Replication of small effect quantitative trait loci for behavioral traits facilitated by estimation of effect size from independent cohorts

Quantitative trait locus (QTL) mapping is often done in a single segregating population, such as a backcross or an intercross. Both QTL location and effect size are then estimated from the same dataset. This approach results in an over-estimate of effect size for two reasons: (1) LOD scores, which are maximized over numerous point-wise tests, are correlated with estimated effect size and (2) small effect QTLs are often undetected in underpowered experiments, yielding inflated effect sizes for detected QTLs (the Beavis effect). When it is impractical to maintain or generate large population sizes, an alternative is to use two populations, one for initial detection and localization and a second for a locus-matched estimate of effect size, not conditioned on significance. Recombinant inbred (RI) panels are eminently suitable for this approach, as each strain genotype can be sampled repeatedly. We present mapping results from the LXS RI panel for two behavioral phenotypes relating to ethanol response: low-dose ethanol activation and loss of righting following high-dose injection. Both the phenotypes were measured in two or three independent cohorts, which were then used to re-estimate effect size. Many small-effect QTLs replicated using this approach, but in all cases, effect size, in the replicate cohorts, was reduced from the initial estimate, often substantially. Such a reduction will have important consequences for power analyses in which sample sizes are determined for subsequent confirmation studies.     

Genetic analysis of the psychomotor stimulant effect of ethanol

Genetic influences on the psychomotor stimulant effect of ethanol may be a key feature of abuse liability. While earlier work has shown the activational effects of ethanol to be under the influence of a relatively uncomplicated additive genetic system, preliminary data from our laboratory suggested the possibility of nonadditive genetic variance. In the present study, a full Mendelian cross was conducted to further characterize gene action and search for quantitative trait loci (QTL) influencing the psychomotor stimulant properties of ethanol. We tested 3062 mice of the six Mendelian cross genotypes (P1, P2, F1, F2, BC1 and BC2) derived from a cross between the C57BL/6J (B6) and C3H/HeJ (C3H) inbred strains of mice. On day 1, mice were injected with saline, put in a holding cage for 5 min, then placed in an activity monitor for 5 min. On day 2, mice were injected with 1.5 g/kg ethanol, and activity again monitored for 5 min. Analysis showed the expected activation in the C3H strain and little activation in the B6 strain, with no effect of sex. Biometrical genetic analysis showed a best-fit model that included the mean (m), additive effect (a), and an epistatic parameter (i = homozygote by homozygote interaction). Analysis showed good evidence for QTL on chromosomes 1 (logarithm of odds (LOD) 3.4-7.5, 88-100 cM), 6 (LOD 9.1-10.4, 46-50 cM) and 15 (LOD 7.3-8.8, 28-32 cM). While the regions on chromosomes 1 and 6 have previously been implicated in several different ethanol-related phenotypes, this is the first report of a QTL influencing the psychomotor stimulant properties of ethanol on chromosome 15. Other studies have identified QTL in this region of chromosome 15 mediating locomotor activation caused by other psychostimulants, including cocaine, amphetamine and phencyclidine.     

Multiple cross mapping (MCM) markedly improves the localization of a QTL for ethanol-induced activation

This study examines the use of multiple cross mapping (MCM) to reduce the interval for an ethanol response QTL on mouse chromosome 1. The phenotype is the acute locomotor response to a 1.5-g/kg i.p. dose of ethanol. The MCM panel consisted of the six unique intercrosses that can be obtained from the C57BL/6J (B6), DBA/2J (D2), BALB/cJ (C) and LP/J (LP) inbred mouse strains (N ≥ 600/cross). Ethanol response QTL were detected only with the B6xD2 and B6xC intercrosses. For both crosses, the D2 and C alleles were dominant and decreased ethanol response. The QTL information was used to develop an algorithm for sorting and editing the chromosome 1 Mit microsatellite marker set ( http://www.jax.org ) . This process yielded a cluster of markers between 82 and 85 cM (MGI). Evidence that the QTL was localized in or near this interval was obtained by the analysis of a sample ( n  = 550) of advanced cross heterogenous stock animals. In addition, it was observed that one of the BXD recombinant inbred strains (BXD-32) had a recombination in the interval of interest which produced the expected change in behavior. Overall, the data obtained suggest that the information available within existing genetic maps coupled with MCM data can be used to reduce the QTL interval. In addition, the MCM data set can be used to interrogate gene expression data to estimate which polymorphisms within the interval of interest are relevant to the QTL.     

