Mapping the mouse genome: current status and future prospects

Resources for Systems Genetics

A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.

[Genetic diversity of Mongolian gerbils (Meriones unguiculatus)]

Genetic diversity of Z:ZCLA Mongolian gerbils, wild Mongolian gerbils and 3 inbred M. gerbil strains was evaluated with 17 microsatellite loci. The genetic variabilities within and between populations were estimated. The results showed that 9 microsatellite DNA, AF200940, AF200941, AF200942, AF200945, AF200946, AF200947, D11Mit128, PKC, and SCN, were amplified efficiently both in Z:ZCLA M. gerbils and the wild M. gerbils. Forty-one alleles were amplified with the number of alleles per locus ranging from 1 to 7. The average expected heterozygosity (He) and polymorphism information content (PIC) of all the loci were 0.5032 and 0.4656, respectively. The mean effective allele number of Z:ZCLA M. gerbils and wild M. gerbils were 2.78 and 2.89. The PIC of Z:ZCLA M. gerbils and the wild M. gerbils were 0.3704 and 0.3893. In the 3 inbred M. gerbils strains, 8 microsatellite DNA were amplified efficiently with 11 alleles. It displayed heterozygosity in AF200941, AF200945, AF200946, D11Mit128, and SCN loci with fragment lengths from 140 to 215 bp; and homozygosity in AF200942, AF200946, and AF200947 with fragment lengths from 203 to 241 bp. All of the 8 microsatellite loci were monomorphic both within and among the strains. These results suggested that the moderate genetic diversity of the conventional closed colony of Z:ZCLA M. gerbils was observed; and inbred M. gerbils strains basically met the re-quest. Microsatellite markers can be used in monitoring of M. gerbils populations.

A comprehensive SNP-based genetic analysis of inbred mouse strains

Dense genetic maps of mammalian genomes facilitate a variety of biological studies including the mapping of polygenic traits, positional cloning of monogenic traits, mapping of quantitative or qualitative trait loci, marker association, allelic imbalance, speed congenic construction, and evolutionary or phylogenetic comparison. In particular, single nucleotide polymorphisms (SNPs) have proved useful because of their abundance and compatibility with multiple high-throughput technology platforms. SNP genotyping is especially suited for the genetic analysis of model organisms such as the mouse because biallelic markers remain fully informative when used to characterize crosses between inbred strains. Here we report the mapping and genotyping of 673 SNPs (including 519 novel SNPs) in 55 of the most commonly used mouse strains. These data have allowed us to construct a phylogenetic tree that correlates and expands known genealogical relationships and clarifies the origin of strains previously having an uncertain ancestry. All 55 inbred strains are distinguishable genetically using this SNP panel. Our data reveal an uneven SNP distribution consistent with a mosaic pattern of inheritance and provide some insight into the changing dynamics of the physical architecture of the genome. Furthermore, these data represent a valuable resource for the selection of markers and the design of experiments that require the genetic distinction of any pair of mouse inbred strains such as the generation of congenic mice, positional cloning, and the mapping of quantitative or qualitative trait loci.

Development of a SNP genotyping panel for genetic monitoring of the laboratory mouse

We have developed a genotyping system for detecting genetic contamination in the laboratory mouse based on assaying single-nucleotide polymorphism (SNP) markers positioned on all autosomes and the X chromosome. This system provides a fast, reliable, and cost-effective way for genetic monitoring, while maintaining a very high degree of confidence. We describe the allelic distribution of 235 SNPs in 48 mouse strains, thereby creating a database of polymorphisms useful for genotyping purposes. The SNP markers used in this study were chosen from publicly available SNP databases. Four genotyping methods were evaluated, and dynamic two-tube allele-specific PCR assays were developed for each marker and tested on a set of 48 inbred mouse strains. The minimal number of assays sufficient to distinguish groups consisting of different numbers of mouse strains was estimated, and a panel of 28 SNPs sufficient to distinguish virtually all of the inbred strains tested was selected. Amplifluor SNP detection assays were developed for these markers and tested on an extended list of 96 strains. This panel was used as a genetic quality control approach to monitor the genotypes of nearly 300 inbred, wild-derived, congenic, consomic, and recombinant inbred strains maintained at The Jackson Laboratory. We have concluded that this marker panel is sufficient for genetic contamination monitoring in colonies containing a large number of genetically diverse mouse strains and that reduced versions of the panel could be implemented in facilities housing a lower number of strains.

