1
|
Sheardown E, Mech AM, Petrazzini MEM, Leggieri A, Gidziela A, Hosseinian S, Sealy IM, Torres-Perez JV, Busch-Nentwich EM, Malanchini M, Brennan CH. Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. Neurosci Biobehav Rev 2022; 135:104559. [PMID: 35124155 PMCID: PMC9016269 DOI: 10.1016/j.neubiorev.2022.104559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/10/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.
Collapse
Affiliation(s)
- Eva Sheardown
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Aleksandra M Mech
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | | | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Saeedeh Hosseinian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Ian M Sealy
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jose V Torres-Perez
- UK Dementia Research Institute at Imperial College London and Department of Brain Sciences, Imperial College London, 86 Wood Lane, London W12 0BZ, UK
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK.
| |
Collapse
|
2
|
Rapid Effects of Selection on Brain-wide Activity and Behavior. Curr Biol 2020; 30:3647-3656.e3. [PMID: 32763165 DOI: 10.1016/j.cub.2020.06.086] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/19/2020] [Accepted: 06/24/2020] [Indexed: 11/21/2022]
Abstract
Interindividual variation in behavior and brain activity is universal and provides substrates for natural selection [1-9]. Selective pressures shift the expression of behavioral traits at the population level [10, 11], but the accompanying changes of the underlying neural circuitry have rarely been identified [12, 13]. Selection likely acts through the genetic and/or epigenetic underpinnings of neural activity controlling the selected behavior [14]. Endocrine and neuromodulatory systems participate in behavioral diversity and could provide the substrate for evolutionary modifications [15-21]. Here, we examined brain-wide patterns of activity in larval zebrafish selectively bred over two generations for extreme differences in habituation of the acoustic startle response (ASR) [22]. The ASR is an evolutionarily conserved defensive behavior induced by strong acoustic/vibrational stimuli. ASR habituation shows great individual variability that is stable over days and heritable [4, 22]. Selection for high ASR habituation leads to stronger sound-evoked activation of ASR-processing brain areas. In contrast, animals selected for low habituation displayed stronger spontaneous activity in ASR-processing centers. Ablation of dopaminergic tyrosine hydroxylase (TH) neurons decreased ASR sensitivity. Independently selected ASR habituation lineages link the effect of behavioral selection to dopaminergic caudal hypothalamus (HC) neurons [23]. High ASR habituation co-segregated with decreased spontaneous swimming phenotypes, but visual startle responses were unaffected. Furthermore, high- and low-habituation larvae differed in stress responses as adults. Thus, selective pressure over a couple of generations on ASR habituation behavior is able to induce substantial differences in brain activity, carrying along additional behaviors as piggyback traits that might further affect fitness in the wild. VIDEO ABSTRACT.
Collapse
|
3
|
Chase KA, Mallari JE, Tan Y, Sittig L. Behavioral Effects of Neuronal, Parent-specific Commd1 Knockout in Mice. Neuroscience 2020; 434:1-7. [PMID: 32200079 DOI: 10.1016/j.neuroscience.2020.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
In this study we focused on gene expression and behavioral differences in mice with brain-specific Commd1 knockout. Commd1 is an imprinted gene with preferential maternal expression, residing within a larger genomic region previously found to affect sensorimotor gating. In this study, individuals harboring a conditional Commd1 mutant allele were bred with Syn1-Cre animals, paying special attention to the parent of origin of the Commd1 mutation. Analysis of mRNA levels of Commd1 and phenotypic tests, including the open field, sensorimotor gating, and the forced swim test, were conducted on offspring with either maternally or paternally derived Commd1 knockout. We found that measurable Commd1 mRNA knockout occurred only in the maternally derived line and affected stereotypy and depressive-like behavior without differences in total locomotion compared to controls. Interestingly, we found that maternal knockout animals exhibited decreased time swimming and increased time immobile when compared to maternal and paternal wild type, and paternal knockout animals. However, there were no differences in climbing behavior between genotypes. This study demonstrates an in vivo behavioral role for Commd1 for the first time and demonstrates the need for careful interpretation of experimental results involving Cre-based knockout systems.
Collapse
Affiliation(s)
- Kayla A Chase
- University of California, Department of Psychiatry, 9500 Gilman Drive, La Jolla, CA 92093, United States; University of Illinois at Chicago, Department of Psychiatry, 900 S. Ashland Ave, Chicago, IL 60612, United States.
| | - Jazlene E Mallari
- University of California, Department of Psychiatry, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Yvette Tan
- University of California, Department of Psychiatry, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Laura Sittig
- University of California, Department of Psychiatry, 9500 Gilman Drive, La Jolla, CA 92093, United States
| |
Collapse
|
4
|
Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (BETHESDA, MD.) 2020; 10:951-965. [PMID: 31974095 PMCID: PMC7056977 DOI: 10.1534/g3.119.400763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (GWAS). We explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F34; n = 428) using a denser marker set and genotyped a new cohort of AIL mice (F39-43; n = 600) for the first time. We identified 36 novel genome-wide significant loci in the F34 and 25 novel loci in the F39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F39-43 cohort. For this subset of traits, we attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner's Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F34 and F39-43 cohorts (n = 1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.
Collapse
Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92092
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110
| | | | - Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA, 90095
| | | | | | - Greta Sokoloff
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IO, 52242
| | - Abraham A Palmer
- Department of Psychiatry,
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92037 and
| |
Collapse
|
5
|
Abstract
In this chapter we will review both the rationale and experimental design for using Heterogeneous Stock (HS) populations for fine-mapping of complex traits in mice and rats. We define an HS as an outbred population derived from an intercross between two or more inbred strains. HS have been used to perform genome-wide association studies (GWAS) for multiple behavioral, physiological, and gene expression traits. GWAS using HS require four key steps, which we review: selection of an appropriate HS population, phenotyping, genotyping, and statistical analysis. We provide advice on the selection of an HS, comment on key issues related to phenotyping, discuss genotyping methods relevant to these populations, and describe statistical genetic analyses that are applicable to genetic analyses that use HS.
