Set Of Recombinant Inbred Strains Research Articles

Xkr8 Modulates Bipolar Cell Number in the Mouse Retina.

The present study interrogated a quantitative trait locus (QTL) on Chr 4 associated with the population sizes of two types of bipolar cell in the mouse retina. This locus was identified by quantifying the number of rod bipolar cells and Type 2 cone bipolar cells across a panel of recombinant inbred (RI) strains of mice derived from two inbred laboratory strains, C57BL/6J (B6/J) and A/J, and mapping a proportion of that variation in cell number, for each cell type, to this shared locus. There, we identified the candidate gene X Kell blood group precursor related family member 8 homolog (Xkr8). While Xkr8 has no documented role in the retina, we localize robust expression in the mature retina via in situ hybridization, confirm its developmental presence via immunolabeling, and show that it is differentially regulated during the postnatal period between the B6/J and A/J strains using qPCR. Microarray analysis, derived from whole eye mRNA from the entire RI strain set, demonstrates significant negative correlation of Xkr8 expression with the number of each of these two types of bipolar cells, and the variation in Xkr8 expression across the strains maps a cis-eQTL, implicating a regulatory variant discriminating the parental genomes. Xkr8 plasmid electroporation during development yielded a reduction in the number of bipolar cells in the retina, while sequence analysis of Xkr8 in the two parental strain genomes identified a structural variant in the 3′ UTR that may disrupt mRNA stability, and two SNPs in the promoter that create transcription factor binding sites. We propose that Xkr8, via its participation in mediating cell death, plays a role in the specification of bipolar cell number in the retina.

Genomic Locus Modulating IOP in the BXD RI Mouse Strains.

Intraocular pressure (IOP) is the primary risk factor for developing glaucoma, yet little is known about the contribution of genomic background to IOP regulation. The present study leverages an array of systems genetics tools to study genomic factors modulating normal IOP in the mouse. The BXD recombinant inbred (RI) strain set was used to identify genomic loci modulating IOP. We measured the IOP in a total of 506 eyes from 38 different strains. Strain averages were subjected to conventional quantitative trait analysis by means of composite interval mapping. Candidate genes were defined, and immunohistochemistry and quantitative PCR (qPCR) were used for validation. Of the 38 BXD strains examined the mean IOP ranged from a low of 13.2mmHg to a high of 17.1mmHg. The means for each strain were used to calculate a genome wide interval map. One significant quantitative trait locus (QTL) was found on Chr.8 (96 to 103 Mb). Within this 7 Mb region only 4 annotated genes were found: Gm15679, Cdh8, Cdh11 and Gm8730. Only two genes (Cdh8 and Cdh11) were candidates for modulating IOP based on the presence of non-synonymous SNPs. Further examination using SIFT (Sorting Intolerant From Tolerant) analysis revealed that the SNPs in Cdh8 (Cadherin 8) were predicted to not change protein function; while the SNPs in Cdh11 (Cadherin 11) would not be tolerated, affecting protein function. Furthermore, immunohistochemistry demonstrated that CDH11 is expressed in the trabecular meshwork of the mouse. We have examined the genomic regulation of IOP in the BXD RI strain set and found one significant QTL on Chr. 8. Within this QTL, there is one good candidate gene, Cdh11.

Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma.