A Titin mutation defines roles for circulation in endothelial morphogenesis

Morphogenesis of the developing vascular network requires coordinated regulation of an extensive array of endothelial cell behaviors. Precisely regulated signaling molecules such as vascular endothelial growth factor (VEGF) direct some of these endothelial behaviors. Newly forming blood vessels also become subjected to novel biomechanical forces upon initiation of cardiac contractions. We report here the identification of a recessive mouse mutation termed shrunken-head (shru) that disrupts function of the Titin gene. Titin was found to be required for the initiation of proper heart contractions as well as for maintaining the correct overall shape and orientation of individual cardiomyocytes. Cardiac dysfunction in shrunken-head mutant embryos provided an opportunity to study the effects of lack of blood circulation on the morphogenesis of endothelial cells. Without blood flow, differentiating endothelial cells display defects in their shapes and patterns of cell-cell contact. These endothelial cells, without exposure to blood circulation, have an abnormal distribution within vasculogenic vessels. Further effects of absent blood flow include abnormal spatial regulation of angiogenesis and elevated VEGF signaling. The shrunken-head mutation has provided an in vivo model to precisely define the roles of circulation on cellular and network aspects of vascular morphogenesis.

Update of Mouse Microsatellite Database of Japan (MMDBJ)

We updated a database of microsatellite marker polymorphisms found in inbred strains of the mouse, most of which were derived from the wild stocks of four Mus musculus subspecies, M. m. domesticus, M. m. musculus, M. m.castaneus and M. m. molossinus. The major aim of constructing this database was to establish the genetic status of these inbred strains as resources for linkage analysis and positional cloning. The inbred strains incorporated in our database are A/J, C57BL/6J, CBA/J, DBA/2J, SM/J, SWR/J, 129Sv/J, MSM/Ms, JF1/Ms, CAST/Ei, NC/Nga, BLG2/Ms, NJL/Ms, PGN2/Ms, SK/CamEi and SWN/Ms, which have not or have only been poorly incorporated in the Whitehead Institute/MIT (WI/MIT) microsatellite database. The number of polymorphic microsatellite loci incorporated in our database is over 1,000 in all strains, and the URL site for our database is located at http:// www.shigen.nig.ac.jp /mouse/mmdbj/mouse.html.

Precision and accuracy of peripheral quantitative computed tomography (pQCT) in the mouse skeleton compared with histology and microcomputed tomography (microCT)

pQCT was evaluated for accuracy of phenotypic characterization of mouse bone in vivo. Bones (tibia, femur, spine) of 27 animals were measured ex vivo with pQCT, microCT, and histomorphometry and of 23 mice in vivo (pQCT). pQCT yielded satisfactory in vivo precision and accuracy in skeletal characterization.

INTRODUCTION

Important aspects of modern skeletal research depend on the phenotypic characterization of genetically manipulated mice, with some approaches requiring in vivo measurement. Peripheral quantitative computed tomography (pQCT) is applicable in vivo and provides opportunities to determine a large variety of bone parameters. Here we test the ex vivo and in vivo reproducibility of pQCT, and its accuracy in comparison with histomorphometry and microcomputed tomography (microCT).

MATERIALS AND METHODS

We examined the tibia, femur, and lumbar spine of 27 mice ex vivo with high-resolution pQCT, using two mouse models (wild-type and ob/ob) with known differences in bone density. Measurements were repeated three times at different days in nine animals. In a second experiment, 23 animals (10 wild-type and 13 bGH transgenic mice) were repeatedly measured in vivo at 12 and 13 weeks of age, respectively.

