzed using the MIXED procedure of SAS, with statistical significance set at P ≤ 0.05. Fixed effects included sex and birth type; starting weight was included as a covariate. There was an effect of birth type on final BW, ADG, HCW, CCW, and body wall thickness (BWT), favoring twin-born lambs. RAM and SS lambs had heavier final BW (P < 0.0001) and ADG (P < 0.0001) than WETHER lambs. RAM lambs had heavier hot (P < 0.01) and cold carcass (P < 0.005) weights than WETHER lambs; SS lambs were intermediate. Dressing percentage was higher (P < 0.004) for WETHER lambs and similar for RAM and SS lambs. RAM and SS lambs had larger REA than WETHER lambs (P < 0.03), but not when adjusted to a common weight (P < 0.71). WETHER lambs produced the fattest carcasses, as evidenced by greater BF (3.8±0.2 mm) than RAM and SS lambs (2.2±0.2 mm and 2.7±0.2 mm, respectively). Sex did not influence BWT, KPH, or leg conformation score. RAM lambs yielded a higher percentage of BCTRC (49.9±0.2%) than WETHER lambs (49.1±0.2%); SS lambs were intermediate (49.6±0.3%). For the second year in a row, RAM and SS lambs demonstrated superior growth and carcass composition compared to WETHER lambs.

Gastro-intestinal parasites, especially Haemonchus contortus, limit the profitability and expansion of the meat goat industry in many states. The objective of the Western MD Pasture Based Meat Goat Production test was to evaluate the performance of meat goat bucklings (mostly Kiko and Kiko crosses), consuming a pasture-based diet, with natural exposure to gastro-intestinal parasites. From 2006–2016, the FAMACHA© system was used to determine need for deworming (scores of 4 and 5) in all kids. Therefore, goats were handled bi-weekly to determine body weights (BW), FAMACHA© scores (FAM) and fecal egg counts (FEC) in eggs per gram (epg), as well as other possible indicators of internal parasitism. Adjacent FAMACHA© scores were used to form 3 groups; kids not requiring treatment (FAM1; FAM 1 and 2), kids intermediate (FAM 3) and kids requiring treatment (FAM 5; FAM 4 and 5). Differences in mean log-transformed FEC (LFEC) and ADG were determined using the PROC MIXED procedure of SAS and included year, FAMACHA© score and FAMACHA© score by year interaction effects. There was an exponential increase in LFEC and decrease in ADG with increasing FAM score groups for most years of the test. LFEC were significantly different for FAM1, FAM3, and FAM5 groups (P

A pasture-based meat goat performance test was conducted at the University of Maryland’s Western Maryland Research & Education Center (39º 30’ N/77º 44’ W) from 2007–2016. The purpose of the test was to evaluate the performance of meat goat bucklings (mostly Kiko and Kiko crosses), consuming a pasture-based diet, with natural exposure to gastro-intestinal parasites. While on test, the goats were handled bi-weekly to determine body weights (BW), FAMACHA© scores (FAM) and body condition (BCS) scores. Coat condition (COAT), dag (DAG) and diarrhea scores (DISCO) and deworming frequency (TX) were also recorded from 2012–2016. Fecal samples were collected bi-weekly to determine individual fecal eggs counts (FEC; 2007–2016) and pooled samples were collected every 28 days for larvae ID (2009–2016). Data came from 811 meat goat kids representing 100 herds in 20 states. Residual correlations among log-transformed FEC (LFEC), FAMACHA© scores, BW, ADG, BCS, coat condition, dag and fecal consistency scores were determined. In addition, deworming frequency by year was determined by PROC FREQ in SAS. The predominant genera of gastrointestinal nematode cultured was Haemonchus contortus ranging from 70–95% over the 10-yrs. Overall, residual correlations (r) of FAMACHA scores with ADG (-0.15), LFEC (0.24), BCS (-0.09), COAT (-0.06), DAG (0.12) and DISCO (0.04) were significant (P

Background We previously reported that acute functional tolerance (AFT) to the hypnotic effects of alcohol was significantly correlated with drinking in the dark (DID) in the LXS recombinant inbred panel, but only in mice that had been pretreated with alcohol. Here, we have conducted quantitative trait locus (QTL) mapping for AFT. DNA sequencing of the progenitor ILS and ISS strains and microarray analyses were also conducted to identify candidate genes and functional correlates. Methods LXS mice were given either saline or alcohol (5 g/kg) on day 1 and then tested for loss of righting reflex AFT on day 2. QTLs were mapped using standard procedures. Two microarray analyses from brain were conducted: (i) naive LXS mice and (ii) an alcohol treatment time course in the ILS and ISS. The full genomes of the ILS and ISS were sequenced to a depth of approximately 30×. Results A significant QTL for AFT in the alcohol pretreatment group was mapped to distal chromosome 4; numerous suggestive QTLs were also mapped. Preference drinking and DID have previously been mapped to the chromosome 4 locus. The credible interval of the significant chromosome 4 QTL spanned 23 Mb and included 716 annotated genes of which 150 had at least 1 nonsynonymous single nucleotide polymorphism or small indel that differed between the ILS and ISS; expression of 48 of the genes was cis-regulated. Enrichment analysis indicated broad functional categories underlying AFT, including proteolysis, transcription regulation, chromatin modification, protein kinase activity, and apoptosis. Conclusions The chromosome 4 QTL is a key region containing possibly pleiotropic genes for AFT and drinking behavior. Given that the region contains many viable candidates and a large number of the genes in the interval fall into 1 or more of the enriched functional categories, we postulate that many genes of varying effect size contribute to the observed QTL effect.