Modulation of the Mesolimbic Dopamine System by Glutamate

Glutamate has been shown to modulate motor behavior, probably via N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors that are involved in the control of the mesolimbic dopamine (DA) system, that is, the ventral tegmental area (VTA)-nucleus accumbens (NAC). In the present study, we investigated the effects of uncompetitive (MK-801) and competitive [DL-2-amino-5-phosphonopentanoic acid (AP-5), CGP 40116] NMDA receptor antagonists and NMDA and AMPA on DA release in the mesolimbic system and on motor behavior. Systemic injection and intrategmental infusion of MK-801 increased DA levels in the VTA, but the systemic administration enhanced DA exclusively in the NAC and increased motor behavior. In contrast, intrategmental infusion of AP-5, but not the systemic administration of its lipophilic analogue CGP 40116, decreased the DA release in the two regions without affecting motor behavior. NMDA and AMPA infusion into the VTA increased DA levels in both areas. This increase was accompanied by a strong motor behavioral stimulation after NMDA but only a moderate increase after AMPA infusion. The present results indicate that mesolimbic DA neurons are controlled by the glutamatergic system and that the effects of uncompetitive and competitive NMDA receptor antagonists on DA release are mediated by an interaction with different brain areas. These findings may account for the different effects of NMDA receptor ligands on motor behavior.     

Harnessing the mouse to unravel the genetics of human disease

Complex traits, i.e. those with multiple genetic and environmental determinants, represent the greatest challenge for genetic analysis, largely due to the difficulty of isolating the effects of any one gene amid the noise of other genetic and environmental influences. Methods exist for detecting and mapping the Quantitative Trait Loci (QTLs) that influence complex traits. However, once mapped, gene identification commonly involves reduction of focus to single candidate genes or isolated chromosomal regions. To reach the next level in unraveling the genetics of human disease will require moving beyond the focus on one gene at a time, to explorations of pleiotropism, epistasis and environment-dependency of genetic effects. Genetic interactions and unique environmental features must be as carefully scrutinized as are single gene effects. No one genetic approach is likely to possess all the necessary features for comprehensive analysis of a complex disease. Rather, the entire arsenal of behavioral genomic and other approaches will be needed, such as random mutagenesis, QTL analyses, transgenic and knockout models, viral mediated gene transfer, pharmacological analyses, gene expression assays, antisense approaches and importantly, revitalization of classical genetic methods. In our view, classical breeding designs are currently underutilized, and will shorten the distance to the target of understanding the complex genetic and environmental interactions associated with disease. We assert that unique combinations of classical approaches with current behavioral and molecular genomic approaches will more rapidly advance the field.     

Enhanced dopaminergic differentiation of human neural stem cells by synergistic effect of Bcl-xL and reduced oxygen tension