Collapse
|
6
|
Gonzales NM, Seo J, Hernandez Cordero AI, St Pierre CL, Gregory JS, Distler MG, Abney M, Canzar S, Lionikas A, Palmer AA. Genome wide association analysis in a mouse advanced intercross line. Nat Commun 2018; 9:5162. [PMID: 30514929 PMCID: PMC6279738 DOI: 10.1038/s41467-018-07642-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
The LG/J x SM/J advanced intercross line of mice (LG x SM AIL) is a multigenerational outbred population. High minor allele frequencies, a simple genetic background, and the fully sequenced LG and SM genomes make it a powerful population for genome-wide association studies. Here we use 1,063 AIL mice to identify 126 significant associations for 50 traits relevant to human health and disease. We also identify thousands of cis- and trans-eQTLs in the hippocampus, striatum, and prefrontal cortex of ~200 mice. We replicate an association between locomotor activity and Csmd1, which we identified in an earlier generation of this AIL, and show that Csmd1 mutant mice recapitulate the locomotor phenotype. Our results demonstrate the utility of the LG x SM AIL as a mapping population, identify numerous novel associations, and shed light on the genetic architecture of mammalian behavior.
Collapse
Affiliation(s)
- Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Jungkyun Seo
- Center for Genomic & Computational Biology, Duke University, Durham, NC, 27708, USA
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Ana I Hernandez Cordero
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jennifer S Gregory
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Margaret G Distler
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Abney
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
7
|
Abstract
Heterogeneous Stock (HS) populations allow for fine-resolution genetic mapping of a variety of complex traits. HS mice and rats were created from breeding together eight inbred strains, followed by maintaining the colony in a manner that minimizes inbreeding. After 50 or more generations of breeding, the resulting animals' chromosomes represent a genetic mosaic of the founders' haplotypes, with the average distance between recombination events in the centiMorgan range. This allows for genetic mapping to only a few Mb, a much smaller region than what can be identified using traditional F2 intercross or backcross mapping strategies. HS animals have been used to fine-map a variety of complex traits including anxiety and fear behaviors, diabetes, asthma, and heart disease, among others. Once a quantitative trait locus (QTL) has been identified, founder sequence and expression analysis can be used to identify underlying causal genes. In the following review, we provide an overview of how HS rats and mice have been used to identify genetic loci, and in some cases the causal genes, underlying complex traits. We discuss the creation and breeding strategies for both HS rats and mice. We then discuss the statistical analyses used to identify genetic loci, as well as strategies to identify causal genes underlying these loci. We end the chapter by discussing limitations faced when using HS populations, including several statistical challenges that have not been fully resolved.
Collapse
Affiliation(s)
- Leah C Solberg Woods
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53130, USA.
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK
| |
Collapse
|
8
|
Lauer AM, Behrens D, Klump G. Acoustic startle modification as a tool for evaluating auditory function of the mouse: Progress, pitfalls, and potential. Neurosci Biobehav Rev 2017; 77:194-208. [PMID: 28327385 PMCID: PMC5446932 DOI: 10.1016/j.neubiorev.2017.03.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/23/2017] [Accepted: 03/13/2017] [Indexed: 12/16/2022]
Abstract
Acoustic startle response (ASR) modification procedures, especially prepulse inhibition (PPI), are increasingly used as behavioral measures of auditory processing and sensorimotor gating in rodents due to their perceived ease of implementation and short testing times. In practice, ASR and PPI procedures are extremely variable across animals, experimental setups, and studies, and the interpretation of results is subject to numerous caveats and confounding influences. We review considerations for modification of the ASR using acoustic stimuli, and we compare the sensitivity of PPI procedures to more traditional operant psychoacoustic techniques. We also discuss non-auditory variables that must be considered. We conclude that ASR and PPI measures cannot substitute for traditional operant techniques due to their low sensitivity. Additionally, a substantial amount of pilot testing must be performed to properly optimize an ASR modification experiment, negating any time benefit over operant conditioning. Nevertheless, there are some circumstances where ASR measures may be the only option for assessing auditory behavior, such as when testing mouse strains with early-onset hearing loss or learning impairments.
Collapse
Affiliation(s)
- Amanda M Lauer
- Department of Otolaryngology-Head and Neck Surgery and Center for Hearing and Balance, Johns Hopkins University, 515 Traylor Building, 720 Rutland Ave., Baltimore, MD 21205, USA.
| | - Derik Behrens
- Cluster of Excellence Hearing4all, Animal Physiology & Behavior Group, Department for Neuroscience, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, Carl Von Ossietzky Str. 9-11, 26111 Oldenburg, Germany
| | - Georg Klump
- Cluster of Excellence Hearing4all, Animal Physiology & Behavior Group, Department for Neuroscience, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, Carl Von Ossietzky Str. 9-11, 26111 Oldenburg, Germany
| |
Collapse
|
9
|
Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nat Genet 2016; 48:919-26. [PMID: 27376237 PMCID: PMC4963286 DOI: 10.1038/ng.3609] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/08/2016] [Indexed: 12/15/2022]
Abstract
Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to obtain genotypes at 92,734 SNPs. We also measured gene expression using RNA sequencing in three brain regions. Our study identified numerous behavioral, physiological and expression quantitative trait loci (QTLs). We integrated the behavioral QTL and eQTL results to implicate specific genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing constitutes a powerful approach to GWAS in mice.