The ILSXISS (LXS) recombinant inbred (RI) panel of mice is a valuable resource for genetic mapping studies of complex traits, due to its genetic diversity and large number of strains. Male and female mice from this panel were used to investigate genetic influences on alcohol consumption in the “drinking in the dark” (DID) model. Male mice (38 strains) and female mice (36 strains) were given access to 20 % ethanol during the early phase of their circadian dark cycle for four consecutive days. The first principal component of alcohol consumption measures on days 2, 3, and 4 was used as a phenotype (DID phenotype) to calculate QTLs, using a SNP marker set for the LXS RI panel. Five QTLs were identified, three of which included a significant genotype by sex interaction, i.e., a significant genotype effect in males and not females. To investigate candidate genes associated with the DID phenotype, data from brain microarray analysis (Affymetrix Mouse Exon 1.0 ST Arrays) of male LXS RI strains were combined with RNA-Seq data (mouse brain transcriptome reconstruction) from the parental ILS and ISS strains in order to identify expressed mouse brain transcripts. Candidate genes were determined based on common eQTL and DID phenotype QTL regions and correlation of transcript expression levels with the DID phenotype. The resulting candidate genes (in particular, Arntl/Bmal1) focused attention on the influence of circadian regulation on the variation in the DID phenotype in this population of mice.

It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to contribute to the alcohol-related phenotypic differences associated with these strains.

Sixty male lambs (East Friesian x Lacaune) from a commercial sheep dairy were used to compare growth and carcass characteristics of short-scrotum (SS), ram (R), and wether (W) lambs. By d 10, every third single, twin, and triplet male was left entire (ram, n = 19), castrated (n = 24), or made short-scrotum (n = 17). After weaning and transport to the Western Maryland Research & Education Center, lambs were maintained as a single group on pasture, with supplemental feeding at 2–3% of BW. Lambs were weighed biweekly. Ultrasonic measurements were determined at d 102. The lambs were slaughtered at d 110. Growth and carcass data were analyzed using PROC GLM and carcass data correlations with PROC CORR. SS lambs had heavier final BW (53.5±1.0 kg) and higher ADG (0.25±0.001 kg/d) than W lambs (50.2±0.6 kg and 0.22±0.001 kg/d, respectively). R lambs were intermediate (51.6±1.0 kg and 0.23±0.001 kg/d, respectively). Sex did not influence ultrasonic backfat (BF), but there was a tendency to influence rib eye area (REA), with W lambs REA smaller than both R and SS lambs (P = 0.07). There was no influence of sex on dressing percentage, body wall thickness, REA, percent kidney and heart fat, leg conformation, or percent boneless closely trimmed retail cuts. There was a tendency (P = 0.10) for SS lambs to have heavier HCW (26.3±0.6 kg) compared to R (24.8±0.6 kg) and W lambs (24.7±0.25 kg). W lambs were fatter (P < 0.02), having greater BF (3.8 ± 0.6 mm) and yield grade (1.9 ± 0.1) than SS (3.0±0.6 mm and 1.6±0.1, respectively) and R lambs (2.8±0.6 mm and 1.5±0.1, respectively). There was strong correlation between ultrasonic and actual carcass measurements (r = 0.7, P < 0.0001), except for REA in SS lambs (r = 0.4; P = 0.1). Compared to W lambs, SS lambs had superior growth and produced leaner carcasses. The short-scrotum procedure may offer a viable alternative to castration.

In prior work, congenic strains carrying the DBA/2Igb (D2) region of chromosome 2 (Chr2) for alcohol preference were bred onto a C57BL/6Ibg (B6) background and as predicted were found to reduce voluntary consumption. Subsequently, interval-specific congenic recombinant strains (ISCRS) were generated and also tested. These ISCRS strains reduced the quantitative trait loci (QTL) interval to a comparatively small 3.4 Mb region. Here, we have exploited an integrative approach using both murine and human populations to critically evaluate candidate genes within this region. First, we used bioinformatics tools to search for genes relevant to alcohol preference within the QTL region. Second, we searched for single nucleotide polymorphisms (SNPs) within exons of every gene in this region. Third, we conducted follow-up microarray analyses to identify differentially expressed genes between the B6 and ISCRS strains in mice from each group. Fourth, we analyzed correlations between the expression level of candidate genes and phenotypes of alcohol preference in a large family of BXD recombinant inbred strains derived from B6 and D2. Finally, we evaluated SNP segregation in both BXD mouse strains and in humans who were heavy alcohol drinkers or non-drinkers. Among several potential candidate genes in this region, we identified activating transcription factor 2 (Atf2) as the most plausible gene that would influence alcohol preference. However, the candidacy of Atf2 was only weakly supported when we used a genetic network approach and by focused reanalysis of genome-wide association study data from European-American and African-American populations. Thus, we cannot conclude that Atf2 plays a role in the regulation of the QTL of mouse Chr2.