Central corneal thickness (CCT) is one of the most heritable ocular traits and it is also a phenotypic risk factor for primary open angle glaucoma (POAG). The present study uses the BXD Recombinant Inbred (RI) strains to identify novel quantitative trait loci (QTLs) modulating CCT in the mouse with the potential of identifying a molecular link between CCT and risk of developing POAG. The BXD RI strain set was used to define mammalian genomic loci modulating CCT, with a total of 818 corneas measured from 61 BXD RI strains (between 60–100 days of age). The mice were anesthetized and the eyes were positioned in front of the lens of the Phoenix Micron IV Image-Guided OCT system or the Bioptigen OCT system. CCT data for each strain was averaged and used to QTLs modulating this phenotype using the bioinformatics tools on GeneNetwork (www.genenetwork.org). The candidate genes and genomic loci identified in the mouse were then directly compared with the summary data from a human POAG genome wide association study (NEIGHBORHOOD) to determine if any genomic elements modulating mouse CCT are also risk factors for POAG.This analysis revealed one significant QTL on Chr 13 and a suggestive QTL on Chr 7. The significant locus on Chr 13 (13 to 19 Mb) was examined further to define candidate genes modulating this eye phenotype. For the Chr 13 QTL in the mouse, only one gene in the region (Pou6f2) contained nonsynonymous SNPs. Of these five nonsynonymous SNPs in Pou6f2, two resulted in changes in the amino acid proline which could result in altered secondary structure affecting protein function. The 7 Mb region under the mouse Chr 13 peak distributes over 2 chromosomes in the human: Chr 1 and Chr 7. These genomic loci were examined in the NEIGHBORHOOD database to determine if they are potential risk factors for human glaucoma identified using meta-data from human GWAS. The top 50 hits all resided within one gene (POU6F2), with the highest significance level of p = 10−6 for SNP rs76319873. POU6F2 is found in retinal ganglion cells and in corneal limbal stem cells. To test the effect of POU6F2 on CCT we examined the corneas of a Pou6f2-null mice and the corneas were thinner than those of wild-type littermates. In addition, these POU6F2 RGCs die early in the DBA/2J model of glaucoma than most RGCs. Using a mouse genetic reference panel, we identified a transcription factor, Pou6f2, that modulates CCT in the mouse. POU6F2 is also found in a subset of retinal ganglion cells and these RGCs are sensitive to injury.

Accumulation, elimination, sequestration, and genetic variation of lead (Pb2+) loads within and between generations of Drosophila melanogaster

We examined accumulation, sequestration, elimination, and genetic variation for lead (Pb) loads within and between generations of Drosophila melanogaster. Flies were reared in control or leaded medium at various doses and tested for their Pb loads at different stages of development (larvae, eclosion, newly-eclosed adults, and mature adults). Pb loads were tested using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). We found that D. melanogaster readily accumulated Pb throughout their lifespan and the levels of accumulation increased with Pb exposure in the medium. Wandering third-instar larvae accumulated more Pb than mature adults; this phenomenon may be due to elimination of Pb in the pupal cases during eclosion and/or depuration in adults post-eclosion. The accumulated Pb in mature adults was not transferred to F1 mature adult offspring. Using a set of recombinant inbred strains, we identified a quantitative trait locus for adult Pb loads and found that genetic variation accounted for 34% of the variance in Pb load. We concluded that D. melanogaster is a useful model organism for evaluating changes in Pb loads during development, as well as between generations. Furthermore, we found that genetic factors can influence Pb loads; this provides an essential foundation for evaluating phenotypic variation induced by the toxic effects of Pb.

A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel.

In this chapter we address the recent explosion in large multilevel population studies such as the METSIM study in humans as well as large panels of animal models such as the Hybrid Mouse Diversity Panel or the BXD set of recombinant inbred strains. These studies have harnessed the increasing affordability of large-scale high-throughput profiling to gather massive quantities of data. These datasets, spread across different -omics levels (genome, transcriptome, etc.), different tissues (e.g. heart, plasma, bone) and different environmental factors (e.g. diet, drugs) each individually have led to a number of novel findings relevant to a variety of complex diseases and other phenotypes. The analysis of these results, however, is often limited to individuals with a comprehensive understanding of database languages such as SQL. In this chapter, we describe the development of a GUI-based database analysis suite, using the Hybrid Mouse Diversity Panel as an example to lay out a series of methods for visualization and integration of large systems genetics datasets. The database is based on the Shiny suite of tools in R, and is transferrable to other SQL-based datasets.

