Inbred Panel Research Articles

Establishing the hybrid rat diversity program: a resource for dissecting complex traits.

Rat models have been a major model for studying complex disease mechanisms, behavioral phenotypes, environmental factors, and for drug development and discovery. Inbred rat strains control for genetic background and allow for repeated, reproducible, cellular and whole animal phenotyping. The Hybrid Rat Diversity Panel (HRDP) was designed to be a powerful panel of inbred rats with genomic, physiological, and behavioral data to serve as a resource for systems genetics. The HRDP consists of 96-98 inbred rat strains aimed to maximize power to detect specific genetic loci associated with complex traits while maximizing the genetic diversity among strains. The panel consists of 32-34 genetically diverse inbred strains and two panels of recombinant inbred panels. To establish the HRDP program, embryo resuscitation and breeding were done to establish colonies for distribution. Whole genome sequencing was performed to achieve 30X coverage. Genomic, phenotype, and strain information is available through the Hybrid Rat Diversity Panel Portal at the Rat Genome Database ( http://rgd.mcw.edu ).

Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet.

Pearl millet is an essential crop worldwide, with noteworthy resilience to abiotic stress, yet the advancement of its breeding remains constrained by the underutilization of molecular-assisted breeding techniques. In this study, we collected 1,455,924 single nucleotide polymorphism (SNP) and 124,532 structural variant (SV) markers primarily from a pearl millet inbred germplasm association panel consisting of 242 accessions including 120 observed phenotypes, mostly related to the yield. Our findings revealed that the SV markers had the capacity to capture genetic diversity not discerned by SNP markers. Furthermore, no correlation in heritability was observed between SNP and SV markers associated with the same phenotype. The assessment of the nine genomic prediction models revealed that SV markers performed better than SNP markers. When using the SV markers as the predictor variable, the genomic BLUP model achieved the best performance, while using the SNP markers, Bayesian methods outperformed the others. The integration of these models enabled the identification of eight candidate accessions with high genomic estimated breeding values (GEBV) across nine phenotypes using SNP markers. Four candidate accessions were identified with high GEBV across 22 phenotypes using SV markers. Notably, accession 'P23' emerged as a consistent candidate predicted based on both SNP and SV markers specifically for panicle number. These findings contribute valuable insights into the potential of utilizing both SNP and SV markers for genomic prediction in pearl millet breeding. Moreover, the identification of promising candidate accessions, such as 'P23', underscores the accelerated prospects of molecular breeding initiatives for enhancing pearl millet varieties.

Integrated GWAS, linkage, and transcriptome analysis to identify genetic loci and candidate genes for photoperiod sensitivity in maize.

Maize photosensitivity and the control of flowering not only are important for reproduction, but also play pivotal roles in the processes of domestication and environmental adaptation, especially involving the utilization strategy of tropical maize in high-latitude regions. In this study, we used a linkage mapping population and an inbred association panel with the photoperiod sensitivity index (PSI) phenotyped under different environments and performed transcriptome analysis of T32 and QR273 between long-day and short-day conditions. The results showed that PSIs of days to tasseling (DTT), days to pollen shedding (DTP), and days to silking (DTS) indicated efficacious interactions with photoperiod sensitivity for maize latitude adaptation. A total of 48 quantitative trait loci (QTLs) and 252 quantitative trait nucleotides (QTNs) were detected using the linkage population and the inbred association panel. Thirteen candidate genes were identified by combining the genome-wide association study (GWAS) approach, linkage analysis, and transcriptome analysis, wherein five critical candidate genes, MYB163, bif1, burp8, CADR3, and Zm00001d050238, were significantly associated with photoperiod sensitivity. These results would provide much more abundant theoretical proofs to reveal the genetic basis of photoperiod sensitivity, which would be helpful to understand the genetic changes during domestication and improvement and contribute to reducing the barriers to use of tropical germplasm.

Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models.

The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.

Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding

Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to ‘Insubria’, ‘Microsperma’, and ‘Scagliolino’ genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.

Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice.