The US meat goat industry lags behind other livestock industries in the use of quantitative genetic evaluation. The Western Maryland Pasture-Based Meat Goat Performance Test was initiated in 2006 at the University of Maryland’s Western Maryland Research & Education Center (39º 30’ N/77º 44’ W). The purpose of the test was to identify genetically-superior meat goat bucks, especially those which exhibited resistance and resilience to internal parasites. From 2006–2016, 736 bucklings, of various breeds and crosses, were evaluated. One hundred producers from 20 states consigned one or bucks. Bi-weekly progress reports, summaries, and other information and data were shared via a blog (https://mdgoattest.blogspot.com), which has 218,346 cumulative page views from 523 blog posts. Many other programs were held in conjunction with the test, including sales, field days, youth programs, and carcass evaluation. Each year, top-performing bucks were identified and sold or retained for breeding, with 86% of consigners using the genetics from top-performing bucks in their breeding programs. Many more producers used the genetics from top-performing bucks by purchasing breeding stock and/or semen from consigners. Per survey data, consigning to the Maryland test improved the reputation of participating herds (80%), increased the demand and selling price for breeding stock (66–72%), and enabled the sale of semen from top-performers (38%). The test enabled participating producers to develop more parasite resistant herds (76%), improve the health and performance of their herds (73%), and improve their knowledge of parasite control (80%). The Western Maryland Pasture-Based Meat Goat Performance Test provided economic value to producers (71%), while contributing to the genetic improvement of the meat goat industry and serving as a valuable resource to producers.

The identification of genes that contribute to polygenic (complex) behavioral phenotypes is a key goal of current genetic research. One approach to this goal is to combine gene expression information with genetic information, i.e., to map chromosomal regions that regulate gene expression levels. This approach has been termed “genetical genomics”, and, when used in conjunction with the identification of genomic regions (QTLs) that regulate the complex physiological trait under investigation, provides a strong basis for candidate gene discovery. In this paper, we describe the implementation of the genetical genomic/phenotypic approach to identify candidate genes for sensitivity to the analgesic effect of morphine in BXD recombinant inbred mice. Our analysis was performed “in silico”, using an online interactive resource called PhenoGen (http://phenogen.ucdenver.edu). We describe in detail the use of this resource, which identified a set of candidate genes, some of whose products regulate the cellular localization and activity of the mu opiate receptor. The results demonstrate how PhenoGen can be used to identify a novel set of genes that can be further investigated for their potential role in pain, morphine analgesia and/or morphine tolerance.

Measures of genetic relatedness are essential to models of evolution by kin selection and determinations of inclusive fitness. Under a kin selection paradigm, individuals are expected to distribute actions influencing the fitness of relatives based on the relatedness of these relatives. In addition, it is necessary to have an accurate measure of relatedness to estimate heritability (h2) of phenotypic characters and to predict the efficacy of selection. Relatedness is often defined as the genotypic correlation between individuals. Assessed on the basis of common ancestry, relatedness can only be determined sensu strictu from pedigree analysis. Recent methodological and statistical advances allow the estimation of relatedness from allele frequency data. Many coefficients of relatedness can be found in the literature; I review and evaluate these, with emphasis on situations for which each is appropriate.

Interval-specific congenic strains (ISCS) allow fine mapping of a quantitative trait locus (QTL), narrowing its confidence interval by an order of magnitude or more. In earlier work, we mapped four QTL specifying differential ethanol sensitivity, assessed by loss of righting reflex because of ethanol (LORE), in the inbred long-sleep (ILS) and inbred short-sleep (ISS) strains, accounting for approximately 50% of the genetic variance for this trait. Subsequently, we generated reciprocal congenic strains in which each full QTL interval from ILS was bred onto the ISS background and vice versa. An earlier paper reported construction and results of the ISCS on the ISS background; here, we describe this process and report results on the ILS background. We developed multiple ISCS for each Lore QTL in which the QTL interval was broken into a number of smaller intervals. For each of the four QTL regions (chromosomes 1, 2, 11 and 15), we were successful in reducing the intervals significantly. Multiple, positive strains were overlapped to generate a single, reduced interval. Subsequently, this reduced region was overlaid on previous reductions from the ISS background congenics, resulting in substantial reductions in all QTL regions by approximately 75% from the initial mapping study. Genes with sequence or expression polymorphisms in the reduced intervals are potential candidates; evidence for these is presented. Genetic background effects can be important in detection of single QTL; combining this information with the generation of congenics on both backgrounds, as described here, is a powerful approach for fine mapping QTL.

BACKGROUND Acute functional tolerance (AFT) develops shortly after ethanol administration, and is determined as the change in brain or blood ethanol concentration (BEC) measured at 2 behavioral or physiological endpoints. Acute functional tolerance studies in some rodent strains support a long-held hypothesis that more sensitive strains develop more within-session tolerance. We used the new, 74-strain L x S recombinant inbred (RI) panel, developed from inbred long-sleep (ILS) and inbred short-sleep (ISS) strains, to revisit this hypothesis and to map quantitative trait loci (QTLs) for AFT. We report replication of QTL regions reported by earlier studies of AFT and preliminary application of a coarse single nucleotide polymorphism map analysis to limit QTL intervals for subsequent candidate gene hypotheses. METHODS Acute functional tolerance was assayed using a test of ataxia: loss and regain of balance on a stationary wooden dowel. Following an initial dose of 1.75 g/kg, BEC was measured at initial loss (BEC(0)) and regain of balance (BEC(1)). A second injection (2.0 g/kg) was administered and blood taken at the second regain of balance (BEC(2)). Acute functional tolerance was calculated as a difference score in 2 ways: (1) between BEC at the 2 successive regains of balance (AFT(1)), or (2) as the difference in BEC at final regain and at initial loss of balance (AFT(2)). We mapped QTLs for BEC(0), a measure of initial sensitivity, and both AFT scores. RESULTS All 4 parental strains (LS, SS, ILS, and ISS) developed tolerance, replicating previous published reports. There were significant sex effects for 3 of these strains. The L x S panel showed a 128-fold range in tolerance, with a few strains showing negative tolerance (sensitization). The ISS surpassed the next highest RI strain by 55% and was more than 4 times greater than SS. Heritability estimates for both AFT measures were close to 0.25 for both sexes. One significant QTL accounting for approximately 18% of phenotypic variance (V(P)), on chromosome 12 (AFT(1)), and 1 suggestive QTL (16% V(P)), on chromosome 16 (AFT(2)), were identified. These QTLs replicated regions reported in other studies. A multiple QTL model incorporating the effects of all significant interacting QTLs was developed, explaining almost 60% of V(P). The chromosome 12 region was further investigated by haplotype analysis, which identified many nonpolymorphic regions within the confidence interval, and possible candidate genes in the polymorphic regions. CONCLUSIONS Both SS and ISS developed greater AFT, assessed by both methods, than LS and ILS; this difference was significant in virtually all sex by strain comparisons. In the L x S RI, there was no correlation between initial sensitivity, measured by BEC at initial loss of balance, and either measure of AFT, on a stationary dowel. These results indicate that in this model system, initial sensitivity does not predict tolerance. Several QTLs for tolerance were identified; candidates in the narrowed chromosome 12 region, which has been reported in 2 other mapping studies, merit additional study.