Sex-dependent genetic effects on immune responses to a parasitic nematode

BackgroundMany disease aetiologies have sex specific effects, which have important implications for disease management. It is now becoming increasingly evident that such effects are the result of the differential expression of autosomal genes rather than sex-specific genes. Such sex-specific variation in the response to Trichuris muris, a murine parasitic nematode infection and model for the human parasitic nematode T. trichiura, has been well documented, however, the underlying genetic causes of these differences have been largely neglected. We used the BXD mouse set of recombinant inbred strains to identify sex-specific loci that contribute to immune phenotypes in T. muris infection.ResultsResponse phenotypes to T. muris infection were found to be highly variable between different lines of BXD mice. A significant QTL on chromosome 5 (TM5) associated with IFN-γ production was found in male mice but not in female mice. This QTL was in the same location as a suggestive QTL for TNF-α and IL-6 production in male mice suggesting a common control of these pro-inflammatory cytokines. A second QTL was identified on chromosome 4 (TM4) affecting worm burden in both male and female cohorts. We have identified several genes as potential candidates for modifying responses to T. muris infection.ConclusionsWe have used the largest mammalian genetic model system, the BXD mouse population, to identify candidate genes with sex-specific effects in immune responses to T. muris infection. Some of these genes may be differentially expressed in male and female mice leading to the difference in immune response between the sexes reported in previous studies. Our study further highlights the importance of considering sex as an important factor in investigations of immune response at the genome-wide level, in particular the bias that can be introduced when generalizing results obtained from only one sex or a mixed sex population. Rather, analyses of interaction effects between sex and genotype should be part of future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-193) contains supplementary material, which is available to authorized users.

Systems genetics analysis of mouse chondrocyte differentiation

One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development. © 2011 American Society for Bone and Mineral Research.

Phenotype and Genetics of Progressive Sensorineural Hearing Loss (Snhl1) in the LXS Set of Recombinant Inbred Strains of Mice

Progressive sensorineural hearing loss is the most common form of acquired hearing impairment in the human population. It is also highly prevalent in inbred strains of mice, providing an experimental avenue to systematically map genetic risk factors and to dissect the molecular pathways that orchestrate hearing in peripheral sensory hair cells. Therefore, we ascertained hearing function in the inbred long sleep (ILS) and inbred short sleep (ISS) strains. Using auditory-evoked brain stem response (ABR) and distortion product otoacoustic emission (DPOAE) measurements, we found that ISS mice developed a high-frequency hearing loss at twelve weeks of age that progressed to lower frequencies by 26 weeks of age in the presence of normal endocochlear potentials and unremarkable inner ear histology. ILS mice exhibited milder hearing loss, showing elevated thresholds and reduced DPOAEs at the higher frequencies by 26 weeks of age. To map the genetic variants that underlie this hearing loss we computed ABR thresholds of 63 recombinant inbred stains derived from the ISS and ILS founder strains. A single locus was linked to markers associated with ISS alleles on chromosome 10 with a highly significant logarithm of odds (LOD) score of 15.8. The 2-LOD confidence interval spans ∼4 Megabases located at position 54–60 Mb. This locus, termed sensorineural hearing loss 1 (Snhl1), accounts for approximately 82% of the phenotypic variation. In summary, this study identifies a novel hearing loss locus on chromosome 10 and attests to the prevalence and genetic heterogeneity of progressive hearing loss in common mouse strains.

Calpain-10 is a component of the obesity-related quantitative trait locus Adip1

Calpain-10 is a component of the obesity-related quantitative trait locus Adip1

Global Exploratory Analysis of Massive Neuroimaging Collections using Microsoft Live Labs Pivot and Silverlight