Neural stem cells constitute a promising source of cells for transplantation in Parkinson's disease, but a protocol for controlled dopaminergic differentiation is not yet available. Here we investigated the effect of the anti-apoptotic protein Bcl-x_L and oxygen tension on dopaminergic differentiation and survival of a human ventral mesencephalic stem cell line (hVM1). hVM1 cells and a Bcl-x_L over-expressing subline (hVMbcl-x_L) were differentiated by sequential treatment with fibroblast growth factor-8, forskolin, sonic hedgehog, and glial cell line-derived neurotrophic factor. After 10 days at 20% oxygen, hVMbcl-x_L cultures contained proportionally more tyrosine hydroxylase(TH)-positive cells than hVM1 control cultures. This difference was significantly potentiated from 11 ± 0.8% to 17.2 ± 0.2% of total cells when the oxygen tension was lowered to 3%. Immunocytochemistry and Q-PCR-analysis revealed expression of several dopaminergic markers besides of TH just as dopamine was detected in the culture medium by HPLC analysis. Although Bcl-x_L-over-expression reduced cell death in the cultures, it did not alter the relative content of GABAergic, neurons, while the content of astroglial cells was reduced in hVMbcl-x_L cell cultures compared with control. We conclude that Bcl-x_L and lowered oxygen tension act in concert to enhance dopaminergic differentiation and survival of human neural stem cells.     

Distribution of the C1473G polymorphism in tryptophan hydroxylase 2 gene in laboratory and wild mice

The neurotransmitter serotonin is implicated in the regulation of various forms of behavior, including aggression, sexual behavior and stress response. The rate of brain serotonin synthesis is determined by the activity of neuronal‐specific enzyme tryptophan hydroxylase 2. The missense C1473G substitution in mouse tryptophan hydroxylase 2 gene has been shown to lower the enzyme activity and brain serotonin level. Here, the C1473G polymorphism was investigated in 84 common laboratory inbred strains, 39 inbred and semi‐inbred strains derived from wild ancestors (mostly from Eurasia) and in 75 wild mice trapped in different locations in Russia and Armenia. Among all the classical inbred strains studied, only substrains of BALB/c, A and DBA, as well as the IITES/Nga and NZW/NSlc strains were homozygous for the 1473G allele. In contrast to laboratory strains, the 1473G allele was not present in any of the samples from wild and wild‐derived mice, although the wild mice varied substantially in the C1477T neutral substitution closely linked to the C1473G polymorphism. According to these results, the frequency of the 1473G allele in natural populations does not exceed 0.5%, and the C1473G polymorphism is in fact a rare mutation that is possibly eliminated by the forces of natural selection.     

茶陵野生稻导入系遗传分析及重要性状相关QTL鉴定

普通野生稻是栽培稻的祖先种,从野生稻中挖掘栽培稻中已丢失或削弱了的优异基因是保证水稻高产稳产的一个重要手段。本研究以茶陵野生稻染色体片段导入系群体为研究材料,使用均匀分布于12条水稻染色体上的136个多态性分子标记,对其遗传背景进行检测。平均每个导入系携带24个导入片段,导入片段平均长度为16.1 cM,导入片段覆盖野生稻基因组的87.89%。结合两个环境中的性状调查,鉴定到与6个产量性状相关的18个QTLs,其中6号染色体上与粒宽有关的QTL在两个环境中被连续检测到。除此之外,还鉴定到5个与发芽期耐冷性有关的QTLs。     

Characterization of the parallel rod floor apparatus to test motor incoordination in mice

Impairment of motor coordination, or ataxia, is a prominent effect of alcohol ingestion in humans. To date, many models have been created to examine this phenomenon in animals. Evidence suggests that the tasks thought to measure this behavior in mice actually measure different components of this complex trait. We have characterized the parallel rod floor apparatus to quantify ethanol-induced motor incoordination. Using genetically heterogeneous mice, we evaluated the influence of rod diameter and inter-rod distance on dose-related ethanol-induced motor incoordination to select parameters that optimized testing procedures. We then used the DBA/2J and C57BL/6J inbred strains of mice to examine the effect of 2 g/kg of ethanol, by serially testing mice on two floor types, separated by 1 week. Finally, we tested eight inbred strains of mice on four floor types to examine patterns of strain sensitivity to 2 g/kg of intraperitoneal ethanol and determined the test parameters that maximized strain effect size. Motor incoordination varied depending on the floor type and strain. When data from strain 129S1/SvlmJ were removed from the analyses because of their extreme behavior, the greatest strain effect size was observed on one floor type during the first 10 min of testing after 2 g/kg of intraperitoneal ethanol. These findings suggest that the parallel rod floor apparatus provides a useful means for examining ethanol-induced motor incoordination in mice but that specific testing procedures are important for optimizing detection of motor incoordination and genetic influences.     