Background: Most mouse quantitative trait loci (QTLs) for behavioral traits have been mapped using populations of mice derived from C57BL/6J (B6) and DBA/2J (D2). It is also important to identify QTLs for behavior in populations derived from other progenitors. We report results from QTL mapping for low-dose (ethanol) locomotor activation (LDA) using the recently developed LXS recombinant inbred (RI) strains, derived from Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) progenitors. The LXS RI panel has additional genetic variation, and greater power due to a larger number of strains, compared with other RI panels and strain crosses. Methods: Mice were tested using a 3-day protocol in which activity levels were monitored for 15 minutes each day. On day 1, baseline activity was recorded; on day 2, mice were injected with saline before testing; and on day 3, mice were injected with 1.8 g/kg ethanol and tested. Results: Several suggestive QTLs were found, on chromosomes 2, 3, 4, 7, 8, 12, and 13; 3 of these QTLs were sex-specific. Conclusions: Two apparently novel LDA QTLs were identified, on chromosomes 4 and 8. The other QTLs appear to replicate previously identified LDA QTLs. These replicated QTLs will be pursued in subsequent studies designed to identify candidate genes.

Animal models offer several advantages for the study of complex human disorders such as alcoholism. No animal model replicates all aspects of alcoholism but different components of the disorder can be investigated using various rodent models. In this article, we review a select subset of the most widely used mouse genetic models in alcohol research. Different genetically defined strains and stocks of mice are useful for genetic, physiologic, behavioral and pharmacological studies of this devastating disorder. In the past decade, numerous genomic regions associated with a tendency for various behavioral components of alcoholism have been identified; recent applications of new methods are shedding light on quantitative trait genes. Many of the underlying genes should be identified in the near future.

In previous studies, we have mapped quantitative trait loci (QTLs) for hypnotic sensitivity to ethanol using a small recombinant inbred (RI) panel and a large F(2) backcross. Alcohol sensitivity is a major predictor of long-term risk for alcoholism. We remapped hypnotic sensitivity using a new set of 75 RI strains, the LXS, derived from Inbred Long Sleep and Inbred Short Sleep strains. We expected to improve mapping resolution in the QTL regions and to identify novel QTLs for loss of the righting reflex due to ethanol. We used three common mapping algorithms (R/qtl, QTL Cartographer, and WebQTL) to map QTLs in the LXS, and we compared the results. Most mapping studies use only a single algorithm, an approach that may result in failure to identify minor QTLs. We confirmed most of our previously reported QTLs, although one major QTL from earlier work (Lore2) failed to replicate, possibly because it represented multiple linked genes separated by recombination in the RI strains. We also report narrowed confidence intervals, based on mapping with a new genetic resource of more than 4000 polymorphic single-nucleotide polymorphism markers. These narrowed confidence intervals will facilitate candidate gene identification and assessment of overlap with human regions specifying risk for alcoholism. Finally, we present an approach for using these RI strains to assess evidence for candidate genes in the narrowed intervals, and we apply this method to a strong candidate, the serotonin transporter.

The Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) mouse strains have a 16-fold difference in duration of loss of the righting response (LORR) following administration of a sedative dose of ethanol. Four quantitative trait loci (QTLs) have been mapped in these strains for this trait. Underlying each of these QTLs must be one or more genetic differences (polymorphisms in either gene coding or regulatory regions) influencing ethanol sensitivity. Because prior studies have tended to focus on differences in coding regions, genome-wide expression profiling in cerebellum was used here to identify candidate genes for regulatory region differences in these two strains. Fifteen differentially expressed genes were found that map to the QTL regions and polymorphisms were identified in the promoter regions of four of these genes by direct sequencing of ILS and ISS genomic DNA. Polymorphisms in the promoters of three of these genes, Slc22a4, Rassf2, and Tax1bp3, disrupt putative transcription factor binding sites. Slc22a4 and another candidate, Xrcc5, have human orthologs that map to genomic regions associated with human ethanol sensitivity in genetic linkage studies. These genes represent novel candidates for the LORR phenotype and provide new targets for future studies into the neuronal processes underlying ethanol sensitivity.