RESULTS

Among metaphyseal sites, the ex vivo precision was highest at the distal femur (RMS CV < 1% for density and < 2% for area). The correlation between density (pQCT) and bone volume fraction (histomorphometry) was r2 = 0.79 (tibia, femur, and spine), and that with microCT was r2 = 0.94 (femur). At the diaphysis, the precision was highest at the femur (< 2% for total and cortical area), and the correlation with microCT was r2 > 0.77. The in vivo precision for bone density (distal femur) was 2.3-5.1%, and that for absolute and relative cortical area (tibia) was 3.1% and 2.2%.

CONCLUSIONS

The results show that pQCT can yield satisfactory precision and accuracy in skeletal characterization of mouse bones, if properly applied. The potential advantage of pQCT is that it provides a large set of parameters on bone properties and that it can be used in vivo, extending the available methodological repertoire for genetic studies.

A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes

Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies.

Genetic epidemiological approaches to the search for osteoporosis genes

Important progress has been made in the identification of specific environmental factors and estimation of hereditary components in bone density, quantitative ultrasound (QUS), and bone turnover indices. By contrast, the search for specific genes that regulate bone mass has progressed rather slowly, and the results are more difficult to interpret and reproduce. This article reviews the genetics of osteoporosis and problems plaguing genetic research. It is argued that the search for genes involved in the expression of osteoporotic phenotypes should be based on linkage studies in relatively homogeneous populations. Strategies for increasing the power of studies, such as making use of information from extended pedigrees and multivariate analysis, are discussed. With the advent of a comprehensive human genetic linkage map, a complete identification of genes for osteoporosis appears feasible. Understanding the genetic mechanisms and their interactions with environmental factors should allow more focused and cost-effective osteoporosis prevention and treatment strategies.

Targeted gene mutations define the roles of insulin and IGF-I receptors in mouse embryonic development

Insulin-like growth factors (IGFs) and their receptors regulate embryonic and post-natal growth. Genetic evidence derived from targeted mouse mutants indicates that both the insulin receptor (IR) and IGF-I receptors (IGF-IRs) are required for mouse embryonic growth. However, the roles of IRs and IGF-IRs are functionally distinct, with IGF-IRs mediating both IGF-I and IGF-II actions, and IRs mediating IGF-II, rather than insulin, action. The combined interactions of IGF-IRs and IRs with IGF-I and IGF-II account for the entirety of the growth effects of these two ligands, and provide the molecular basis for IGFs-mediated intrauterine growth and differentiation. Genetic ablation experiments of insulin receptor substrate-1 (IRS-1) and -2 (IRS-2), two important molecules in the IR and IGF-IR signaling pathways, are also beginning to shed light onto the mechanisms accounting for the specificity of IR and IGF-IR signaling. IRS-1-deficient mice are growth retarded, while IRS-2-deficient mice develop diabetes, indicating that the two molecules play a more specific role than previously recognized in IGF-IR and IR signaling.

Single-gene influences on brain and behavior

As traditional behavioral genetics analysis merges with neurogenetics, the field of neurobehavioral genetics, focusing on single-gene effects, comes into being. New biotechnology has greatly accelerated gene discovery and the study of gene function in relation to brain and behavior. More than 7,000 genes in mice and 10,000 in humans have now been documented, and extensive information about the genetics of several species is readily available on the World Wide Web. Based on knowledge of the DNA sequence of a gene, a targeted mutation with the capacity to disable it can be created. These knockouts--also called null mutants--are employed in the study of a wide range of phenotypes, including learning and memory, appetite and obesity, and circadian rhythms. The era of examining single-gene effects from a reductionistic perspective is waning, and research with interacting arrays of genes in various environmental contexts is demonstrating a need for systems-oriented theory.

