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1.
Genomewide association studies (GWAS) aim to identify genetic markers strongly associated with quantitative traits by utilizing linkage disequilibrium (LD) between candidate genes and markers. However, because of LD between nearby genetic markers, the standard GWAS approaches typically detect a number of correlated SNPs covering long genomic regions, making corrections for multiple testing overly conservative. Additionally, the high dimensionality of modern GWAS data poses considerable challenges for GWAS procedures such as permutation tests, which are computationally intensive. We propose a cluster‐based GWAS approach that first divides the genome into many large nonoverlapping windows and uses linkage disequilibrium network analysis in combination with principal component (PC) analysis as dimensional reduction tools to summarize the SNP data to independent PCs within clusters of loci connected by high LD. We then introduce single‐ and multilocus models that can efficiently conduct the association tests on such high‐dimensional data. The methods can be adapted to different model structures and used to analyse samples collected from the wild or from biparental F2 populations, which are commonly used in ecological genetics mapping studies. We demonstrate the performance of our approaches with two publicly available data sets from a plant (Arabidopsis thaliana) and a fish (Pungitius pungitius), as well as with simulated data. 相似文献
2.
The inbred strains BALB/cWah1 and 129P1/ReJ both show incomplete penetrance for absent corpus callosum (CC); about 14% of adult mice have no CC at all. Their F(1) hybrid offspring are normal, which proves that the strains differ at two or more loci pertinent to absent CC. Twenty-three recombinant inbred lines were bred from the F(2) cross of BALB/c and 129, and several of these expressed a novel and severe phenotype after only three or four generations of inbreeding - total absence of the CC and severe reduction of the hippocampal commissure (HC) in every adult animal. As inbreeding progressed, intermediate sizes of the CC and the HC remained quite rare. This striking phenotypic distribution in adults arose from developmental thresholds in the embryo. CC axons normally cross to the opposite hemisphere via a tissue bridge in the septal region at midline, where the HC forms before CC axons arrive. The primary defect in callosal agenesis in the BALB/c and 129 strains is severe retardation of fusion of the hemispheres in the septal region, and failure to form a CC is secondary to this defect. The putative CC axons arrive at midline at the correct time and place in all groups, but in certain genotypes, the bridge is not yet present. The relative timing of axon growth and delay of the septal bridge create a narrow critical period for forming a normal brain. 相似文献
3.
Absence epilepsy is a common form of idiopathic generalized epilepsy whose etiology is poorly understood because of genetic and phenotypic heterogeneity. The inbred mouse strain C3H/He exhibits spontaneous absence seizures characterized by spike and wave discharges (SWD) on the electroencephalogram concomitant with behavioral arrest. Previous studies using the C3H/HeJ (HeJ) substrain identified a mutation in the Gria4 gene as a major susceptibility locus. In the present study, we found that two closely related substrains C3H/HeOuJ (OuJ) and C3H/HeSnJ, which have a similar SWD incidence as HeJ, do not contain the Gria4 mutation. Further analysis of backcross mice segregating OuJ and C57BL/6J alleles shows that, unlike the HeJ substrain, OuJ does not have a major locus for SWD but has suggestive loci at best that would explain only a fraction of the phenotypic variance. These results illustrate how the genetic etiology of a common neurological disorder can differ between substrains with similar phenotypes. We infer that all C3H strains are sensitized to SWD and that additional mutations affecting SWD arose or were fixed independently in the years since the substrains diverged. 相似文献
4.
A. P. Nagtegaal S. Spijker T. T. H. Crins Neuro‐Bsik Mouse Phenomics Consortium J. G. G. Borst 《Genes, Brain & Behavior》2012,11(8):911-920
The DBA/2J inbred strain of mice has been used extensively in hearing research as it suffers from early‐onset, progressive hearing loss. Initially, it mostly affects high frequencies, but already at 2–3 months hearing loss becomes broad. In search for hearing loss genes other than Cadherin 23 (otocadherin) and fascin‐2, which make a large contribution to the high‐frequency deficits, we used a large set of the genetic reference population of BXD recombinant inbred strains. For frequencies 4, 8, 16 and 32 kHz, auditory brainstem response hearing thresholds were longitudinally determined from 2–3 up to 12 weeks of age. Apart from a significant, broad quantitative trait locus (QTL) for high‐frequency hearing loss on chromosome 11 containing the fascin‐2 gene, we found a novel, small QTL for low‐frequency hearing loss on chromosome 18, from hereon called ahl9. Real‐time quantitative polymerase chain reaction of organs of Corti, isolated from a subset of strains, showed that a limited number of genes at the QTL were expressed in the organ of Corti. Of those genes, several showed significant expression differences based on the parental line contributing to the allele. Our results may aid in the future identification of genes involved in low‐frequency, early‐onset hearing loss. 相似文献
5.