The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact potygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

Background The inbred long-sleep (ILS) and inbred short-sleep (ISS) strains of mice are widely studied as a model of initial sensitivity to alcohol. Recently, a large comparative DNA sequencing study of candidate genes located within the four Lore quantitative trait loci (QTLs) associated with the ethanol-induced loss of righting reflex in ILS and ISS mice has identified eight genes that contain coding region differences corresponding to amino acid changes. Here, recently developed interval-specific congenic recombinant mice (ISCRs) have been used to map these genes in relationship to newly narrowed QTL regions. Methods Regions of candidate genes containing DNA differences corresponding to previously identified amino acid changes between ISS and ILS mice were amplified from either genomic DNA or complementary DNA from ISCR mice using polymerase chain reaction. The products were purified and directly sequenced to determine the genotypes for each polymorphism. On the basis of these genotypic data, each candidate gene was determined to be located either within or outside of recently narrowed Lore QTL intervals. Results Of these eight candidates with protein-coding differences, five are now excluded from their respective Lore intervals. The other three (Znf142, Ptprn, and Znf133) have been localized to the narrowed QTL intervals. Conclusions These three central nervous system genes (Znf142, Ptprn, and Znf133) represent promising candidates for involvement in the differential sensitivity to alcohol exhibited between ILS and ISS mice. This study also demonstrates how the combination of high-throughput comparative gene sequencing and concomitant genetic fine mapping of QTL regions with ISCRs can be an effective tool for accelerating the process of moving from QTL to gene.

Background: We have identified four major genes or quantitative trait loci (QTLs) that determine duration of loss of righting reflex (LORR), induced by sedative doses of ethanol:Lore1, Lore2, Lore4, and Lore5. Together these genes explain more than 50% of the phenotypic variance for sensitivity to the sedative/hypnotic effects of ethanol between the Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) strains of mice. The derivation of these strains is reviewed here. Methods: Each QTL has been bred onto the opposite background (ILS or ISS) through 10 rounds of backcrossing by using QTL-marker-assisted counter selection to produce reciprocal congenic strains. Mice were genotyped for markers that flanked each of the QTLs. Selection for the donor at the desired QTL, and against donor markers at the other four QTLs, allowed rapid fixation of the genetic background. Phenotypic assessment in the ISS-recipient congenic strains was conducted throughout the backcross. Results: By the N5 generation, phenotypic assessments failed to detect significant effects in some sublines; these sublines were discarded and positive lines split to create new replicate sublines. In the N10, all sublines retained the phenotypic difference between heterozygotes and ISS homozygotes; however, the expected additive effect was not found in the Lore1 congenics. On the ILS background, each Lore was captured, as shown by the expected differential LORR. Two strains on the ILS background, and one on the ISS, exhibited the differential effect on blood ethanol concentration associated with the donor strain. Conclusions: Congenic strains represent an important resource for confirmation of previously identified QTLs, for identification and mapping of additional phenotypes, and for exclusion of candidate genes. QTL-marker-assisted selection rapidly stabilized the genetic background within four generations (based on phenotypic assessments); however, phenotypic selection during the backcrossing to generate congenic strains did not contribute to the successful capture of the ISS QTLs.

Low initial response to alcohol has been shown to be among the best predictors of development of alcoholism. A similar phenotypic measure, difference in initial sensitivity to ethanol, has been used for the genetic selection of two mouse strains, the Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice, and for the subsequent identification of four quantitative trait loci (QTLs) for alcohol sensitivity. We now report the application of high throughput comparative gene sequencing in the search for genes underlying these four QTLs. To carry out this search, over 1.7 million bases of comparative DNA sequence were generated from 68 candidate genes within the QTL intervals, corresponding to a survey of over 36,000 amino acids. Eight central nervous system genes, located within these QTLs, were identified that contain a total of 36 changes in protein coding sequence. Some of these coding variants are likely to contribute to the phenotypic variation between ILS/ISS animals, including sensitivity to alcohol, providing specific new genetic targets potentially important to the neuronal actions of alcohol.

Mouse strains congenic for individual quantitative trait loci (QTLs) conferring hypnotic sensitivity to ethanol were constructed by backcrossing genotypically selected ILS × ISS N2 individuals to either inbred Long Sleep (ILS) or inbred Short Sleep (ISS) mice. We used a novel ``speed congenic'' approach in which N2 mice were genotyped for markers flanking each of the five originally identified QTLs. Genotypic selection for ISS regions at four of the five QTLs, and for ILS/ISS at the fifth QTL, allowed rapid fixation of the genetic background. We call this strategy ``QTL-Marker-Assisted Counter Selection'' or QMACS. By the N4 generation, phenotypic assessments showed that in some sublines the QTL had not been captured; these sublines were discarded and positive lines split to create new replicate sublines. One QTL, on Chromosome (Chr) 8, was not confirmed. At the N8, virtually all sublines on the remaining QTLs retained the phenotypic difference between heterozygotes and ISS homozygotes. Small numbers of interim congenics were produced at the N6 and later generations in which the ILS QTL was made homozygous on the ISS background; as expected, these congenic mice showed an increased sleep time. For later backcrosses (after the N4), the parents were selected on the basis of phenotype as well as genotype. The parent-offspring correlation over all QTLs was significant, supporting the use of phenotypic selection in congenic construction.