Comparative genomics and host resistance against infectious diseases

The large size and complexity of the human genome have limited the identification and functional characterization of components of the innate immune system that play a critical role in front-line defense against invading microorganisms. However, advances in genome analysis (including the development of comprehensive sets of informative genetic markers, improved physical mapping methods, and novel techniques for transcript identification) have reduced the obstacles to discovery of novel host resistance genes. Study of the genomic organization and content of widely divergent vertebrate species has shown a remarkable degree of evolutionary conservation and enables meaningful cross-species comparison and analysis of newly discovered genes. Application of comparative genomics to host resistance will rapidly expand our understanding of human immune defense by facilitating the translation of knowledge acquired through the study of model organisms. We review the rationale and resources for comparative genomic analysis and describe three examples of host resistance genes successfully identified by this approach.

Quantitative trait loci affecting peak bone mineral density in mice

Peak bone mass is a major determinant of risk of osteoporotic fracture. Family and twin studies have found a strong genetic component to the determination of bone mineral density (BMD). However, BMD is a complex trait whose expression is confounded by environmental influences and polygenic inheritance. The number, locations, and effects of the individual genes contributing to natural variation in this trait are all unknown. Experimental animal models provide a means to circumvent complicating environmental factors, and the development of dense genetic maps based on molecular markers now provides opportunities to resolve quantitative genetic variation into individual regions of the genome influencing a given trait (quantitative trait loci, QTL). To begin to identify the heritable determinants of BMD, we have examined genetically distinct laboratory mouse strains raised under strict environmental control. Mouse whole-body bone mineral content by dual-energy X-ray absorptiometry (DXA) correlated strongly with skeletal calcium content by ashing, and peak whole-body BMD by DXA in female mice occurred at approximately 80-90 days of age. We therefore determined mean body weight and peak whole body BMD values in 12-week-old female mice from a panel of 24 recombinant inbred (RI) BXD strains, derived from a cross between C57BL/6 and DBA/2 progenitors. The distribution of body weight and BMD values among the strains clearly indicated the presence of strong genetic influences on both of these traits, with an estimated narrow sense heritability of 60% and 35%, respectively. The patterns of differences in body weight and peak whole body BMD in the BXD strains were then integrated with a large database of genetic markers previously defined in the RI BXD strains to generate chromosome map sites for QTL. After correction for redundancy among the significant correlations, QTL analysis of the BXD RI strain series provisionally identified 10 chromosomal sites linked to peak bone mass development in the female. Several of the identified sites map near genes encoding hormones, structural proteins, and cell surface receptors that are intricately involved in skeletal homeostasis. Four QTL for body weight were also identified. One of these loci was also strongly linked to inherited variation in BMD. This finding suggests that body weight and peak BMD may be influenced by linked genes or perhaps by common genes with pleiotropic effects. Our phenotyping in the RI BXD strains has allowed us to map a number of specific genetic loci strongly related to the acquisition of peak BMD. Confirmation of these findings will likely result in the understanding of which genes control skeletal health.

Mouse models of genetic disease: new approaches, new paradigms

The mouse mutant resource is a valuable tool for gene function studies in the post-genomics era. However, despite a seemingly large catalogue of mouse mutants, it is recognized that we have access to mutations at only a small fraction of the total number of mouse genes. There is a phenotype gap that needs to be narrowed by the implementation of large-scale, systematic mutagenesis programmes in the mouse. Both genotype-driven and phenotype-driven approaches can be employed to recover new mouse mutations. Genotype-driven approaches include large-scale genome-wide mutagenesis by gene trapping in embryonic stem cells. For genotype-driven approaches, the initial focus is on the characterization of the mutational change to the genome. Identification of the mutated gene is relatively trivial, but the genotype-driven route provides little indication of the likely phenotypic outcome of the mutation. In contrast, phenotype-driven approaches employ mutagenesis procedures that emphasize the recovery of novel phenotypes without prior assumptions about the underlying gene or pathway that has been disrupted--although identifying the underlying gene may not be trivial. One phenotype-driven approach includes chemical mutagenesis using N-ethyl-N-nitrosourea (ENU). ENU mutagenesis programmes are increasingly being brought to bear on increasing the breadth and depth of the mouse mutant resource, and in so doing narrowing the phenotype gap.