从HeLa细胞中分离的人的Elongator复合物在组成及与RNAPⅡ的作用方式上与酵母的E- longator复合物十分相似,但对其功能研究极少。为了研究人的Elongator复合物催化亚基Elp3的功能,将人elp3等基因转入酵母elp3基因缺失的突变菌株(elp3Δ菌株),并对转化菌株进行功能互补实验和ssa3和pho5基因表达分析,结果表明人elp3基因可显著恢复突变菌株对高温和Caffeine的敏感性,在低磷条件下显著补偿了突变株pho5基因表达延迟的缺陷,并可在热激条件下提高ssa3基因的表达。含酵母elp3非HAT区和人elp3 HAT区的融合yhelp3对上述缺陷有着更强的补偿能力。而HAT区催化结构域缺失的yhelp3HAT没有任何补偿能力,表明人Elp3亚基可能与酵母的该亚基功能相似,人Elp3的HAT活性也为其行使功能所必需。 相似文献
6.
Ryoko Hashimoto Birger Voigt Yuji Ishimaru Ryoji Hokao Shigeru Chiba Tadao Serikawa Masashi Sasa Takashi Kuramoto 《Experimental Animals》2013,62(3):181-187
Amygdala kindling is useful for modeling human epilepsy development. It has been knownthat genetic factors are involved in the development of amygdala kindling. The purpose ofthis study was to identify the loci that are responsible for the development of amygdalakindling. To achieve this, rat strains from a LEXF/FXLE recombinant inbred (RI) strainpanel were used. The phenotypes of amygdala kindling-related parameters for seven RIstrains and parental LE/Stm and F344/Stm strains were determined. They included theafterdischarge threshold (ADT), the afterdischarge duration (ADD), and the kindling rate,an incidence of development of kindling. Quantitative trait loci (QTL) analysis wasperformed to identify linkage relationships between these phenotypes and 1,033 SNPmarkers. Although no significant differences in pre-kindling ADT and ADD were observed, asignificant difference in the kindling rate was found for the LEXF/FXLE RI strain. TwoQTLs for the amygdala kindling rate (Agkr1 and Agkr2)were identified on rat chromosome 2. These findings clearly prove the existence of geneticinfluences that are involved in kindling development and suggest that substantial geneticcomponents contribute to the progression of partial seizures into generalizedseizures. 相似文献
7.
从HeLa细胞中分离的人的Elongator复合物在组成及与RNAPⅡ的作用方式上与酵母的Elongator复合物十分相似．但对其功能研究极少。为了研究人的Elongator复合物催化亚基Elp3的功能,将人elp3等基因转入酵母elp3基因缺失的突变菌株（elp3△菌株）,并对转化菌株进行功能互补实验和ssa和pho5基因表达分析,结果表明人elp3基因可显著恢复突变菌株对高温和Caffeine的敏感性．在低磷条件下显著补偿了突变株ph05基因表达延迟的缺陷．并可在热激条件下提高ssa3基因的表达。含酵母elp3非HAT区和人elp3 HAT区的融合yhelp3对上述缺陷有着更强的补偿能力。而HAT区催化结构域缺失的yhelp3HAT-没有任何补偿能力．表明人Elp3亚基可能与酵母的该亚基功能相似．人Elp3的HAT活性也为其行使功能所必需。 相似文献
8.
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. 相似文献
9.
Thi Dong Binh Tran Christian Monroy Hernandez Hoan Nguyen Susan Wright Center for Systems Neurogenetics of Addiction Lisa M. Tarantino Elissa J. Chesler George M. Weinstock Yanjiao Zhou Jason A. Bubier 《Genes, Brain & Behavior》2023,22(3):e12845
The gut-brain axis is increasingly recognized as an important pathway involved in cocaine use disorder. Microbial products of the murine gut have been shown to affect striatal gene expression, and depletion of the microbiome by antibiotic treatment alters cocaine-induced behavioral sensitization in C57BL/6J male mice. Some reports suggest that cocaine-induced behavioral sensitization is correlated with drug self-administration behavior in mice. Here, we profile the composition of the naïve microbiome and its response to cocaine sensitization in two collaborative cross (CC) strains. These strains display extremely divergent behavioral responses to cocaine sensitization. A high-responding strain, CC004/TauUncJ (CC04), has a gut microbiome that contains a greater amount of Lactobacillus than the cocaine-nonresponsive strain CC041/TauUncJ (CC41). The gut microbiome of CC41 is characterized by an abundance of Eisenbergella, Robinsonella and Ruminococcus. In response to cocaine, CC04 has an increased Barnsiella population, while the gut microbiome of CC41 displays no significant changes. PICRUSt functional analysis of the functional potential of the gut microbiome in CC04 shows a significant number of potential gut-brain modules altered after exposure to cocaine, specifically those encoding for tryptophan synthesis, glutamine metabolism, and menaquinone synthesis (vitamin K2). Depletion of the microbiome by antibiotic treatment revealed an altered cocaine-sensitization response following antibiotics in female CC04 mice. Depleting the microbiome by antibiotic treatment in males revealed increased infusions for CC04 during a cocaine intravenous self-administration dose–response curve. Together these data suggest that genetic differences in cocaine-related behaviors may involve the microbiome. 相似文献
10.