Collapse
Affiliation(s)
- Clarissa C Parker
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.,Department of Psychology, Middlebury College, Middlebury, Vermont, USA.,Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.,Natural History Museum of Denmark, Copenhagen University, Copenhagen, Denmark
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.,AncestryDNA, San Francisco, California, USA
| | - Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Emily Leung
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Yeonhee J Park
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Emmanuel Aryee
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Joe Davis
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - David A Blizard
- Department of Biobehavioral Health, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Cheryl L Ackert-Bicknell
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA.,Department of Orthopedics and Rehabilitation, University of Rochester, Rochester, New York, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Palo Alto, California, USA.,Department of Biology, Stanford University, Palo Alto, California, USA.,Howard Hughes Medical Institute, Stanford University, Palo Alto, California, USA
| | - Abraham A Palmer
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.,Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, USA.,Department of Psychiatry, University of California, San Diego, La Jolla, California, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
10
|
Sittig LJ, Carbonetto P, Engel KA, Krauss KS, Palmer AA. Integration of genome-wide association and extant brain expression QTL identifies candidate genes influencing prepulse inhibition in inbred F1 mice. GENES BRAIN AND BEHAVIOR 2016; 15:260-70. [PMID: 26482417 DOI: 10.1111/gbb.12262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Abstract
Genetic association mapping in structured populations of model organisms can offer a fruitful complement to human genetic studies by generating new biological hypotheses about complex traits. Here we investigated prepulse inhibition (PPI), a measure of sensorimotor gating that is disrupted in a number of psychiatric disorders. To identify genes that influence PPI, we constructed a panel of half-sibs by crossing 30 females from common inbred mouse strains with inbred C57BL/6J males to create male and female F1 offspring. We used publicly available single nucleotide polymorphism (SNP) genotype data from these inbred strains to perform a genome-wide association scan using a dense panel of over 150,000 SNPs in a combined sample of 604 mice representing 30 distinct F1 genotypes. We identified two independent PPI-associated loci on Chromosomes 2 and 7, each of which explained 12-14% of the variance in PPI. Searches of available databases did not identify any plausible causative coding polymorphisms within these loci. However, previously collected expression quantitative trait locus (eQTL) data from hippocampus and striatum indicated that the SNPs on Chromosomes 2 and 7 that showed the strongest association with PPI were also strongly associated with expression of several transcripts, some of which have been implicated in human psychiatric disorders. This integrative approach successfully identified a focused set of genes which can be prioritized for follow-up studies. More broadly, our results show that F1 crosses among common inbred strains can be used in combination with other informatics and expression datasets to identify candidate genes for complex behavioral traits.
Collapse
Affiliation(s)
- L J Sittig
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - P Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - K A Engel
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - K S Krauss
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - A A Palmer
- Department of Human Genetics, University of Chicago, Chicago, IL.,Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| |
Collapse
|
11
|
High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice. Genetics 2015; 198:103-16. [PMID: 25236452 DOI: 10.1534/genetics.114.167056] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic influences on anxiety disorders are well documented; however, the specific genes underlying these disorders remain largely unknown. To identify quantitative trait loci (QTL) for conditioned fear and open field behavior, we used an F2 intercross (n = 490) and a 34th-generation advanced intercross line (AIL) (n = 687) from the LG/J and SM/J inbred mouse strains. The F2 provided strong support for several QTL, but within wide chromosomal regions. The AIL yielded much narrower QTL, but the results were less statistically significant, despite the larger number of mice. Simultaneous analysis of the F2 and AIL provided strong support for QTL and within much narrower regions. We used a linear mixed-model approach, implemented in the program QTLRel, to correct for possible confounding due to familial relatedness. Because we recorded the full pedigree, we were able to empirically compare two ways of accounting for relatedness: using the pedigree to estimate kinship coefficients and using genetic marker estimates of "realized relatedness." QTL mapping using the marker-based estimates yielded more support for QTL, but only when we excluded the chromosome being scanned from the marker-based relatedness estimates. We used a forward model selection procedure to assess evidence for multiple QTL on the same chromosome. Overall, we identified 12 significant loci for behaviors in the open field and 12 significant loci for conditioned fear behaviors. Our approach implements multiple advances to integrated analysis of F2 and AILs that provide both power and precision, while maintaining the advantages of using only two inbred strains to map QTL.
Collapse
|
12
|
Nikolskiy I, Conrad DF, Chun S, Fay JC, Cheverud JM, Lawson HA. Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. BMC Genomics 2015; 16:415. [PMID: 26016481 PMCID: PMC4445795 DOI: 10.1186/s12864-015-1592-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/28/2015] [Indexed: 12/04/2022] Open
Abstract
Background The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity. Results We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length. Conclusions We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1592-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Igor Nikolskiy
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Justin C Fay
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | | | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| |
Collapse
|
13
|
Dickson PE, Ndukum J, Wilcox T, Clark J, Roy B, Zhang L, Li Y, Lin DT, Chesler EJ. Association of novelty-related behaviors and intravenous cocaine self-administration in Diversity Outbred mice. Psychopharmacology (Berl) 2015; 232:1011-24. [PMID: 25238945 PMCID: PMC4774545 DOI: 10.1007/s00213-014-3737-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/28/2014] [Indexed: 01/22/2023]
Abstract
RATIONALE The preference for and reaction to novelty are strongly associated with addiction to cocaine and other drugs. However, the genetic variants and molecular mechanisms underlying these phenomena remain largely unknown. Although the relationship between novelty- and addiction-related traits has been observed in rats, studies in mice have failed to demonstrate this association. New, genetically diverse, high-precision mouse populations including Diversity Outbred (DO) mice provide an opportunity to assess an expanded range of behavioral variation enabling detection of associations of novelty- and addiction-related traits in mice. METHODS To examine the relationship between novelty- and addiction-related traits, male (n = 51) and female (n = 47) DO mice were tested on open field exploration, hole board exploration, and novelty preference followed by intravenous cocaine self-administration (IVSA; ten 2-h sessions of fixed ratio 1 and one 6-h session of progressive ratio). RESULTS We observed high variation of cocaine IVSA in DO mice with 43 % reaching and 57 % not reaching conventional acquisition criteria. As a group, mice that did not reach these criteria still demonstrated significant lever discrimination. Mice experiencing catheter occlusion or other technical issues (n = 17) were excluded from the analysis. Novelty-related behaviors were positively associated with cocaine IVSA. Multivariate analysis of associations among novelty- and addiction-related traits revealed a large degree of shared variance (45 %). CONCLUSIONS Covariation among cocaine IVSA and novelty-related phenotypes in DO mice indicates that this relationship is amenable to genetic dissection. The high genetic precision and phenotypic diversity in the DO may facilitate discovery of previously undetectable mechanisms underlying predisposition to develop addiction disorders.