Event Abstract Back to Event Global Exploratory Analysis of Massive Neuroimaging Collections using Microsoft Live Labs Pivot and Silverlight Robert W. Williams1*, Lei Yan1, Xiaodong Zhou1, Lu Lu1, Arthur Centeno1, Leonard Kuan2, Michael Hawrylycz2 and Glenn D. Rosen3 1 University of Tennessee Health Science Center, Department of Anatomy and Neurobiology, Center for Integrative and Translational Genomics, United States 2 The Allen Institute for Brain Science, United States 3 Beth Israel Deaconess Medical Center/Harvard Medical School, Department of Neurology, United States Introduction: The Mouse Brain Library (www.mbl.org) consists of high resolution images generated for 200 genetically well defined strains of mice, 2200 cases, 8800 Nissl-stained slides, and ~120,000 coronal and horizontal sections of the brain. The MBL includes representatives for most sets of recombinant inbred strains, (BXD, LXS, AXB, BXH, CXB). This collection provides a solid foundation for studies of the genetic control of brain structure, function, and behavior (Lu et al. 2001; Yang et al., 2008; Rosen et al., 2009). A key challenge is how to deliver massive image collections such as the MBL, Allen Brain Atlas projects, and BrainMaps using modern web services. In this work we tested Microsoft Live Labs Pivot (www.getpivot.com ) as an image distribution portal. Pivot provides a unique method for delivering and exploring very large collections of high-resolution images. Methods and Results: Large slides of 30-µm celloidin sections were imaged using a 20x objective (NA 0.75) and an Aperio Scanscope CS scanner at an in-plane resolution of 1-µm/pixel and at 150-µm steps along the cutting axis. Images were segmented to extract single sections. SVS format image were converted into Advanced Forensic format (AFF), JPEG2000, and Silverlight deep zoom (DZI) pyramids. A DVI is 2x larger than its JPEG parent. DZIs were assembled into a set of Pivot image collections. Metadata for sorting and display were extracted from MBL and GeneNetwork.org data tables. Metadata types include thousands of genotypes and phenotypes for all strains, as well as data for individual cases (sex, age, body weight, brain weight, litter size). Spatial coordinate tags for each section using INCF Waxholm space and BIRNLex neuroanatomical terms are being added. A Pivot server was installed on a Linux CentOS 5 8-core system (Dell R610) running Tomcat and MySQL. The system was tested on Vista and Windows 7 using a Pivot browser (www.getpivot.com) and runs well on Mac OS X 10.6 using the VMWARE Fusion 3 virtual machine. Link to http://mbl.pivotcollections.org to view the MBL. The MBL collection is large and unwieldy and our current interface (www.mbl.org) does not provide sufficient sorting flexibility and speed to effectively explore or analyze the collection. A good exploratory interface would provide both forest and tree views and a way to effectively scan the entire collection for variation in traits such as ventricular volume, callosal architecture, cortical lamination, and differences in the cytology in specific nuclei in a matter of minutes, not hours or days. Pivot is optimal for these types of rapid review and exploratory tasks. The collection can be filtered, sorted, and viewed at a wide range of magnifications—from thumbnails of whole slide to full zooms of subnuclei—almost instantly. The collection can be split, filtered, and sorted using a range of continuous and discrete metadata variables (sex, age, strain, genotype, behavior) Limitations with the current Pivot implementation can be divided into two categories: those associated with the interface itself (no nested displays, a limit of 15 displayed categories, no graphic overlay for marking or annotation), and those associated with secondary analytic and statistical functions that would typically be used to test hypotheses (no dynamic output of group statistics nor tests for differences among groups using ANOVA or t tests) Discussion: Pivot is a superb web service architecture that provides very fluid access to massive neuroimaging databases. It is extremely well suited for both the dissemination of massive 2D collections and direct exploratory analysis as part of a web service. Pivot has also been extremely helpful as part of quality control workflow and has enabled us to search for neuroanatomical differences and patterns of variation among strains of mice in ways that far surpass any other web interface.