目的 分离和培养 6 15小鼠的ES细胞集落 ,为建系打下基础。方法 以PMEF为饲养层分离 6 15小鼠的ES细胞集落 ,进行无饲养层培养 ,并对其进行初步鉴定。结果 ES细胞集落的出现率和传代成功率为 2 2 6 %和 0 94 % ,其ALP染色阳性 ,具有稳定的二倍体核型 ,可自发分化为多种类型的细胞。结论 成功分离和培养了6 15小鼠的ES细胞集落 相似文献
11.
Arka Chakraborty Pradeep Kumar Mandal Namasivayam Gautham 《Acta Crystallographica. Section F, Structural Biology Communications》2012,68(10):1169-1174
The crystal structure of the decamer sequence d(CCGGGACCGG)4 has previously been reported at 2.16 Å resolution as a four‐way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four‐way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent‐mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures. 相似文献
12.
Many animal species have been domesticated over the course of human history and became tame as a result of domestication. Tameness is a behavioral characteristic with 2 potential components: (1) reluctance to avoid humans and (2) motivation to approach humans. However, the specific behavioral characteristics selected during domestication processes remain to be clarified for many species. To quantify these 2 different components of tameness separately, we established 3 behavioral tests: the ‘active tame’, ‘passive tame’ and ‘stay‐on‐hand’ tests. We subjected genetically diverse mouse strains to these tests, including 10 wild strains (BFM/2Ms, PGN2/Ms, HMI/Ms, BLG2/Ms, NJL/Ms, KJR/Ms, SWN/Ms, CHD/Ms, MSM/Ms and CAST/Ei), a fancy strain (JF1/Ms) and 6 standard laboratory strains (C3H/HeNJcl, CBA/J, BALB/cAnNCrlCrlj, DBA/2JJcl, 129+Ter/SvJcl and C57BL/6JJcl). To analyze the effects of domestication, these 17 strains were divided into 2 groups: domesticated strains (fancy and laboratory strains) and wild strains. Significant differences between strains were observed in all traits, and the calculated estimates of broad‐sense heritability were 0.15–0.72. These results illustrate that tameness in mice is significantly influenced by genetic background. In addition, they clearly show the differences in the features of tameness in domesticated and wild strains. Most of the domesticated strains showed significantly greater reluctance to avoid humans than wild strains, whereas there was no significant difference in the level of motivation to approach humans between these 2 groups. These results might help to clarify the genetic basis of tameness in mice . 相似文献
13.
Bonné AC den Bieman MG Gillissen GF Kren V Krenová D Bílá V Zídek V Kostka V Musilová A Pravenec M van Zutphen BF van Lith HA 《Biochemical genetics》2003,41(3-4):77-89
The amplified fragment length polymorphism (AFLP) technique has been used to enhance marker density in a large set of recombinant inbred strains (H × B and B × H) derived from a spontaneously hypertensive rat (SHR/OlaIpcv) and a Brown-Norway (BN.lx/Cub) inbred strain. Thirteen different primer combinations were tested and a total of 191 polymorphic bands were detected. From these polymorphic bands 89 AFLP markers could be assigned to specific chromosomes. Several of these AFLP markers were mapped to regions with low marker density, thus filling up gaps in the existing genetic map of these recombinant inbred strains. These results substantiate the value of the AFLP technology in increasing marker density in genetic maps. 相似文献
14.
Hemoglobin phenotypes A and B were determined by polyacrylamide gel electrophoresis of erythrocyte lysates from 29 inbred strains of rats. Fourteen strains have phenotype A and fifteen have phenotype B, which are characterized by five and six hemoglobin bands, respectively. Breeding studies showed that the phenotypes are codominant and that they segregate in a simple Mendelian fashion in the (A×B) F1×A backcross. Sex and hemoglobin phenotype assort independently, and the hemoglobin phenotype is not linked to the major histocompatibility complex (RT1) and to two erythrocyte alloantigenic systems (RT2 and RT3).This work was supported by National Institutes of Health Grant CA 18659. 相似文献
15.