Dopamine inhibition of human tyrosine hydroxylase type 1 is controlled by the specific portion in the N-terminus of the enzyme

Tyrosine hydroxylase (TH), which converts L-tyrosine to L-DOPA, is a rate-limiting enzyme in the biosynthesis of catecholamines; its activity is regulated by feedback inhibition by catecholamine products including dopamine. To investigate the specific portion of the N-terminus of TH that determines the efficiency of dopamine inhibition, wild-type and N-terminal 35-, 38-, and 44-amino acid-deleted mutants (del-35, del-38, and del-44, respectively) of human TH type 1 were expressed as a maltose binding protein fusion in Escherichia coli and purified as a tetrameric form by affinity and size-exclusion chromatography. The fused-form wild-type enzyme possessed almost the same specific enzymatic activity as the previously reported recombinant nonfused form. Although maximum velocities of all N-terminus-deleted forms were about one-fourth of the wild-type value, there was no difference in Michaelis constants for L-tyrosine or (6R)-(L-erythro-1',2'-dihydroxypropyl)-2-amino-4-hydroxy-5,6,7,8-tetrahy dropteridine (6RBPH4) among the four enzymes. The iron contents incorporated into the three N-terminus-deleted mutants were significantly lower than that of wild type. However, there was no substantial difference in incorporated iron contents among the three mutants. The deletion of up to no less than 38 amino acid residues in the N-terminus made the enzyme more resistant to dopamine inhibition than the wild-type or del-35 TH form. Dopamine bound to the del-38 more than to the del-35 TH form. However, when incubation with dopamine was followed by further inhibition with the cofactor 6RBPH4 dopamine was expelled more readily from the del-38 than from the del-35 TH form. These observations suggest that the amino acid sequence Gly36-Arg37-Arg38 plays a key role in determining the competition between dopamine and 6RBPH4 and affects the efficiency of dopamine inhibition of the catalytic activity.     

Retrograde Axonal Transport of Dopamine Beta Hydroxylase Antibodies by Neurons in the Trigeminal Ganglion

In this study we describe a population of neurons in the adult rat trigeminal ganglion (TG) that express dopamine beta-hydroxylase (DBH) and tyrosine hydroxylase (TH), and transport anti-DBH from their terminals. We have used NGF and NT3 labeled with biotin and anti-p75^NTR labeled with FITC to examine the transport of neurotrophins and their receptors by these cells. In both the superior cervical ganglion (SCG) and the TG all neurons that transported anti-DBH transported NGF. While 100% of the DBH positive neurons in the TG also transported NT3, approximately 25% of these neurons in the SCG failed to transport NT3. In the SCG virtually all the neurons transported anti-p75^NTR with the neurotrophins while in the TG more than 25% of these neurons failed to transport anti-p75^NTR with the neurotrophins. These findings suggest that DBH positive neurons in the TG depend upon target-derived NGF and NT3 for their noradrenergic phenotype.     

Genetic dissection of quantitative trait locus for ethanol sensitivity in long- and short-sleep mice

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.     

Quantitative genetics of feeding behavior in two ecological races of the pea aphid, Acyrthosiphon pisum