Genetic differences among mammalian hosts and among strains of Mycobacterium tuberculosis (Mtb) are well-established determinants of tuberculosis (TB) patient outcomes. The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of complex host-pathogen interactions. To identify host and pathogen genetic determinants of Mtb pathogenesis, we infected members of the highly diverse BXD family of strains with a comprehensive library of Mtb transposon mutants (TnSeq). Members of the BXD family segregate for Mtb-resistant C57BL/6J (B6 or B) and Mtb-susceptible DBA/2J (D2 or D) haplotypes. The survival of each bacterial mutant was quantified within each BXD host, and we identified those bacterial genes that were differentially required for Mtb fitness across BXD genotypes. Mutants that varied in survival among the host family of strains were leveraged as reporters of "endophenotypes," each bacterial fitness profile directly probing specific components of the infection microenvironment. We conducted quantitative trait loci (QTL) mapping of these bacterial fitness endophenotypes and identified 140 host-pathogen QTL (hpQTL). We located a QTL hotspot on chromosome 6 (75.97-88.58 Mb) associated with the genetic requirement of multiple Mtb genes: Rv0127 (mak), Rv0359 (rip2), Rv0955 (perM), and Rv3849 (espR). Together, this screen reinforces the utility of bacterial mutant libraries as precise reporters of the host immunological microenvironment during infection and highlights specific host-pathogen genetic interactions for further investigation. To enable downstream follow-up for both bacterial and mammalian genetic research communities, all bacterial fitness profiles have been deposited into GeneNetwork.org and added into the comprehensive collection of TnSeq libraries in MtbTnDB.

Collaborative cross strain CC011/UncJ as a novel mouse model of T2-high, severe asthma

Among asthmatics, there is significant heterogeneity in the clinical presentation and underlying pathophysiological mechanisms, leading to the recognition of multiple disease endotypes (e.g., T2-high vs. T2-low). This heterogeneity extends to severe asthmatics, who may struggle to control symptoms even with high-dose corticosteroid treatment and other therapies. However, there are limited mouse models available to model the spectrum of severe asthma endotypes. We sought to identify a new mouse model of severe asthma by first examining responses to chronic allergen exposure among strains from the Collaborative Cross (CC) mouse genetics reference population, which contains greater genetic diversity than other inbred strain panels previously used for models of asthma. Mice from five CC strains and the often-used classical inbred strain BALB/cJ were chronically exposed to house dust mite (HDM) allergen for five weeks followed by measurements of airway inflammation. CC strain CC011/UncJ (CC011) exhibited extreme responses to HDM including high levels of airway eosinophilia, elevated lung resistance, and extensive airway wall remodeling, and even fatalities among ~ 50% of mice prior to study completion. Compared to BALB/cJ mice, CC011 mice had stronger Th2-mediated airway responses demonstrated by significantly elevated total and HDM-specific IgE and increased Th2 cytokines during tests of antigen recall, but not enhanced ILC2 activation. Airway eosinophilia in CC011 mice was completely dependent upon CD4+ T-cells. Notably, we also found that airway eosinophilia in CC011 mice was resistant to dexamethasone steroid treatment. Thus, the CC011 strain provides a new mouse model of T2-high, severe asthma driven by natural genetic variation likely acting through CD4+ T-cells. Future studies aimed at determining the genetic basis of this phenotype will provide new insights into mechanisms underlying severe asthma.

Genotype-by-environment interactions for starch, mineral, and agronomic traits in pearl millet hybrids evaluated across five locations in West Africa.

Pearl millet is a staple cereal grown in the harshest environments of arid and semi-arid regions of Asia and sub-Saharan Africa. It is the primary source of calories for millions of people in these regions because it has better adaptation to harsh environmental conditions and better nutritional traits than many other cereals. By screening the pearl millet inbred germplasm association panel (PMiGAP), we earlier reported the best genotypes with the highest concentration of slowly digestible and resistant starch in their grains. In the current study, we tested these 20 top-performing pearl millet hybrids, identified based on starch data, in a randomised block design with three replications at five locations in West Africa, viz. Sadore and Konni (Niger), Bambey (Senegal), Kano (Nigeria), and Bawku (Ghana). Phenotypic variability was assessed for agronomic traits and mineral traits (Fe and Zn). Analysis of variance demonstrated significant genotypic, environmental, and GEI effects among five testing environments for agronomic traits (days to 50% flowering, panicle length, and grain yield), starch traits (rapidly digestible starch, slowly digestible starch, resistant starch, and total starch), and mineral trait (iron and zinc). Starch traits, such as rapidly digestible starch (RDS) and slowly digestible starch (SDS), showed nonsignificant genotypic and environmental interactions but high heritability, indicating the lower environmental influence on these traits in the genotype × testing environments. Genotype stability and mean performance across all the traits were estimated by calculating the multi-trait stability index (MTSI), which showed that genotypes G3 (ICMX207070), G8 (ICMX207160), and G13 (ICMX207184) were the best performing and most stable among the five test environments.