The purpose of this study is to investigate whether expression profiles of alcoholism-relevant genes in different parts of the brain are correlated differently with those in the liver. Four experiments were conducted. First, we used gene expression profiles from five parts of the brain (striatum, prefrontal cortex, nucleus accumbens, hippocampus, and cerebellum) and from liver in a population of recombinant inbred mouse strains to examine the expression association of 10 alcoholism-relevant genes. Second, we conducted the same association analysis between brain structures and the lung. Third, using five randomly selected, nonalcoholism-relevant genes, we conducted the association analysis between brain and liver. Finally, we compared the expression of 10 alcoholism-relevant genes in hippocampus and cerebellum between an alcohol preference strain and a wild-type control. We observed a difference in correlation patterns in expression levels of 10 alcoholism-relevant genes between different parts of the brain with those of liver. We then examined the association of gene expression between alcohol dehydrogenases (Adh1, Adh2, Adh5, and Adh7) and different parts of the brain. The results were similar to those of the 10 genes. Then, we found that the association of those genes between brain structures and lung was different from that of liver. Next, we found that the association patterns of five alcoholism-nonrelevant genes were different from those of 10 alcoholism-relevant genes. Finally, we found that the expression level of 10 alcohol-relevant genes is influenced more in hippocampus than in cerebellum in the alcohol preference strain. Our results show that the expression of alcoholism-relevant genes in liver is differently associated with the expression of genes in different parts of the brain. Because different structural changes in different parts of the brain in alcoholism have been reported, it is important to investigate whether those structural differences in the brains of those with alcoholism are due to the difference in the associations of gene expression between genes in liver and in different parts of the brain.

Numerous algorithms for the identification and genetic mapping of quantitative trait loci (QTL) have been developed. Methods for confirming QTL maps involve either examination of independent segregating populations or the construction of congenic lines differing only in the QTL of interest. Because these projects require a minimum of several years or thousands of marker assessments in laboratory mice, an alternative, faster congenic method has been proposed. In a preliminary study, we tested this method for confirming QTLs identified in crosses between the ILS and ISS selected lines of mice for differential sensitivity to the hypnotic effects of ethanol. Herein, we report the construction of "segregating congenic" strains in which each QTL is made homozygous in a single generation, whereas the remainder of the genetic background is allowed to segregate. Sensitivity to ethanol among the progeny of such mice is consistent with predictions. Phenotypic variation is high, as expected, due to the background segregation, and statistical significance was attained in only 2 of 7 comparisons. Such segregating congenic populations may be a valuable research tool for confirming QTL map positions and for subsequent assessment of individual pathways and mechanisms of action of individual QTLs.

Initial insensitivity to alcohol is a strong predictor of human alcoholism, a widespread and heritable health problem. The Long Sleep and Short Sleep lines of mice were developed by genetic selection for high or low alcohol sensitivity. We have identified seven quantitative trait loci (QTLs) specifying differences in alcohol sensitivity using intercross progeny from these selected strains. These QTLs (Lorel-Lore7) together account for approximately 60% of the total genetic variance for this trait. This represents the first report of linkages for genes influencing alcohol action in any mammalian system using stringent, genome-wide mapping criteria.

We are mapping the genes (quantitative trait loci or QTLs) that are responsible for individual differences in ethanol sensitivity, measured as the duration of loss of righting, reflex (LORR) and blood ethanol concentrations upon recovery of the righting reflex (BEC). The Long-Sleep (LS) and Short-Sleep (SS) selected lines of mice manifest an 18-fold difference in LORR and serve as a rodent model for ethanol sensitivity. The LS x SS recombinant inbred (RI) series, developed from LS and SS lines, are an important resource for QTL mapping of ethanol-related responses. The current report summarizes the initial QTL analysis of LORR and BEC in the LS x SS strains and compares the results of correlational analysis with an interval-mapping approach. The data provide strong evidence for QTLs that influence ethanol sensitivity on mouse chromosomes 1 and 2 and possible QTLs on chromosomes 1, 3, 4, 5, 6, 7, 12, 13, 16, and 18. These results are compared to those from an F2 cross which confirms QTLs on chromosomes 1, 2, 4, and 18.

Results By using the keyword alcohol, we identified a total of 39 genetic elements in the region between markers D2Mit56 and D2Mit10. Among these genetic elements, we found seven with potential function in alcohol preference (Table 1). We then examined the SNPs, insertions and deletions, and gene expression levels of those seven genes. Conclusions Our current data suggest that the Atf2 and Titin genes are potentially the most alcohol relevant genes. However, further experiments and examination are still needed to confirm their candidacy. Several other candidate genes are also in the process of being identified.

Genetic influences on the predisposition to complex behavioral or physiological traits can reflect genetic polymorphisms that lead to altered gene product function, and/or variations in gene expression levels. We have explored quantitative variations in an animal's alcohol consumption, using a genetical genomic/phenomic approach. In our studies, gene expression is correlated with amount of alcohol consumed, and genomic regions that regulate the alcohol consumption behavior and the quantitative levels of gene expression (behavioral and expression quantitative trait loci [QTL]) are determined and used as a filter to identify candidate genes predisposing the behavior. We determined QTLs for alcohol consumption using the LXS panel of recombinant inbred mice. We then identified genes that were: 1) differentially expressed between five high and five low alcohol-consuming lines or strains of mice; and 2) were physically located in, or had an expression QTL (eQTL) within the alcohol consumption QTLs. Comparison of mRNA and protein levels in brains of high and low alcohol consuming mice led us to a bioinformatic examination of potential regulation by microRNAs of an identified candidate transcript, Gnb1 (G protein beta subunit 1). We combined our current analysis with our earlier work identifying candidate genes for the alcohol consumption trait in mice, rats and humans. Our overall analysis leads us to postulate that the activity of the GABAergic system, and in particular GABA release and GABA receptor trafficking and signaling, which involves G protein function, contributes significantly to genetic variation in the predisposition to varying levels of alcohol consumption. This article is part of a Special Issue entitled 'Trends in neuropharmacology: in memory of Erminio Costa'.