Collapse
Affiliation(s)
| | - Juliet Ndukum
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Troy Wilcox
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - James Clark
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Brittany Roy
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Lifeng Zhang
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
| | - Yun Li
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
| | - Da-Ting Lin
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
| | | |
Collapse
|
14
|
Gonzales NM, Palmer AA. Fine-mapping QTLs in advanced intercross lines and other outbred populations. Mamm Genome 2014; 25:271-92. [PMID: 24906874 DOI: 10.1007/s00335-014-9523-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/25/2014] [Indexed: 12/16/2022]
Abstract
Quantitative genetic studies in model organisms, particularly in mice, have been extremely successful in identifying chromosomal regions that are associated with a wide variety of behavioral and other traits. However, it is now widely understood that identification of the underlying genes will be far more challenging. In the last few years, a variety of populations have been utilized in an effort to more finely map these chromosomal regions with the goal of identifying specific genes. The common property of these newer populations is that linkage disequilibrium spans relatively short distances, which permits fine-scale mapping resolution. This review focuses on advanced intercross lines (AILs) which are the simplest such population. As originally proposed in 1995 by Darvasi and Soller, an AIL is the product of intercrossing two inbred strains beyond the F2 generation. Unlike recombinant inbred strains, AILs are maintained as outbred populations; brother-sister matings are specifically avoided. Each generation of intercrossing beyond the F2 further degrades linkage disequilibrium between adjacent makers, which allows for fine-scale mapping of quantitative trait loci (QTLs). Advances in genotyping technology and techniques for the statistical analysis of AILs have permitted rapid advances in the application of AILs. We review some of the analytical issues and available software, including QTLRel, EMMA, EMMAX, GEMMA, TASSEL, GRAMMAR, WOMBAT, Mendel, and others.
Collapse
Affiliation(s)
- Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | | |
Collapse
|
15
|
Abstract
Quantitative trait locus (QTL) mapping in animal populations has been a successful strategy for identifying genomic regions that play a role in complex diseases and traits. When conducted in an F2 intercross or backcross population, the resulting QTL is frequently large, often encompassing 30 Mb or more and containing hundreds of genes. To narrow the locus and identify candidate genes, additional strategies are needed. Congenic strains have proven useful but work less well when there are multiple tightly linked loci, frequently resulting in loss of phenotype. As an alternative, we discuss the use of highly recombinant outbred models for directly fine-mapping QTL to only a few megabases. We discuss the use of several currently available models such as the advanced intercross (AI), heterogeneous stocks (HS), the diversity outbred (DO), and commercially available outbred stocks (CO). Once a QTL has been fine-mapped, founder sequence and expression QTL mapping can be used to identify candidate genes. In this regard, the large number of alleles found in outbred stocks can be leveraged to identify causative genes and variants. We end this review by discussing some important statistical considerations when analyzing outbred populations. Fine-resolution mapping in outbred models, coupled with full genome sequence, has already led to the identification of several underlying causative genes for many complex traits and diseases. These resources will likely lead to additional successes in the coming years.
Collapse
Affiliation(s)
- Leah C Solberg Woods
- Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| |
Collapse
|
16
|
Schauwecker PE. Microarray-assisted fine mapping of quantitative trait loci on chromosome 15 for susceptibility to seizure-induced cell death in mice. Eur J Neurosci 2013; 38:3679-90. [PMID: 24001120 DOI: 10.1111/ejn.12351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/08/2013] [Indexed: 11/30/2022]
Abstract
Prior studies with crosses of the FVB/NJ (FVB; seizure-induced cell death-susceptible) mouse and the C57BL/6J (B6; seizure-induced cell death-resistant) mouse revealed the presence of a quantitative trait locus (QTL) on chromosome 15 that influenced susceptibility to kainic acid-induced cell death (Sicd2). In an earlier study, we confirmed that the Sicd2 interval harbors gene(s) conferring strong protection against seizure-induced cell death through the creation of the FVB.B6-Sicd2 congenic strain, and created three interval-specific congenic lines (ISCLs) that encompass Sicd2 on chromosome 15 to fine-map this locus. To further localise this Sicd2 QTL, an additional congenic line carrying overlapping intervals of the B6 segment was created (ISCL-4), and compared with the previously created ISCL-1-ISCL-3 and assessed for seizure-induced cell death phenotype. Whereas all of the ISCLs showed reduced cell death associated with the B6 phenotype, ISCL-4, showed the most extensive reduction in seizure-induced cell death throughout all hippocampal subfields. In order to characterise the susceptibility loci on Sicd2 by use of this ISCL and identify compelling candidate genes, we undertook an integrative genomic strategy of comparing exon transcript abundance in the hippocampus of this newly developed chromosome 15 subcongenic line (ISCL-4) and FVB-like littermates. We identified 10 putative candidate genes that are alternatively spliced between the strains and may govern strain-dependent differences in susceptibility to seizure-induced excitotoxic cell death. These results illustrate the importance of identifying transcriptomics variants in expression studies, and implicate novel candidate genes conferring susceptibility to seizure-induced cell death.