Effects of isolation housing stress and mouse strain on intravenous cocaine self-administration, sensory stimulus self-administration, and reward preference

Sensory stimuli are natural rewards in mice and humans. Consequently, preference for a drug reward relative to a sensory reward may be an endophenotype of addiction vulnerability. In this study, we developed a novel behavioral assay to quantify the preference for intravenous drug self-administration relative to sensory stimulus self-administration. We used founder strains of the BXD recombinant inbred mouse panel (C57BL/6J, DBA/2J) and a model of stress (isolation vs enriched housing) to assess genetic and epigenetic effects. Following 10 weeks of differential housing, all mice were tested under three reward conditions: sensory rewards available, cocaine rewards available, both rewards available. When a single reward was available (sensory stimuli or cocaine; delivered using distinct levers), DBA/2J mice self-administered significantly more rewards than C57BL/6J mice. When both rewards were available, DBA/2J mice exhibited a significant preference for cocaine relative to sensory stimuli; in contrast, C57BL/6J mice exhibited no preference. Housing condition influenced sensory stimulus self-administration and strain-dependently influenced inactive lever pressing when both rewards were available. Collectively, these data reveal strain effects, housing effects, or both on reward self-administration and preference. Most importantly, this study reveals that genetic mechanisms underlying preference for a drug reward relative to a nondrug reward can be dissected using the full BXD panel.

Which mouse multiparental population is right for your study? The Collaborative Cross inbred strains, their F1 hybrids, or the Diversity Outbred population.

Multiparental populations (MPPs) encompass greater genetic diversity than traditional experimental crosses of two inbred strains, enabling broader surveys of genetic variation underlying complex traits. Two such mouse MPPs are the Collaborative Cross (CC) inbred panel and the Diversity Outbred (DO) population, which are descended from the same eight inbred strains. Additionally, the F1 intercrosses of CC strains (CC-RIX) have been used and enable study designs with replicate outbred mice. Genetic analyses commonly used by researchers to investigate complex traits in these populations include characterizing how heritable a trait is, i.e. its heritability, and mapping its underlying genetic loci, i.e. its quantitative trait loci (QTLs). Here we evaluate the relative merits of these populations for these tasks through simulation, as well as provide recommendations for performing the quantitative genetic analyses. We find that sample populations that include replicate animals, as possible with the CC and CC-RIX, provide more efficient and precise estimates of heritability. We report QTL mapping power curves for the CC, CC-RIX, and DO across a range of QTL effect sizes and polygenic backgrounds for samples of 174 and 500 mice. The utility of replicate animals in the CC and CC-RIX for mapping QTLs rapidly decreased as traits became more polygenic. Only large sample populations of 500 DO mice were well-powered to detect smaller effect loci (7.5-10%) for highly complex traits (80% polygenic background). All results were generated with our R package musppr, which we developed to simulate data from these MPPs and evaluate genetic analyses from user-provided genotypes.

Intravenous fentanyl self-administration in male and female C57BL/6J and DBA/2J mice

The genetic mechanisms underlying fentanyl addiction, a highly heritable disease, are unknown. Identifying these mechanisms will lead to better risk assessment, early diagnosis, and improved intervention. To this end, we used intravenous fentanyl self-administration to quantify classical self-administration phenotypes and addiction-like fentanyl seeking in male and female mice from the two founder strains of the BXD recombinant inbred mouse panel (C57BL/6J and DBA/2J). We reached three primary conclusions from these experiments. First, mice from all groups rapidly acquired intravenous fentanyl self-administration and exhibited a dose–response curve, extinction burst, and extinction of the learned self-administration response. Second, fentanyl intake (during acquisition and dose response) and fentanyl seeking (during extinction) were equivalent among groups. Third, strain effects, sex effects, or both were identified for several addiction-like behaviors (cue-induced reinstatement, stress-induced reinstatement, escalation of intravenous fentanyl self-administration). Collectively, these data indicate that C57BL/6J and DBA/2J mice of both sexes were able to acquire, regulate, and extinguish intravenous fentanyl self-administration. Moreover, these data reveal novel strain and sex effects on addiction-like behaviors in the context of intravenous fentanyl self-administration in mice and indicate that the full BXD panel can be used to identify and dissect the genetic mechanisms underlying these effects.