Much of the diversity of herbivorous insects stems from the adaptive divergence of populations onto different host plants. This often involves the evolution of specialized patterns of host acceptance that in turn lead to assortative mating for insects that mate exclusively on their hosts. Here, we explore the genetic architecture of feeding behavior in a herbivorous insect that has become a model for the study of incipient speciation, the pea aphid (Acyrthosiphon pisum). We use crosses between individuals specialized to either alfalfa or red clover in order to perform both a biometrical analysis and a quantitative trait locus (QTL) analysis of key feeding behaviors. For each character in each environment, Castle-Wright's estimator for the number of effective factors segregating ranged from 0.11 to 2.54. Similarly, between 0 and 3 QTLs were detected. In one case, a single QTL explained over 50% of the variance in the F2, suggesting that at least one gene (or a complex of tightly linked genes) has a major effect on feeding behavior in the pea aphid. However, the identified QTL explain only 23-73% of the genetic variance for these characters thus additional genes of minor effect are also involved. We found a variety of modes of gene action, including several cases of non-additive gene action. Our results suggest that feeding behavior in pea aphids is neither simple nor highly polygenic. The oligogenetic basis of variation in feeding behavior may facilitate host shifts, providing one explanation for the frequent divergence and speciation of herbivorous insects.     

Analysis of the mouseAmy locus in recombinant inbred mouse strains

Pancreatic and salivary amylase cDNA probes have been used to search for new DNA fragment length variation among a total of 43 inbred mouse strains. Fragment length differences found with three restriction endonucleases grouped the strains into two major classes. The segregation of these variant fragments has been analyzed among several sets of recombinant inbred strains and is presented here. Previously reported differences for strains YBR and CE have been confirmed. New segregation data for carbonic anhydrase, a locus near the proximal end of mouse chromosome 3, are presented.     

Assignment of the gene for dipeptidase 2 to Mus musculus chromosome 18 by somatic cell hybridization

Evidence is presented for the assignment of the gene for dipeptidase 2 to Mus musculus chromosome 18 by synteny testing and karyotypic analysis of Chinese hamster × mouse somatic cell hybrid clones. DIP-2 and chromosome 18 were expressed concordantly in 24/24 clones examined (ten primary clones and 14 secondary clones). Synteny testing indicated that DIP-2 was not expressed concordantly with the expression of any marker enzymes.This work was supported by NIH grant USPHS GM 09966.     

Abnormal anxiety-related behavior in serotonin transporter null mutant mice: the influence of genetic background

Serotonin transporter (5-HTT) null mutant mice provide a model system to study the role genetic variation in the 5-HTT plays in the regulation of emotion. Anxiety-like behaviors were assessed in 5-HTT null mutants with the mutation placed on either a B6 congenic or a 129S6 congenic background. Replicating previous findings, B6 congenic 5-HTT null mutants exhibited increased anxiety-like behavior and reduced exploratory locomotion on the light ↔ dark exploration and elevated plus-maze tests. In contrast, 129S6 congenic 5-HTT null mutant mice showed no phenotypic abnormalities on either test. 5-HTT null mutants on the 129S6 background showed reduced 5-HT_1A receptor binding (as measured by quantitative autoradiography) and reduced 5-HT_1A receptor function (as measured by 8-OH-DPAT-indcued hypothermia). These data confirm that the 5-HTT null mutation produced alterations in brain 5-HT function in mice on the 129S6 background, thereby discounting the possibility that the absence of an abnormal anxiety-like phenotype in these mice was due to a suppression of the mutation by 129 modifier genes. Anxiety-like behaviors in the light ↔ dark exploration and elevated plus-maze tests were significantly higher in 129S6 congenic +/+ mice as compared to B6 congenic +/+ mice. This suggests that high baseline anxiety-like behavior in the 129S6 strain might have precluded detection of the anxiety-like effects of the 5-HTT null mutation on this background. Present findings provide further evidence linking genetic variation in the 5-HTT to abnormalities in mood and anxiety. Furthermore, these data highlight the utility of conducting behavioral phenotyping of mutant mice on multiple genetic backgrounds.     