Collapse
Affiliation(s)
- P E Schauwecker
- Department of Cell and Neurobiology, USC Keck School of Medicine, 1333 San Pablo Street, BMT 403, Los Angeles, CA, 90033, USA
| |
Collapse
|
17
|
Assessment of behaviors modeling aspects of schizophrenia in Csmd1 mutant mice. PLoS One 2012; 7:e51235. [PMID: 23284669 PMCID: PMC3524225 DOI: 10.1371/journal.pone.0051235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 10/31/2012] [Indexed: 11/27/2022] Open
Abstract
Schizophrenia is a debilitating psychotic disorder that affects up to 1.5% of the population worldwide. Two recent studies in humans identified genome-wide significant associations between schizophrenia and single-nucleotide polymorphisms (SNPs) in an intron of CSMD1. The effect of deleting CSMD1 on mouse behavior is unknown. The present study utilized mice with a mutant Csmd1 allele in which the first exon had been ablated (KO mice). All Csmd1 transcripts that included the first exon were absent in the brains of KO mice, but there was persistent expression of at least one other transcript that does not include the first exon. Wild type (WT), heterozygous (HET), and KO mice were assessed using several well-established behavioral paradigms that model aspects of schizophrenia. Csmd1 KO mice did not differ from wild-type littermates for sensorimotor gating (measured as prepulse inhibition), social interaction, anhedonia (measured by sucrose preference), or sensitivity to the locomotor stimulant effects of the dopaminergic agent d-amphetamine. These data demonstrate that loss of Csmd1 transcripts that include the first exon does not alter multiple well-established behaviors that model aspects of schizophrenia. The SNP most strongly associated with schizophrenia in humans is between exons 3 and 4; therefore, ablation of exon 1 appeared to be a logical animal model. Nevertheless, future studies should consider alternative mouse models including gain-of-function mutations, and loss-of-function mutations that target alternative transcripts of Csmd1.
Collapse
|
18
|
Abstract
In mammals, milk provision is crucial to offspring survival and growth from birth to weaning. Milk deficiency early in life may cause death or changes in the progeny metabolism that later may lead to obesity and metabolic disorders. This study investigates milk ejection (ME) the first day after birth (D1) in F(2) females from the intercross of LG/J and SM/J inbred mice strains. The absence of milk in F(3) pups' stomach at D1 is directly associated with their survival (p < 0.001) and growth pattern (p < 0.001) in the early stages of life. Furthermore, late growth pattern is also affected by this lack of nutrients at D1 because pups that survive this absence, mostly males, are heavier at weaning (p < 0.001) which, after necropsy, is shown to be due to significant higher total fat deposition (p < 0.01). We performed QTL analysis for ME at D1 in these F(2) females. Maternal performance of ME revealed a complex genetic architecture which even though it contains only a single QTL (accounting for 8 % of the variation in ME), it is totally context-dependent on the genetic background. We discovered many regions involved in epistatic interactions that together with the single QTL explain 19 % of the genetic variation for this trait. Milk ejection is an important component of maternal care, and understanding the mechanisms modulating its variation, along with other maternal features, may help to disentangle the complexity that is the mother/offspring relationship.
Collapse
|
19
|
Solberg Woods LC, Holl KL, Oreper D, Xie Y, Tsaih SW, Valdar W. Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiol Genomics 2012; 44:1013-26. [PMID: 22947656 DOI: 10.1152/physiolgenomics.00040.2012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Type 2 diabetes (T2D) is a disease of relative insulin deficiency resulting from both insulin resistance and beta cell failure. We have previously used heterogeneous stock (HS) rats to fine-map a locus for glucose tolerance. We show here that glucose intolerance in the founder strains of the HS colony is mediated by different mechanisms: insulin resistance in WKY and an insulin secretion defect in ACI, and we demonstrate a high degree of variability for measures of insulin resistance and insulin secretion in HS rats. As such, our goal was to use HS rats to fine-map several diabetes-related traits within a region on rat chromosome 1. We measured blood glucose and plasma insulin levels after a glucose tolerance test in 782 male HS rats. Using 97 SSLP markers, we genotyped a 68 Mb region on rat chromosome 1 previously implicated in glucose and insulin regulation. We used linkage disequilibrium mapping by mixed model regression with inferred descent to identify a region from 198.85 to 205.9 that contains one or more quantitative trait loci (QTL) for fasting insulin and a measure of insulin resistance, the quantitative insulin sensitivity check index. This region also encompasses loci identified for fasting glucose and Insulin_AUC (area under the curve). A separate <3 Mb QTL was identified for body weight. Using a novel penalized regression method we then estimated effects of alternative haplotype pairings under each locus. These studies highlight the utility of HS rats for fine-mapping genetic loci involved in the underlying causes of T2D.
Collapse
Affiliation(s)
- Leah C Solberg Woods
- Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Paek MJ, Kang UG. How many genes are involved in schizophrenia? A simple simulation. Prog Neuropsychopharmacol Biol Psychiatry 2012; 38:302-9. [PMID: 22561393 DOI: 10.1016/j.pnpbp.2012.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 01/09/2023]
Abstract
We attempted to estimate how many genes are involved in schizophrenia using a simulation based on the polygenic threshold model. The basic assumptions were as follows: (1) All genes involved are transmitted independently; (2) every locus is composed of two alleles - one pathogenic and the other non-pathogenic; (3) all pathogenic alleles are dominant; (4) the two alleles at any locus are in Hardy-Weinberg Equilibrium (HWE) in the general population (GP) but not within the patient (PP) or non-patient (NP) subpopulations; (5) the number of affected loci determines the disease genetically; and (6) only a fraction of genetically determined individuals actually becomes ill. A range of the total number of disease-related genes (N) and threshold genetic load (T) was set for the simulation. Assuming that the number of affected loci follows a binomial distribution, the mean gene frequencies satisfying a disease prevalence of 1.12% in the GP were sought for various N and T combinations. Based on these gene frequencies, the odds ratio and the incidence rate in relatives under random mating were calculated. These results were then compared with real genetic epidemiologic data to obtain best-fit estimates for N and T. The results indicated that a polygenic threshold model with an N greater than 100 and a T in the range of 0.3-0.8 fits the empirical data. It was estimated that at least several hundreds of study subjects are required to yield a statistically significant frequency difference for a single gene between the patient and the control groups.