Behavioral phenotypes revealed during reversal learning are linked with novel genetic loci in diversity outbred mice

Impulsive behavior and impulsivity are heritable phenotypes that are strongly associated with risk for substance use disorders. Identifying the neurogenetic mechanisms that influence impulsivity may also reveal novel biological insights into addiction vulnerability. Our past studies using the BXD and Collaborative Cross (CC) recombinant inbred mouse panels have revealed that behavioral indicators of impulsivity measured in a reversal-learning task are heritable and are genetically correlated with aspects of intravenous cocaine self-administration. Genome-wide linkage studies in the BXD panel revealed a quantitative trait locus (QTL) on chromosome 10, but we expect to identify additional QTL by testing in a population with more genetic diversity. To this end, we turned to Diversity Outbred (DO) mice; 392 DO mice (156 males, 236 females) were phenotyped using the same reversal learning test utilized previously. Our primary indicator of impulsive responding, a measure that isolates the relative difficulty mice have with reaching performance criteria under reversal conditions, revealed a genome-wide significant QTL on chromosome 7 (max LOD score = 8.73, genome-wide corrected p<0.05). A measure of premature responding akin to that implemented in the 5-choice serial reaction time task yielded a suggestive QTL on chromosome 17 (max LOD score = 9.14, genome-wide corrected <0.1). Candidate genes were prioritized (2900076A07Rik, Wdr73 and Zscan2) based upon expression QTL data we collected in DO and CC mice and analyses using publicly available gene expression and phenotype databases. These findings may advance understanding of the genetics that drive impulsive behavior and enhance risk for substance use disorders.

A Locus on Chromosome 15 Contributes to Acute Ozone-induced Lung Injury in Collaborative Cross Mice.

Ozone (O3)-induced respiratory toxicity varies considerably within the human population and across inbred mouse strains, indicative of gene-environment interactions (GxE). Though previous studies have identified several quantitative trait loci (QTL) and candidate genes underlying responses to O3 exposure, precise mechanisms of susceptibility remain incompletely described. We sought to update our understanding of the genetic architecture of O3 responsiveness using the Collaborative Cross (CC) recombinant inbred mouse panel. We evaluated hallmark O3-induced inflammation and injury phenotypes in 56 CC strains after exposure to filtered air or 2 ppm O3, and performed focused genetic analysis of variation in lung injury, as reflected by protein in lung lavage fluid. Strain-dependent responses to O3 were clear, and QTL mapping revealed two novel loci on Chr (Chromosomes) 10 (peak, 26.2 Mb; 80% confidence interval [CI], 24.6-43.6 Mb) and 15 (peak, 47.1 Mb; 80% CI, 40.2-54.9 Mb), the latter surpassing the 95% significance threshold. At the Chr 15 locus, C57BL/6J and CAST/EiJ founder haplotypes were associated with higher lung injury responses compared with all other CC founder haplotypes. With further statistical analysis and a weight of evidence approach, we delimited the Chr 15 QTL to an ∼2 Mb region containing 21 genes (10 protein coding) and nominated three candidate genes, namely Oxr1, Rspo2, and Angpt1. Gene and protein expression data further supported Oxr1 and Angpt1 as priority candidate genes. In summary, we have shown that O3-induced lung injury is modulated by genetic variation, identified two high priority candidate genes, and demonstrated the value of the CC for detecting GxE.

Hybrid Rat Diversity Program (HRDP): A rat resource for mapping complex traits

Rats are a major model for studying complex disease mechanisms, behavioral phenotypes, environmental factors, and for drug development and discovery. Inbred rat strains control for genetic background and allow for repeated, reproducible molecular, cellular, and whole animal phenotyping. Genetic susceptibility to disease, sensitivity to environmental elements, and pharmacogenomics are critical components of the concepts of precision medicine. The Hybrid Rat Diversity Program (HRDP) is a resource that combines the power of genetic stability within strains, power for genomic mapping strategies, and strength in an animal model that mirrors many human disease traits. The HRDP was designed to include 96 inbred rat strains with genomic and physiological diversity to maximize power to detect specific genetic loci associated with complex traits while maximizing the genetic diversity among strains. The 96 strain panel consists of 33 genetically diverse inbred strains and two panels of recombinant inbred panels: FEXL/LEXF (33 strains, Japan) and HXB/BXH (30 strains, Czech Republic). Embryo resuscitation and breeding is well underway at the Medical College of Wisconsin (MCW) with 55 strains available. Whole genome sequencing for 54 of the 96 strains is complete, having been generated on am Illumina NovaSeq S4 to achieve 30X coverage. An additional 14 related substrains have been sequenced. Liver and brain transcriptome analysis is underway through PhenoGen (http://phenogen.ucdenver.edu) at the University of Colorado. Genomic, phenotype, and strain information will be made available through the Hybrid Rat Diversity Panel portal at the Rat Genome Database (http://rgd.mcw.edu). The HRDP will provide a genetically stable population of rat strains with fully sequenced genomes, transcriptomes for brain and liver, and general phenotypic characterization to be used for systems genetic studies and fine mapping of complex traits.

Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel

Post transcriptional modifications of RNA are powerful mechanisms by which eukaryotes expand their genetic diversity. For instance, researchers estimate that most transcripts in humans undergo alternative splicing and alternative polyadenylation. These splicing events produce distinct RNA molecules, which in turn yield distinct protein isoforms and/or influence RNA stability, translation, nuclear export, and RNA/protein cellular localization. Due to their pervasiveness and impact, we hypothesized that alternative splicing and alternative polyadenylation in brain can contribute to a predisposition for voluntary alcohol consumption. Using the HXB/BXH recombinant inbred rat panel (a subset of the Hybrid Rat Diversity Panel), we generated over one terabyte of brain RNA sequencing data (total RNA) and identified novel splice variants (via StringTie) and alternative polyadenylation sites (via aptardi) to determine the transcriptional landscape in the brains of these animals. After establishing an analysis pipeline to ascertain high quality transcripts, we quantitated transcripts and integrated genotype data to identify candidate transcript coexpression networks and individual candidate transcripts associated with predisposition to voluntary alcohol consumption in the two-bottle choice paradigm. For genes that were previously associated with this trait (e.g., Lrap, Ift81, and P2rx4) (Saba et al., Febs. J., 282, 3556–3578, Saba et al., Genes. Brain. Behav., 20, e12698), we were able to distinguish between transcript variants to provide further information about the specific isoforms related to the trait. We also identified additional candidate transcripts associated with the trait of voluntary alcohol consumption (i.e., isoforms of Mapkapk5, Aldh1a7, and Map3k7). Consistent with our previous work, our results indicate that transcripts and networks related to inflammation and the immune system in brain can be linked to voluntary alcohol consumption. Overall, we have established a pipeline for including the quantitation of alternative splicing and alternative polyadenylation variants in the transcriptome in the analysis of the relationship between the transcriptome and complex traits.

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

BackgroundThe teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals.ResultsWe exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines.ConclusionsWe present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.

Working memory and pattern separation in founder strains of the BXD recombinant inbred mouse panel

Working memory and pattern separation are fundamental cognitive abilities which, when impaired, significantly diminish quality of life. Discovering genetic mechanisms underlying innate and disease-induced variation in these cognitive abilities is a critical step towards treatments for common and devastating neurodegenerative conditions such as Alzheimer's disease. In this regard, the trial-unique nonmatching-to-location assay (TUNL) is a touchscreen operant conditioning procedure allowing simultaneous quantification of working memory and pattern separation in mice and rats. In the present study, we used the TUNL assay to quantify these cognitive abilities in C57BL/6J and DBA/2J mice. These strains are the founders of the BXD recombinant inbred mouse panel which enables discovery of genetic mechanisms underlying phenotypic variation. TUNL testing revealed that pattern separation was significantly influenced by mouse strain, whereas working memory was not. Moreover, horizontal distance and vertical distance between choice-phase stimuli had dissociable effects on TUNL performance. These findings provide novel data on mouse strain differences in pattern separation and support previous findings of equivalent working memory performance in C57BL/6J and DBA/2J mice. Although working memory of the BXD founder strains was equivalent in this study, working memory of BXD strains may be divergent because of transgressive segregation. Collectively, data presented here indicate that pattern separation is heritable in the mouse and that the BXD panel can be used to identify mechanisms underlying variation in pattern separation.

Incorporating genetic diversity to improve alignment of mouse models to human Alzheimer’s disease