A high-resolution microsatellite map of the mouse genome

The European Collaborative Interspecific Backcross (EUCIB) resource was constructed for the purposes of high-resolution genetic mapping of the mouse genome (). The large Mus spretus/C57BL/6 backcross of 982 progeny has a genetic resolution of 0.3 cM at the 95% confidence level ( approximately 500 kb in the mouse genome). We have used the EUCIB mapping resource to develop a genome-wide high-resolution genetic map incorporating 3368 microsatellites. The microsatellites are distributed among 2302 genetically separated bins with 1.46 markers per bin on average. Average bin separation is 0.61 cM. This high-resolution genetic map will aid the construction of a robust physical map of the mouse genome.

Comparative mapping of the Brassica S locus region and its homeolog in Arabidopsis. Implications for the evolution of mating systems in the Brassicaceae

The crucifer family includes self-incompatible genera, such as Brassica, and self-fertile genera, such as Arabidopsis. To gain insight into mechanisms underlying the evolution of mating systems in this family, we used a selective comparative mapping approach between Brassica campestris plants homozygous for the S8 haplotype and Arabidopsis. Starting with markers flanking the self-incompatibility genes in Brassica, we identified the homeologous region in Arabidopsis as a previously uncharacterized segment of chromosome 1 in the immediate vicinity of the ethylene response gene ETR1. A total of 26 genomic and 21 cDNA markers derived from Arabidopsis yeast artificial and bacterial artificial chromosome clones were used to analyze this region in the two genomes. Approximately half of the cDNAs isolated from the region represent novel expressed sequence tags that do not match entries in the DNA and protein databases. The physical maps that we derived by using these markers as well as markers isolated from bacteriophage clones spanning the S8 haplotype revealed a high degree of synteny at the submegabase scale between the two homeologous regions. However, no sequences similar to the Brassica S locus genes that are known to be required for the self-incompatibility response were detected within this interval or other regions of the Arabidopsis genome. This observation is consistent with deletion of self-recognition genes as a mechanism for the evolution of autogamy in the Arabidopsis lineage.

Physical and genetic maps of the deafwaddler region on distal mouse Chr 6

The deafwaddler (dfw) mutation, displaying motor ataxia and profound deafness, arose spontaneously in a C3H/HeJ colony and was mapped previously to distal mouse Chr 6. In this study, a high-resolution genetic map was generated by positioning 10 microsatellite markers and 5 known genes on a 968-meioses intersubspecific backcross segregating for dfw [(CAST/Ei(-)+/+ x C3HeB/ FeJ-dfw/dfw) x C3HeB/FeJ-dfw/dfw], giving the following marker order and sex-averaged distances: D6Mit64-(0.10 + 0.10 cM)-Pang-(1.24 + 0.36 cM)-Itpr1-(0.62 + 0.25 cM)-D6Mit108-(0.52 + 0.23 cM)-D6Mit54-(0.21 + 0.15 cM)-D6Mit23, D6Mit107, D6Mit328-(0.72 + 0.27 cM)-D6Mit11-(0.21 + 0.15 cM)-dfw-(0.93 + 0.31 cM)-Gat4, D6Mit55-(0.10 + 0.10 cM)-D6Mit63-(0.31 + 0.18 cM)-Syn2-(0.62 + 0.25 cM)-D6Mit44 (Rho). Female and male genetic maps are similar immediately surrounding the dfw locus, but show marked differences in other areas. A yeast artificial chromosome-based physical map suggests that the closest markers flanking the dfw locus, D6Mit11 (proximal) and Gat4, D6Mit55 (distal), are contained within 650-950 kb. The human homologues of the flanking loci Itpr1 (proximal) and Syn2 (distal) map to chromosome 3p25-p26, suggesting that the human homologue of the dfw gene is located within this same region.