Collapse
Affiliation(s)
- Myung Jae Paek
- Department of Psychiatry, The Armed Forces Capital Hospital, Seongnam, Republic of Korea
| | | |
Collapse
|
21
|
Chiavegatto S, Sauce B, Ambar G, Cheverud JM, Peripato AC. Hypothalamic expression of Peg3 gene is associated with maternal care differences between SM/J and LG/J mouse strains. Brain Behav 2012; 2:365-76. [PMID: 22950040 PMCID: PMC3432959 DOI: 10.1002/brb3.58] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/27/2012] [Accepted: 04/04/2012] [Indexed: 11/17/2022] Open
Abstract
Maternal care is essential in mammals, and variations in the environment provided by mothers may directly influence the viability of newborns and emotional behavior later in life. A previous study investigated genetic variations associated with maternal care in an intercross of LG/J and SM/J inbred mouse strains and identified two single-locus QTLs (quantitative trait loci). Here, we selected three candidate genes located within these QTLs intervals; Oxt on chromosome 2, and FosB and Peg3 on chromosome 7 and tested their association with maternal care. LG/J females showed impaired postpartum nest building and pup retrieval, a one-day delay in milk ejection, reduced exploratory activity, and higher anxiety-like behavior when compared to SM/J females. The nucleotide sequences of Oxt and FosB were similar between strains, as were their hypothalamic expression levels. Conversely, Peg3 nucleotide sequences showed four nonsynonymous replacement substitutions on LG/J dams, T11062G, G13744A, A13808G, and G13813A, and a 30 base pair (10 aa) in tandem repeat in the coding region with three copies in SM/J and five copies in LG/J. Maternal care impaired LG/J mothers express 37% lower Peg3 mRNA levels in the hypothalamus on the second postpartum day. We also found an association of the Peg3 repeat-variant and poor maternal care in F(2) heterozygote females derived from a LG/J × SM/J intercross. These results may suggest that the maternally imprinted Peg3 gene is responsible for the single-locus QTL on chromosome 7 that has been shown to influence maternal care in these strains. Furthermore, these data provide additional support for an epigenetic regulation of maternal behavior.
Collapse
Affiliation(s)
- Silvana Chiavegatto
- Department of Pharmacology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
- Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
- National Institute for Developmental Psychiatry for Childhood and Adolescence (INCT‐CNPq), Brazil
| | - Bruno Sauce
- Department of Genetics and Evolution, Biological Science and Health Center, Federal University of Sao Carlos, Sao Carlos, SP, Brazil
| | - Guilherme Ambar
- Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - James M. Cheverud
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 63110, St. Louis, Missouri
| | - Andrea C. Peripato
- Department of Genetics and Evolution, Biological Science and Health Center, Federal University of Sao Carlos, Sao Carlos, SP, Brazil
- Department of Biosciences, Federal University of Sao Paulo, Santos, SP, Brazil
| |
Collapse
|
22
|
Sauce B, de Brito RA, Peripato AC. Genetic architecture of nest building in mice LG/J × SM/J. Front Genet 2012; 3:90. [PMID: 22654894 PMCID: PMC3361010 DOI: 10.3389/fgene.2012.00090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 05/07/2012] [Indexed: 11/13/2022] Open
Abstract
Maternal care is critical to offspring growth and survival, which is greatly improved by building an effective nest. Some suggest that genetic variation and underlying genetic effects differ between fitness-related traits and other phenotypes. We investigated the genetic architecture of a fitness-related trait, nest building, in F2 female mice intercrossed from inbred strains SM/J and LG/J using a QTL analysis for six related nest phenotypes (Presence and Structure pre- and postpartum, prepartum Material Used and postpartum Temperature). We found 15 direct-effect QTLs explaining from 4 to 13% of the phenotypic variation in nest building, mostly with non-additive effect. Epistatic analyses revealed 71 significant epistatic interactions which together explain from 28.4 to 75.5% of the variation, indicating an important role for epistasis in the adaptive process of nest building behavior in mice. Our results suggest a genetic architecture with small direct effects and a larger number of epistatic interactions as expected for fitness-related phenotypes.
Collapse
Affiliation(s)
- Bruno Sauce
- Department of Genetics and Evolution, Center of Health and Biological Sciences, Federal University of Sao Carlos Sao Carlos, Brazil
| | | | | |
Collapse
|
23
|
Parker CC, Cheng R, Sokoloff G, Palmer AA. Genome-wide association for methamphetamine sensitivity in an advanced intercross mouse line. GENES, BRAIN, AND BEHAVIOR 2012; 11:52-61. [PMID: 22032291 PMCID: PMC3368015 DOI: 10.1111/j.1601-183x.2011.00747.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitivity to the locomotor stimulant effects of methamphetamine (MA) is a heritable trait that utilizes neurocircuitry also associated with the rewarding effects of drugs. We used the power of a C57BL/6J × DBA/2J F(2) intercross (n = 676) and the precision of a C57BL/6J × DBA/2J F(8) advanced intercross line (Aap: B6, D2-G8; or F(8) AIL; n = 552) to identify and narrow quantitative trait loci (QTLs) associated with sensitivity to the locomotor stimulant effects of MA. We used the program QTLRel to simultaneously map QTL in the F(2) and F(8) AIL mice. We identified six genome-wide significant QTLs associated with locomotor activity at baseline and seven genome-wide significant QTLs associated with MA-induced locomotor activation. The average per cent decrease in QTL width between the F(2) and the integrated analysis was 65%. Additionally, these QTLs showed a distinct temporal specificity within each session that allowed us to further refine their locations, and identify one QTL with a 1.8-LOD support interval of 1.47 Mb. Next, we utilized publicly available bioinformatics resources to exploit strain-specific sequence data and strain- and region-specific expression data to identify candidate genes. These results illustrate the power of AILs in conjunction with sequence and gene expression data to investigate the genetic underpinnings of behavioral and other traits.