There is evidence that the peptide urocortin 1 (Ucn1) may be involved in mediating some of the effects of ethanol. The purpose of the present study was to characterize Ucn1 immunoreactivity in mice selectively bred for either high or low sensitivity to ethanol-induced sedation, with additional differences in their response to ethanol- induced hypothermia. The brains of naive male mice of the inbred long sleep/short sleep (ILS/ISS) selected lines were analyzed by immunohistochemistry. Significant differences were found between lines in the number of Ucn1-containing cells in the non-preganglionic Edinger- Westphal nucleus (npEW, the main source of Ucn1 in the brain); with the ISS mice having more cells. However, significant differences in the optical density of Ucn1 immunoreactivity in individual npEW cells and differ- ences in cell area were also found between lines, with ILS mice having a greater density of Ucn1 per cell and having larger cells in the npEW. Importantly, the ILS mice also had a significantly greater number of Ucn1-positive terminal fibers than ISS mice in the lateral septum and the dorsal raphe nucleus, projection areas of Ucn1- containing neurons. These results suggest that the greater sensitivity of ILS than ISS mice to the hypothermic effects of ethanol could be mediated by stronger innerv- ation of the dorsal raphe by Ucn1-containing fibers. In addition, these results lend further support to previous findings implicating Ucn1-containing projections from npEWtothe dorsalrapheinethanol-inducedhypothermia.

Objective: In previous work, we created congenic strains that carry the DBA/2IBG (D2) region for alcohol preference on chromosome 2, on an otherwise C57BL/6IBG (B6) background. Here, we report construction and testing of interval-specific congenic recombinant strains (ISCRSs) for the purpose of narrowing the quantitative trait loci (QTL) interval. Methods: ISCRSs were derived by identifying mice that carry recombination events in the D2 interval, during the backcrossing for congenics. Recombinant mice were backcrossed to B6, and progeny that carry the reduced chromosome 2 region were tested for its effect on the alcohol preference phenotype. Results: We developed multiple ISCR strains, which spanned the QTL interval. Three of these showed the D2 phenotype of reduced alcohol consumption. The overlap of two of these strains reduced the QTL interval from 66.8 to 3.5 Mb. A third positive ISCRS suggests the possibility of a second, linked QTL. Conclusions: Use of ISCRSs can narrow a QTL region to a few Mb. This reduced interval size will facilitate identification of candidate genes, through bioinformatics, gene expression, and DNA sequencing strategies. Potential difficulties, including reduced power as a result of variable phenotypes or small effect size, are discussed.

Background: Ethanol enhances γ-aminobutyric acid (GABA) A receptor-mediated responses in the brain, and this enhancement is greater in a mouse line behaviourally more sensitive to ethanol (long sleep) than in a line (short sleep) hehaviorally less ethanol sensitive (assayed by loss of righting; sleep time). Quantitative trait locus (QTL) analysis of inbred long sleep (ILS) and inbred short sleep (ISS) phenotypes revealed four chromosomal regions (Lorel, Lore2, Lore4, and Lore5) that together account for approximately 50% of ethanol-induced sleep-time variance. Congenic strains were generated, each of which is homozygous for one of four ISS Lore QTLs on the ILS background. These congenic mouse strains are ideally suited for asking which QTL regions might correlate with other phenotypes that differ between ILS and ISS mice. Here we used the congenics to investigate altered GABA A , responses to ethanol. Methods: Evoked GABA A receptor-mediated inhibitory postsynaptic currents (IPSCs) were measured by whole-cell voltage-clamp recording procedures in CA1 pyramidal neurons in hippocampal brain slices. Results: GABA A IPSC responses in hippocampal brain slices from ILS mice were significantly enhanced by 80 mM ethanol, whereas those from ISS mice were not affected. ILS.Lore2 S and ILS.Lore5 S congenic strains were significantly enhanced by 80 mM ethanol, similar to the background (control) ILS mice. However, ethanol had no significant effect on GABA A responses in ILS.Lore1 S and ILS.Lore4 S congenic mice, similar to the ISS mice, thus reflecting the influence of ISS alleles on the ILS phenotype. Conclusions: Our results suggest that alleles located in the Lorel and Lore4 QTL regions confer ethanol sensitivity of GABA A receptor-mediated IPSCs. Thus, for these QTLs, GABA A IPSCs may represent an endophenotype of sedative/hypnotic sensitivity to ethanol. Although the Lore2 and Lore5 QTL regions have a significant effect on sleep time, they do not play a significant role in the differential ethanol enhancement of GABA A IPSCs between ILS and ISS mice.

The set of LXS recombinant inbred (RI) strains is a new and exceptionally large mapping panel that is suitable for the analysis of complex traits with comparatively high power. This panel consists of 77 strains-more than twice the size of other RI sets--and will typically provide sufficient statistical power (beta = 0.8) to map quantitative trait loci (QTLs) that account for approximately 25% of genetic variance with a genomewide p0.05. To characterize the genetic architecture of this new set of RI strains, we genotyped 330 MIT microsatellite markers distributed on all autosomes and the X Chromosome and assembled error-checked meiotic recombination maps that have an average F2-adjusted marker spacing of approximately 4 cM. The LXS panel has a genetic structure consistent with random segregation and subsequent fixation of alleles, the expected 3-4 x map expansion, a low level of nonsyntenic association among loci, and complete independence among all 77 strains. Although the parental inbred strains-Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS)--were derived originally by selection from an 8-way heterogeneous stock selected for differential sensitivity to sedative effects of ethanol, the LXS panel is also segregating for many other traits. Thus, the LXS panel provides a powerful new resource for mapping complex traits across many systems and disciplines and should prove to be of great utility in modeling the genetics of complex diseases in human populations.

International audience; This white paper by eighty members of the Complex Trait Consortium presents a community's view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?