IRS-PCR-based genetic mapping of the huntingtin interacting protein gene (HIP1) on mouse chromosome 5

Huntington's disease (HD) is a devastating central nervous system disorder. Even though the gene responsible has been positionally cloned recently, its etiology has remained largely unclear. To investigate potential disease mechanisms, we conducted a search for binding partners of the HD-protein huntingtin. With the yeast two-hybrid system, one such interacting factor, the huntingtin interacting protein-1 (HIP-1), was identified (Wanker et al. 1997; Kalchman et al. 1997) and the human gene mapped to 7q11.2. In this paper we demonstrate the localization of the HIP1 mouse homologue (Hip1) into a previously identified region of human-mouse synteny on distal mouse Chromosome (Chr) 5, both employing an IRS-PCR-based mapping strategy and traditional fluorescent in situ hybridization (FISH) mapping.

A yeast artificial chromosome (YAC) library containing 10 haploid chicken genome equivalents

We report the construction of a YAC library that provides 10-fold redundant coverage of the chicken genome. The library was made by transforming S. cerevisiae AB1380 with YAC constructs consisting of partially digested and size fractionated (>465 kb) EcoRI genomic fragments ligated to pCGS966 YAC vector arms. The primary library provides 8.5-fold redundant coverage and consists of 16,000 clones arrayed in duplicate 96-well microtiter plates and gridded on nylon membranes at high density (18,000 clones/484cm2). The average insert size, 634 kb, was derived from size fractionation of a random sample of 218 YACs. Hybridization of five unlinked chicken genes to colony blots revealed six or more positive clones. This is consistent with the theoretical expectation from average insert sizes and number of clones. A second collection of clones consists of a further 20,000 colonies, of which 20% contain inserts larger than 450 kb and 80% contain only coligated vector arms. We estimate that these clones provide a further 1.5-fold redundant coverage of the chicken genome; thus, the total collection of 36,000 clones provides 10-fold redundant coverage of the chicken genome. The library is intended as a resource for fine-scale analysis of the organization of the chicken genome and is presently being used to construct a contig map of chicken Chromosome (Chr) 16, which contains the MHC and nucleolar organizer.

High-throughput microsatellite analysis using fluorescent dUTPs for high-resolution genetic mapping of the mouse genome

The use of fluorescent end-labeled primers has proved successful for rapid, semiautomated genotyping of microsatellite loci. However, custom synthesis is expensive and costs can be prohibitive when a wide range of markers is to be analyzed for only a few genotypings. This particularly applies to high-resolution genetic mapping in the mouse either in the construction of global maps or in the production of local high-resolution genetic maps for positional cloning. We demonstrate here the use of fluorescent dUTPs for cost-effective, high-throughput microsatellite genotyping in the mouse. This alternative to the use of fluorescent end-labeled primers for semiautomated genotyping is potentially applicable to the construction of linkage maps in other species.

Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases

Molecular and fragment ion data of intact 8- to 43-kDa proteins from electrospray Fourier-transform tandem mass spectrometry are matched against the corresponding data in sequence data bases. Extending the sequence tag concept of Mann and Wilm for matching peptides, a partial amino acid sequence in the unknown is first identified from the mass differences of a series of fragment ions, and the mass position of this sequence is defined from molecular weight and the fragment ion masses. For three studied proteins, a single sequence tag retrieved only the correct protein from the data base; a fourth protein required the input of two sequence tags. However, three of the data base proteins differed by having an extra methionine or by missing an acetyl or heme substitution. The positions of these modifications in the protein examined were greatly restricted by the mass differences of its molecular and fragment ions versus those of the data base. To characterize the primary structure of an unknown represented in the data base, this method is fast and specific and does not require prior enzymatic or chemical degradation.