Collapse
Affiliation(s)
| | - Riyan Cheng
- Department of Human Genetics, the University of Chicago, IL 60637
| | - Greta Sokoloff
- Department of Human Genetics, the University of Chicago, IL 60637
| | - Abraham A. Palmer
- Department of Human Genetics, the University of Chicago, IL 60637
- Department of Psychiatry and Behavioral Neuroscience, the University of Chicago, IL 60637
| |
Collapse
|
24
|
Genome-wide association for fear conditioning in an advanced intercross mouse line. Behav Genet 2012; 42:437-48. [PMID: 22237917 DOI: 10.1007/s10519-011-9524-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/27/2011] [Indexed: 01/06/2023]
Abstract
Fear conditioning (FC) may provide a useful model for some components of post-traumatic stress disorder (PTSD). We used a C57BL/6J × DBA/2J F(2) intercross (n = 620) and a C57BL/6J × DBA/2J F(8) advanced intercross line (n = 567) to fine-map quantitative trait loci (QTL) associated with FC. We conducted an integrated genome-wide association analysis in QTLRel and identified five highly significant QTL affecting freezing to context as well as four highly significant QTL associated with freezing to cue. The average percent decrease in QTL width between the F(2) and the integrated analysis was 59.2%. Next, we exploited bioinformatic sequence and expression data to identify candidate genes based on the existence of non-synonymous coding polymorphisms and/or expression QTLs. We identified numerous candidate genes that have been previously implicated in either fear learning in animal models (Bcl2, Btg2, Dbi, Gabr1b, Lypd1, Pam and Rgs14) or PTSD in humans (Gabra2, Oprm1 and Trkb); other identified genes may represent novel findings. The integration of F(2) and AIL data maintains the advantages of studying FC in model organisms while significantly improving resolution over previous approaches.
Collapse
|
25
|
Tarantino LM, Eisener-Dorman AF. Forward genetic approaches to understanding complex behaviors. Curr Top Behav Neurosci 2012; 12:25-58. [PMID: 22297575 PMCID: PMC6989028 DOI: 10.1007/7854_2011_189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Assigning function to genes has long been a focus of biomedical research.Even with complete knowledge of the genomic sequences of humans, mice and other experimental organisms, there is still much to be learned about gene function and control. Ablation or overexpression of single genes using knockout or transgenic technologies has provided functional annotation for many genes, but these technologies do not capture the extensive genetic variation present in existing experimental mouse populations. Researchers have only recently begun to truly appreciate naturally occurring genetic variation resulting from single nucleotide substitutions,insertions, deletions, copy number variation, epigenetic changes (DNA methylation,histone modifications, etc.) and gene expression differences and how this variation contributes to complex phenotypes. In this chapter, we will discuss the benefits and limitations of different forward genetic approaches that capture the genetic variation present in inbred mouse strains and present the utility of these approaches for mapping QTL that influence complex behavioral phenotypes.
Collapse
|
26
|
Powell SB, Weber M, Geyer MA. Genetic models of sensorimotor gating: relevance to neuropsychiatric disorders. Curr Top Behav Neurosci 2012; 12:251-318. [PMID: 22367921 PMCID: PMC3357439 DOI: 10.1007/7854_2011_195] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sensorimotor gating, or the ability of a sensory event to suppress a motor response, can be measured operationally via prepulse inhibition (PPI) of the startle response. PPI is deficient in schizophrenia patients as well as other neuropsychiatric disorders, can be measured across species, and has been used widely as a translational tool in preclinical neuropharmacological and genetic research. First developed to assess drug effects in pharmacological and developmental models, PPI has become one of the standard behavioral measures in genetic models of schizophrenia and other neuropsychiatric disorders that exhibit PPI deficits. In this chapter we review the literature on genetic models of sensorimotor gating and discuss the utility of PPI as a tool in phenotyping mutant mouse models. We highlight the approaches to genetic mouse models of neuropsychiatric disease, discuss some of the important caveats to these approaches, and provide a comprehensive table covering the more recent genetic models that have evaluated PPI.