Previous work by our labs, and others, reveal the benefits of incorporating diverse mouse strains to better model human Alzheimer's disease (AD). For instance, mouse models of AD on genetically distinct wild-derived mouse strains demonstrated robust differences in immune response to amyloid and neurodegeneration, better representing the phenotypic spectrum of AD than previous models. To further investigate the importance of genetic diversity, as part of MODEL-AD, we generated AD-relevant mouse models on Collaborative Cross (CC) lines background, a recombinant inbred mouse panel created from eight highly diverse founder strains.C57BL/6J (B6J) mice homozygous for humanized APOE4 allele and carrying mutant APP and PS1 alleles (APPswe , PS1de9 ) were crossed to five CC strains that were selected based on variation in AD-relevant genes. Cohorts of male and female B6JCCnF1.APOE4.APP/PS1 mice and controls were aged to 8 months (a mid-point for amyloid deposition in B6.APP/PS1 mice) and brain hemispheres processed for RNA-Seq and neuropathological assessment. Expectation Maximization for Allele Specific Expression (EMASE) tool was used to quantify transcriptome-wide expression at allelic level. Differential expression and KEGG pathway enrichment analysis were performed to determine altered molecular processes in CC strains. Strain specific transcriptional signatures were mapped to co-expression gene modules of human Late-Onset AD (LOAD) from the AMP-AD consortium. Neuropathological assessment included characterization of plaque deposition, Tau pathology, glial activation, neurodegeneration and cerebrovascular health.RNA-Seq analysis revealed up-regulation of neuroinflammation related pathways (lysosome, complement and coagulation cascades) in all CC strains as an effect of mutant APP and PS1 transgenes in presence of APOE4 allele. On the other hand, we observed significant CC strain and sex specific variation in immune (Fc gamma R-mediated phagocytosis) and metabolic (glycosphingolipid biosynthesis) response to amyloid pathogenesis. Alignment with human LOAD signatures revealed high strain and sex specific variation in correlation with synaptic signaling, cell cycle and DNA repair related gene modules. Overall, novel AD mouse models that incorporated CC lines demonstrated increased alignment to human AD-like transcriptomic signatures compared to B6J.This work builds on previous work highlighting the strengths of including multiple diverse mouse strains to better model complex neurodegenerative disorders such as AD and related dementias.

Heritable variation in locomotion, reward sensitivity and impulsive behaviors in a genetically diverse inbred mouse panel.

Drugs of abuse, including alcohol and stimulants like cocaine, produce effects that are subject to individual variability, and genetic variation accounts for at least a portion of those differences. Notably, research in both animal models and human subjects point toward reward sensitivity and impulsivity as being trait characteristics that predict relatively greater positive subjective responses to stimulant drugs. Here we describe use of the eight collaborative cross (CC) founder strains and 38 (reversal learning) or 10 (all other tests) CC strains to examine the heritability of reward sensitivity and impulsivity traits, as well as genetic correlations between these measures and existing addiction-related phenotypes. Strains were all tested for activity in an open field and reward sensitivity (intake of chocolate BOOST®). Mice were then divided into two counterbalanced groups and underwent reversal learning (impulsive action and waiting impulsivity) or delay discounting (impulsive choice). CC and founder mice show significant heritability for impulsive action, impulsive choice, waiting impulsivity, locomotor activity, and reward sensitivity, with each impulsive phenotype determined to be non-correlating, independent traits. This research was conducted within the broader, inter-laboratory effort of the Center for Systems Neurogenetics of Addiction (CSNA) to characterize CC and DO mice for multiple, cocaine abuse related traits. These data will facilitate the discovery of genetic correlations between predictive traits, which will then guide discovery of genes and genetic variants that contribute to addictive behaviors.

Strain and sex dependent effects of isolation housing relative to environmental enrichment on operant sensation seeking in mice

Sensation seeking is a multidimensional phenotype that predicts the development of drug addiction in humans and addiction-like drug seeking in rodents. Several lines of evidence suggest that chronic stress increases sensation seeking and addiction-like drug seeking through common genetic mechanisms. Discovery and characterization of these mechanisms would reveal how chronic stress interacts with the genome to influence sensation seeking and how drugs of abuse hijack these fundamental reward mechanisms to drive addiction. To this end, we tested the hypothesis that chronic isolation housing stress (relative to environmental enrichment) influences operant sensation seeking as a function of strain, sex, or their interaction. To determine if the BXD recombinant inbred panel could be used to identify genetic and epigenetic mechanisms underlying any identified gene-by-environment interactions, we used mice from the two BXD founder strains. Following 10 weeks of differential housing, we assessed operant sensation seeking using several reinforcement schedules. The primary finding from this study was that DBA/2J but not C57BL/6J mice were significantly vulnerable to an isolation-induced increase (relative to environmental enrichment) in sensation seeking during extinction when the sensory reward was no longer available; this effect was significantly more robust in females. These data reveal a previously unknown isolation-induced effect on extinction of operant sensation seeking that is sex-dependent, addiction-relevant, and that can be dissected using the BXD recombinant inbred panel.