James H. Thorpe Susana C. M. Teixeira Benjamin C. Gale Christine J. Cardin 《Acta Crystallographica. Section D, Structural Biology》2002,58(3):567-569
DNA‐strand exchange is a vital step in the recombination process, of which a key intermediate is the four‐way DNA Holliday junction formed transiently in most living organisms. Here, the single‐crystal structure at a resolution of 2.35 Å of such a DNA junction formed by d(CCGGTACCGG)2, which has crystallized in a more highly symmetrical packing mode to that previously observed for the same sequence, is presented. In this case, the structure is isomorphous to the mismatch sequence d(CCGGGACCGG)2, which reveals the roles of both lattice and DNA sequence in determining the junction geometry. The helices cross at the larger angle of 43.0° (the previously observed angle for this sequence was 41.4°) as a right‐handed X. No metal cations were observed; the crystals were grown in the presence of only group I counter‐cations. 相似文献
16.
Singh R. P. Singh S. 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1985,70(1):80-84
Summary Sixty families from two tomato triple test crosses (S120 x EC61747 and EC31513 x Tusa Ruby) were raised in complete randomized blocks in two replications and two environments (two fertilizer levels). Jinks and Perkins' (1970) analysis was used to detect and estimate the additive, dominance and epistatic components of genetic variation for flowering time, maturity period, number of branches per plant, final height, shape index of fruit, locule number, number of fruits per plant, yield per plant and weight per fruit. The j & 1 type epistasis was more important than the i type epistasis in the first cross, while in the second cross the two components of epistasis played almost equal roles in the control of characters studied. Both the D (additive) and H (dominance) components were significant for most of the characters in both crosses and in both the environments. The D component was relatively more important than the H component in the first cross, while the situation was just the reverse in the second cross. Dominance was directional in 8 out of 36 cases. Ambidirectional dominance was observed in 27 cases. A real absence of dominance was observed in one case only. 相似文献
17.
A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F2 population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome‐wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome‐wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken. 相似文献
18.
D. V. Osipova A. V. Kulikov K. Mekada A. Yoshiki M. P. Moshkin E. V. Kotenkova N. K. Popova 《Genes, Brain & Behavior》2010,9(5):537-543
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. 相似文献
19.
The C57BL/6JOlaHsd and 129S2/SvHsd mice were tested in a battery designed for behavioral phenotyping of genetically modified mice. The study was performed in order to reveal the effect of training history on the behavior by comparison with the experimentally naïve mice in the same tests. Significant strain differences were obtained in all experiments. Previous handling and testing reduced exploratory activity and emotionality significantly in the mice. The coordination ability was better and nociceptive sensitivity was increased in the trained mice. The contextual fear was reduced whereas the cued fear was enhanced in the experienced mice. The training history did not alter initial learning in the water maze. However, after reversal learning the naïve mice displayed significant preference for both old and new platform locations, whereas the battery animals did not exhibit preference to the old location. The experienced mice appeared to be less active in the forced swimming test and exhibited decreased conditioned taste aversion. The influence of test history was strain-dependent in certain cases. Therefore, the experience has substantial consequences on the behavior, mainly by reducing exploratory activity, and the previous experience of the animals has always to be considered in the analysis of genetically modified mice. 相似文献
20.
Crabbe JC Cotnam CJ Cameron AJ Schlumbohm JP Rhodes JS Metten P Wahlsten D 《Genes, Brain & Behavior》2003,2(4):201-213
Mice from 8 to 21 inbred strains were tested for sensitivity to ethanol intoxication using a range of doses and three different measures: the screen test, the dowel test and a test of grip strength. Strains differed under nearly all conditions. For the dowel test, two dowel widths were employed, and mice were tested immediately or 30 min after ethanol. For the dowel and screen tests, low doses failed to affect some strains, and the highest doses failed to discriminate among mice, maximally affecting nearly all. For grip strength, a single ethanol dose was used, and mice of all strains were affected. Pharmacokinetic differences among strains were significant, but these could not account for strain differences in intoxication. For doses and test conditions in the middle range, there were only modest correlations among strain means within a test. In addition, genotypic correlations across tests were modest to quite low. These results suggest that different specific versions of a test reflect the influence of different genes, and that genetic influences on different tests were also distinct. 相似文献