Collapse
Affiliation(s)
- Susan B. Powell
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0804, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
| | - Martin Weber
- Department of Neuroscience, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080-4990, USA
| | - Mark A. Geyer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0804, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
| |
Collapse
|
27
|
Loos M, Staal J, Pattij T, Smit AB, Spijker S. Independent genetic loci for sensorimotor gating and attentional performance in BXD recombinant inbred strains. GENES BRAIN AND BEHAVIOR 2011; 11:147-56. [DOI: 10.1111/j.1601-183x.2011.00754.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
28
|
Parker CC, Cheng R, Sokoloff G, Lim JE, Skol AD, Abney M, Palmer AA. Fine-mapping alleles for body weight in LG/J × SM/J F₂ and F(34) advanced intercross lines. Mamm Genome 2011; 22:563-71. [PMID: 21761260 PMCID: PMC3308133 DOI: 10.1007/s00335-011-9349-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/21/2011] [Indexed: 01/17/2023]
Abstract
The present study measured variation in body weight using a combined analysis in an F(2) intercross and an F(34) advanced intercross line (AIL). Both crosses were derived from inbred LG/J and SM/J mice, which were selected for large and small body size prior to inbreeding. Body weight was measured at 62 (± 5) days of age. Using an integrated GWAS and forward model selection approach, we identified 11 significant QTLs that affected body weight on ten different chromosomes. With these results we developed a full model that explained over 18% of the phenotypic variance. The median 1.5-LOD support interval was 5.55 Mb, which is a significant improvement over most prior body weight QTLs. We identified nonsynonymous coding SNPs between LG/J and SM/J mice in order to further narrow the list of candidate genes. Three of the genes with nonsynonymous coding SNPs (Rad23b, Stk33, and Anks1b) have been associated with adiposity, waist circumference, and body mass index in human GWAS, thus providing evidence that these genes may underlie our QTLs. Our results demonstrate that a relatively small number of loci contribute significantly to the phenotypic variance in body weight, which is in marked contrast to the situation in humans. This difference is likely to be the result of strong selective pressure and the simplified genetic architecture, both of which are important advantages of our system.
Collapse
Affiliation(s)
- Clarissa C. Parker
- Department of Human Genetics, University of Chicago, 920 E 58th St., CLSC-507D, Chicago, IL 60637, USA
| | - Riyan Cheng
- Department of Human Genetics, University of Chicago, 920 E 58th St., CLSC-507D, Chicago, IL 60637, USA
| | - Greta Sokoloff
- Department of Human Genetics, University of Chicago, 920 E 58th St., CLSC-507D, Chicago, IL 60637, USA
| | - Jackie E. Lim
- Departments of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew D. Skol
- Department of Medicine, Section for Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Mark Abney
- Department of Human Genetics, University of Chicago, 920 E 58th St., CLSC-507D, Chicago, IL 60637, USA
| | - Abraham A. Palmer
- Department of Human Genetics, University of Chicago, 920 E 58th St., CLSC-507D, Chicago, IL 60637, USA
- Departments of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
29
|
Kas MJ, Kahn RS, Collier DA, Waddington JL, Ekelund J, Porteous DJ, Schughart K, Hovatta I. Translational Neuroscience of Schizophrenia: Seeking a Meeting of Minds Between Mouse and Man. Sci Transl Med 2011; 3:102mr3. [DOI: 10.1126/scitranslmed.3002917] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
30
|
Cheng R, Abney M, Palmer AA, Skol AD. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet 2011; 12:66. [PMID: 21794153 PMCID: PMC3160955 DOI: 10.1186/1471-2156-12-66] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components. Results We have successfully used the package to analyze many datasets, including F34 body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU. Conclusions QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.
Collapse
Affiliation(s)
- Riyan Cheng
- Department of Human Genetics, The University of Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
31
|
Brennan CH. Zebrafish behavioural assays of translational relevance for the study of psychiatric disease. Rev Neurosci 2011; 22:37-48. [PMID: 21615260 DOI: 10.1515/rns.2011.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Understanding the pathogenesis of the complex behavioural disorders that constitute psychiatric disease is a major challenge for biomedical research. Assays in rodents have contributed significantly to our understanding of the neural basis of behavioural disorders and continue to be one of the main focuses for the development of novel therapeutics. Now, owing to their genetic tractability and optical transparency (allowing in vivo imaging of circuit function) and the rapid expansion of genetic tools, zebrafish are becoming increasingly popular for behavioural genetic research. The increased development of behavioural assays in zebrafish raises the possibility of exploiting the advantages of this system to identify molecular mechanisms contributing to behavioural phenotypes associated with psychiatric disorders as well as potential therapeutics. This mini-review describes behavioural paradigms in zebrafish that can be used to address endophenotypes associated with psychiatric disease. The content reflects the interests of the author and covers tests of cognitive functions, response choice and inhibition, social interaction and executive function.
Collapse
Affiliation(s)
- Caroline H Brennan
- Queen Mary University of London, Biological and Experimental Psychology Group, School of Biological and Chemical Sciences, Mile End, London E1 4NS, UK.
| |
Collapse
|
32
|
Sokoloff G, Parker CC, Lim JE, Palmer AA. Anxiety and fear in a cross of C57BL/6J and DBA/2J mice: mapping overlapping and independent QTL for related traits. GENES BRAIN AND BEHAVIOR 2011; 10:604-14. [PMID: 21554534 DOI: 10.1111/j.1601-183x.2011.00699.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anxiety, like other psychiatric disorders, is a complex neurobehavioral trait, making identification of causal genes difficult. In this study, we examined anxiety-like behavior and fear conditioning (FC) in an F(2) intercross of C57BL/6J and DBA/2J mice. We identified numerous quantitative trait loci (QTL) influencing anxiety-like behavior in both open field (OF) and FC tests. Many of these QTL were mapped back to the same chromosomal regions, regardless of behavior or test. For example, highly significant overlapping QTL on chromosome 1 were found in all FC measures as well as in center time measures in the OF. Other QTL exhibited strong temporal profiles over testing, highlighting dynamic relationship between genotype, test and changes in behavior. Next, we implemented a factor analysis design to account for the correlated nature of the behaviors measured. OF and FC behaviors loaded onto four main factors representing both anxiety and fear behaviors. Using multiple QTL modeling, we calculated the percentage variance in anxiety and fear explained by multiple QTL using both additive and interactive terms. Quantitative trait loci modeling resulted in a broad description of the genetic architecture underlying anxiety and fear accounting for 14-37% of trait variance. Factor analysis and multiple QTL modeling showed both unique and shared QTL for anxiety and fear; suggesting a partially overlapping genetic architecture for these two different models of anxiety.
Collapse
Affiliation(s)
- G Sokoloff
- Department of Human Genetics, The University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|