Headlong into a genomic singularity

Headlong into a genomic singularity

Embrace diversity! Systems genetics-enabled discovery of disease networks

identify robust and strain-, sex-, and strain*sex-dependent responses to the diet. Global analysis of the expression data by ANOVA revealed extensive impact of both strain and sex on dietary responses in liver. The main effect of diet was apparent in the differential expression of almost 57% of genes on the arrays. Among the top co-regulated of these, the authors showed using Gene Ontology (GO) enrichment analyses that the expected effects of diet-mediated suppression of cholesterol biosynthesis occurred in all strains and that other specific biological systems functional involvements were also strongly implicated. Valuable data emerge from the ability to identify sets of genes that are reflective of strain-, sex-, and strain*sexdependent effects of diet, attributable in part from the statistical power of the study design in which the underlying genetic variations imparted systematic effects at the level of biological pathways and processes. When strain is taken into account, the majority of significantly enriched GO categories reflected a powerful correlation between effects of diet on immune function, such as antigen processing and presentation. The authors suggest that these changes may be related to diet-induced liver damage, which was indicated by changes expression of damage-related genes and by an increase in circulating levels of glutamate dehydrogenase. However, these changes may also broadly reflect genetic correlation between pathways that mediate immune responses and the development of diet-induced atherogenic plaques, the formation and propagation of which are driven by immune responses. Integrating the expression data with information about the incidence, severity, and phenotypic details of atherosclerotic lesions in this same set of strains should shed additional light on this possibility. Other important follow-on studies may also determine if strainspecific patterns of immune gene expression in liver are paralleled by qualitatively similar effects on lymphocyte populations, atherogenic lesions, and insulin pathway-associated tissues. Importantly, the authors have also provided a publicly accessible database that can be mined in a number of ways. For example, this resource could be used to select strains with divergent responses to diet (e.g., sensitive and resistant to liver damage) or to identify coexpression networks centered around a gene(s) of specific interest. It could also be used to extract supportive evidence for genes implicated in processes related

Genomic Analysis of Left Ventricular Remodeling

The left ventricle (LV) of the heart remodels in response to hemodynamic load through the processes of physiological or pathophysiological hypertrophy.1–3 Despite extensive study of the molecular basis of cardiac hypertrophy and LV remodeling,1,4 the mainstay of medical treatment of maladaptive remodeling remains based on therapies initially devised for treating hypertension. The limited progress in the development of specific therapies for LV remodeling has led some to refer to “the impossible task of developing a new treatment for heart failure” and is the reason why, in part, device therapies have received such recent attention.5–8 To gain a better understanding of the biology of maladaptive LV remodeling, with a view to identifying therapeutic targets, new paradigms and experimental approaches are needed, and genomics provides one such methodology. Genomics is the study of genome-scale data sets, at the DNA or RNA level, and when combined with studies of physiological traits or disease phenotypes, genomics can be used to infer molecular insights. Unlike single-gene studies, which are the favored hypothesis-driven design,4 genomic approaches examine variation in up to gigabases of sequences to find statistical associations between transcripts and traits in a hypothesis-free system. These hypothesis-free studies have often been criticized as unfocused, but following the successes of genome-wide association studies (GWAS) and the recent achievements of integrated genetic and genomic analyses, a new era of genomic experimentation presents itself.9–14 It is notable that GWAS and integrated genomic studies in humans often identify regions associated with disease rather than specific genes and that effect sizes are small; nevertheless, these data remain highly informative.15–17 In this article, we review the genomic analysis of LV remodeling in the context of the recent past, the state of the art, and the imminent use of next-generation sequencing. A glossary of terms is …