Quantitative trait loci (QTLs) for many alcohol- and drug-related traits have been mapped using well-accepted mapping techniques. The ultimate goal of gene identification necessitates confirmation of the QTL and reduction of the interval surrounding the QTL; both can be accomplished in congenic strains. These strains carry a chromosomal region introgressed from a donor strain onto the genetic background of a second, recipient strain. Multiple generations of backcrossing reduce the unlinked donor genome to less than 0.1%. Then, phenotypic comparisons between mice congenic for the donor region and controls from the recipient strain allow confirmation of the QTL effect. Animals with recombinations in the donor region can be used to generate interval-specific congenic recombinant lines. Numerous congenic strains are currently being developed in which chromosomal regions carrying QTLs for alcohol- and drug-related traits have been transferred from one strain onto a second strain. The purpose of this review is to summarize the chromosomal regions, donor and recipient strains, and results obtained from these congenics. Most researchers developing such strains are willing to share these resources to facilitate localization of the genetic bases of other phenotypes.

The whole genome scan for quantitative trait loci (QTLs) specifying peak bone mass was performed with the F2 intercrosses of SAMP6, an established murine model of senile osteoporosis, exhibiting a significantly lower peak bone mass, and SAMP2, exhibiting a higher peak bone mass. Cortical thickness index (CTI), a parameter of bone mass of femurs, was measured in 488 F2 progeny at 4 months of age, when the animals attained peak bone mass by microphotodensitometry. Genetic markers were typed at 90 loci spanning all chromosomes except the Y. By interval mapping of 246 male F2 mice, two loci were identified with significant linkage to peak bone mass, one on Chromosome (Chr) 11 and another on Chr 13, with a maximum lod score of 10.8 (22.2% of the total variance) and 5.8 (10.0%), respectively. Another locus on the X Chr was suggestive of a QTL associated oppositely with a low peak bone mass to the SAMP2 allele. This association was consistent with the distribution of peak bone mass in the F1 and F2. These findings should be useful to elucidate the genetics of osteoporosis.

We present the strain distribution patterns (SDPs) of 118 SSLP markers and three pigmentation genes that have been characterized in 27 strains from the LSXSS RI series. This coarse map provides a resource for linkage studies of phenotypes that are heritable in the LSXSS RI series. The LSXSS recombinant inbred (RI) strains were derived from the Long-Sleep (LS) and Short-Sleep (SS) selected lines of mice that were selected for differential sensitivity to ethanol but are also differentially sensitive to a variety of other alcohols, barbiturates, sedative hypnotics, and general anesthetics. Since the parents were not inbred, two atypical factors are present in these SDPs. First, more than two alleles are frequently found in these RIs, and second, some alleles can be uniquely associated with one or the other parent while other alleles may be found in both parental lines. To validate the markers found in the parental line, we genotyped all parental mice from one generation of both the LS and SS lines, thus leading to a set of marker SDPs that are useful for further phenotypic association and identification of provisional QTLs.

Familial correlations for general cognitive ability wer estimated for three ethnic groups tested in the Hawaii Family Study of Cognition (Americans of European, Japanese, and Chinese ancestry). Assuming multivariate normality of family data, separate observed covariance matrices were computed for families of different size, ethnicity, and child's gender and then equated to their expectations using a log-likelihood ratio statistic. Resulting maximum-likelihood estimates of familial correlations are highly similar to previously reported product-moment and intraclass correlations; however, standard errors for the maximum-likelihood estimates are somewhat smaller. More importantly, the estimation procedure employed in the present study facilitates tests of alternative hypotheses. Using this approach, hypotheses of homogeneity of familial correlations among the three ethnic groups and of homogeneity among the various parent-offspring correlations (mother-son, mother-daughter, father-son, father-daughter) and sibling correlations (son-daughter, son-son, and daughter-daughter) were rejected.

The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs. Electronic supplementary material The online version of this article (doi:10.1007/s00335-016-9663-6) contains supplementary material, which is available to authorized users.

Our laboratory has developed an online interactive resource called PhenoGen ( http://phenogen.ucdenver.edu ) which provides an archive of brain and other organ gene expression data from a panel of 20 common inbred mouse strains, and three recombinant inbred (RI) panels (two mouse and one rat). DNA microarray data can also be uploaded to the site where numerous analytical tools can be implemented. An important advantage to the archived data is that each array represents data from a single animal and each strain was sampled 4-7 times, providing an estimate of genetic variance (heritability) of individual transcript levels. These panels also allow genetic mapping of expression QTLs. Overlap of eQTLs with phenotypic QTLs provides a powerful approach to candidate gene identification. These methods are briefly described here and we encourage the use of our site for both scientific discovery and as a teaching tool in quantitative genetics.

Background Many quantitative trait loci (QTL) influencing mouse model phenotypes for alcoholism have been mapped genetically. However, the gene(s) comprising the QTL (QTG) are largely unknown. In previous work, Bennett and colleagues created congenic strains carrying the DBA/2IBG (D2) region for alcohol preference (AP) on chromosome 2, on a C57BL/6IBG (B6) background [1]. Subsequently, interval specific congenic recombinant strains (ISCRS), in which the full D2 QTL region was broken into smaller, partially overlapping regions of introgression, were generated and tested. With information from two ISCRS, the QTL has been mapped onto mouse chromosome 2 (Chr2) in a region of 3.4Mb by using C57BL/6J (B6) x DBA/2J (D2) recombinant inbred (RI) strains as well as by using F2 populations. Several candidate genes, Gad1, Atp5g3, Atf2, Sp3 and Sp9, have been evaluated but none of them has been confirmed for a definitive role in the regulation of the QTL of AP on Chr2 [2,3].