Effects of Dibutyryl Cyclic AMP and Retinoic Acid on the Differentiation of Dopamine Neurons: Prevention of Cell Death by Dibutyryl Cyclic AMP

Abstract: Immature neurons, including fetal and tumoral cells, are used for investigating neuronal differentiation in vitro. The human neuroblastoma cell line NB69 could be induced to differentiate to dopamine or acetylcholine neurons by different compounds, including neurotrophins and activators of the protein kinases. In these NB69 cells dibutyryl cyclic AMP (dbcAMP) at 2 m M reduced the division rate and increased the levels of catecholamines, tyrosine hydroxylase (TH) activity, and monoamine oxidase activity. The dbcAMP also increased cell size, dendritic arborization, density of the sites for high-affinity dopamine uptake, and activity of choline acetyltransferase. In fetal rat midbrain neurons treatment with dbcAMP increased the levels of dopamine and the number of TH-immunoreactive neurons in the culture. When embryonic day 14 fetal midbrain neurons, previously exposed to 1 µ M retinoic acid (a compound that severely reduces the number of fetal midbrain dopamine neurons), were treated with dbcAMP, the levels of dopamine and the number of TH-immunoreactive cells returned to normal levels. This suggests that dbcAMP induces the differentiation to dopamine neurons of quiescent progenitor or facilitates expression of the dopamine phenotype in immature neurons. Therefore, dbcAMP not only differentiates uncommitted immature dopamine neurons, but also reverses the antidopaminergic effects of retinoic acid. These properties of dbcAMP could be of therapeutic value in Parkinson's disease.     

不同发育时期小麦粒重性状QTL的动态分析

利用6044×01-35构建的重组自交系(RIL)群体为试验材料,对小麦粒重性状进行发育动态QTL分析。结果表明,在小麦花后子粒灌浆的7个不同时期,两个试验点共检测到16个与粒重性状相关的QTL。其中开花后20d检测到的单穗粒重QTL位于2A染色体上,解释率达12%,遗传效应超过10;两环境下控制千粒重QTL在7个时期均被检测到。花后的各个时期均能在Xgwm448-Xgpw7399标记区间定位到千粒重QTL。其中花后10d检测到1个千粒重QTL,位于2A染色体的Xgwm448-Xgpw7399标记区间,解释较大的表型变异,达到18%。Qtl8、Qtl13和Qtl14均定位在Xgwm448-Xgpw7399标记区间的同一位置,共同解释11%的表型变异。花后20d和花后25d均检测到1个QTL,位于2A染色体的Xgwm372-Xgwm95标记区间的不同位点,均能解释4%的表型变异。花后40d检测到1个QTL,位于1D染色体的Xwmc93-Xgpw2224标记区间,解释1%的表型变异。从连锁群的位置上看,控制千粒重的QTL主要集中在2A染色体的Xgwm448-Xgpw7399标记区间,这是一个控制千粒重QTL的富集区域,以期进行精细定位和图位克隆。     

Genetic and behavioral differences among five inbred mouse strains commonly used in the production of transgenic and knockout mice

Five strains of mice commonly used in transgenic and knockout production were compared with regard to genetic background and behavior. These strains were: C57BL/6J, C57BL/6NTac, 129P3/J (formerly 129/J), 129S6/SvEvTac (formerly 129/SvEvTac) and FVB/NTac. Genotypes for 342 microsatellite markers and performance in three behavioral tests (rotorod, open field activity and habituation, and contextual and cued fear conditioning) were determined. C57BL/6J and C57BL/6NTac were found to be true substrains; there were only 12 microsatellite differences between them. Given the data on the genetic background, one might predict that the two C57BL/6 substrains should be very similar behaviorally. Indeed, there were no significant behavioral differences between C57BL/6J and C57BL/6NTac. Contrary to literature reports on other 129 strains, 129S6/SvEvTac often performed similarly to C57BL/6 strains, except that it was less active. FVB/NTac showed impaired rotorod learning and cued fear conditioning. Therefore, both 129S6/SvEvTac and C57BL/6 are recommended as background strains for targeted mutations when researchers want to evaluate their mice in any of these three behavior tests. However, any transgene on the FVB/NTac background should be transferred to B6. Habituation to the open field was analyzed using the parameters: total distance, center distance, velocity and vertical activity. Contrary to earlier studies, we found that all strains habituated to the open field in at least two of these parameters (center distance and velocity).