Gene mapping of sperm quality parameters in recombinant inbred strains of mice

The aim of this study was to map chromosomal regions containing hypothetical genes responsible for the following parameters of mouse semen quality: (1) the percentage of sperm with abnormal head morphology, (2) the level of dead spermatozoa, (3) the percentage of sperm tails with residual cytoplasmic droplets, and (4) the percentage of sperm with impaired sperm tail membrane integrity. We also analyzed any possible correlations between these parameters. The most appropriate animal model for mapping genes controlling quantitative traits (QTL, quantitative trait locus) is a set of recombinant inbred (RI) strains. The set of RI strains used in this study was derived from crosses between two inbred mouse strains, KE and CBA/Kw, which differ significantly in fertility parameters and gamete quality. We analyzed the four parameters of sperm quality in male mice from two parental strains and from 12 RI strains. The strain distribution pattern (SDP) of 187 polymorphic microsatellite markers was prepared for 20 chromosomes of the mouse genome in 12 RI strains. We correlated the SDP of these markers with the values of sperm quality parameters, using MapManager QTX software (ver. b18). The mapping procedure indicated that the percentage of sperm with abnormal head morphology is controlled by gene(s) located in chromosomal regions 11q24, 11q31 and 6q15.6. There was also a strong correlation between male body weight and the hypothetical gene(s) in chromosomal region 18q47. A detailed analysis of the genes located in these regions enabled us to prepare a list of candidate genes. We discuss the basis of the correlation between the measured parameters.

Evaluation of LEXF/FXLE rat recombinant inbred strains for genetic dissection of complex traits

Recombinant inbred (RI) strains are formed from an outcross between two well-characterized inbred stains followed by at least 20 generations of inbreeding. RI strains can be utilized for the analysis of many complex phenotypic traits. The LEXF/FXLE RI strain set consists of 34 RI strains derived by reciprocal crossing of LE/Stm and F344/Stm. Here we report on genetic dissections of complex traits using this RI set and their parental strains. We have developed strain distribution patterns for 232 informative simple sequence length polymorphism markers. The framework map covers the rat genome except for chromosome Y. Seventy-six phenotype parameters, which included physiological and behavioral traits, were examined for these RI lines. Quantitative trait locus (QTL) analysis of these parameters revealed 27 significant and 91 suggestive QTLs, illustrating the potential of this RI resource for the detection of underlying gene functions for various phenotypes. Although this RI set was originally developed to study susceptibility to chemical-induced tumors, it has been shown to be equally powerful for a wide spectrum of traits. The LEXF/FXLE RI strains have been deposited at the National Bio Resource Project for the Rat in Japan and are maintained under specific pathogen-free conditions. They are available at http://www.anim.med.kyoto-u.ac.jp/nbr.

A Simple Method for Combining Genetic Mapping Data from Multiple Crosses and Experimental Designs

BackgroundOver the past decade many linkage studies have defined chromosomal intervals containing polymorphisms that modulate a variety of traits. Many phenotypes are now associated with enough mapping data that meta-analysis could help refine locations of known QTLs and detect many novel QTLs.Methodology/Principal FindingsWe describe a simple approach to combining QTL mapping results for multiple studies and demonstrate its utility using two hippocampus weight loci. Using data taken from two populations, a recombinant inbred strain set and an advanced intercross population we demonstrate considerable improvements in significance and resolution for both loci. 1-LOD support intervals were improved 51% for Hipp1a and 37% for Hipp9a. We first generate locus-wise permuted P-values for association with the phenotype from multiple maps, which can be done using a permutation method appropriate to each population. These results are then assigned to defined physical positions by interpolation between markers with known physical and genetic positions. We then use Fisher's combination test to combine position-by-position probabilities among experiments. Finally, we calculate genome-wide combined P-values by generating locus-specific P-values for each permuted map for each experiment. These permuted maps are then sampled with replacement and combined. The distribution of best locus-specific P-values for each combined map is the null distribution of genome-wide adjusted P-values.Conclusions/SignificanceOur approach is applicable to a wide variety of segregating and non-segregating mapping populations, facilitates rapid refinement of physical QTL position, is complementary to other QTL fine mapping methods, and provides an appropriate genome-wide criterion of significance for combined mapping results.

Simulating the Collaborative Cross: Power of Quantitative Trait Loci Detection and Mapping Resolution in Large Sets of Recombinant Inbred Strains of Mice

It has been suggested that the collaborative cross, a large set of recombinant inbred strains derived from eight inbred mouse strains, would be a powerful resource for the dissection of complex phenotypes. Here we use simulation to investigate the power of the collaborative cross to detect and map small genetic effects. We show that for a fixed population of 1000 individuals, 500 RI lines bred using a modified version of the collaborative cross design are adequate to map a single additive locus that accounts for 5% of the phenotypic variation to within 0.96 cM. In the presence of strong epistasis more strains can improve detection, but 500 lines still provide sufficient resolution to meet most goals of the collaborative cross. However, even with a very large panel of RILs, mapping resolution may not be sufficient to identify single genes unambiguously. Our results are generally applicable to the design of RILs in other species.

Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis.

The set of LXS recombinant inbred (RI) strains is a new and exceptionally large mapping panel that is suitable for the analysis of complex traits with comparatively high power. This panel consists of 77 strains-more than twice the size of other RI sets--and will typically provide sufficient statistical power (beta = 0.8) to map quantitative trait loci (QTLs) that account for approximately 25% of genetic variance with a genomewide p < 0.05. To characterize the genetic architecture of this new set of RI strains, we genotyped 330 MIT microsatellite markers distributed on all autosomes and the X Chromosome and assembled error-checked meiotic recombination maps that have an average F2-adjusted marker spacing of approximately 4 cM. The LXS panel has a genetic structure consistent with random segregation and subsequent fixation of alleles, the expected 3-4 x map expansion, a low level of nonsyntenic association among loci, and complete independence among all 77 strains. Although the parental inbred strains-Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS)--were derived originally by selection from an 8-way heterogeneous stock selected for differential sensitivity to sedative effects of ethanol, the LXS panel is also segregating for many other traits. Thus, the LXS panel provides a powerful new resource for mapping complex traits across many systems and disciplines and should prove to be of great utility in modeling the genetics of complex diseases in human populations.

Genetic map of AFLP markers in the rat (Rattus norvegicus) derived from the H x B/Ipcv and B x H/Cub sets of recombinant inbred strains.

The amplified fragment length polymorphism (AFLP) technique has been used to enhance marker density in a large set of recombinant inbred strains (H x B and B x H) derived from a spontaneously hypertensive rat (SHR/OlaIpcv) and a Brown-Norway (BN.lx/Cub) inbred strain. Thirteen different primer combinations were tested and a total of 191 polymorphic bands were detected. From these polymorphic bands 89 AFLP markers could be assigned to specific chromosomes. Several of these AFLP markers were mapped to regions with low marker density, thus filling up gaps in the existing genetic map of these recombinant inbred strains. These results substantiate the value of the AFLP technology in increasing marker density in genetic maps.

Genome scanning of the HXB/BXH sets of recombinant inbred strains of the rat for quantitative trait loci associated with conditioned taste aversion.

In the current study, we searched for quantitative trait loci (QTL) responsible for a conditioned taste aversion (CTA) measured as a decrease in the intake of a saccharin conditioned stimulus followed by an i.p. injection of 0.15 M LiCl (lithium chloride) (2 ml/100 g body weight). A genome scanning for QTL associated with CTA was performed in the HXB/BXH sets of recombinant inbred (RI) strains derived from the Brown Norway (BN-Lx) rat and the spontaneously hypertensive rat (SHR). The BN-Lx progenitor showed a significantly stronger CTA (8.3+/-2.8%) than the SHR progenitor (27.8+/-3.3%, p < .0001). The distribution of CTA values among RI strains was continuous, suggesting a polygenic mode of inheritance. Genome scanning of RI strains with more than 700 gene markers revealed a significant association of CTA with the D2Cebr11s4 marker on chromosome 2 (LRS = 22.7) and with the D4Cebrp149s8 marker on chromosome 4 (LRS = 23.4). The chromosome 2 putative QTL was confirmed by detecting a significant difference in CTA between the SHR progenitor (27.8+/-3.3%) and the SHR-2 (SHR.BN-D2Rat171/D2Arb24) congenic strain (13.1+/-4.4%, p < .01) that are genetically identical except for a segment of chromosome 2 that was transferred onto the genetic background of the SHR from the BN strain.