GENE-LINK: a program in PASCAL for backcross genetic analysis

Mendel: a simple excel workbook to compare the observed and expected distributions of genotypes/phenotypes in transgenic and knockout mouse crosses involving up to three unlinked loci by means of a χ2 test

The analysis of transgenic and knockout mice always involves the establishment of matings with individuals carrying different loci, segregating independently, whose presence is expected among the progeny, according to a Mendelian distribution. The appearance of distorted inheritance ratios suggests the existence of unexpected lethal or sub-lethal phenotypes associated with some genotypes. These situations are common in a number of cases, including: testing transgenic founder mice for germ-line transmission of their transgenes; setting up heterozygous crosses to obtain homozygous individuals, both for transgenic and knockout mice; establishing matings between floxed mouse lines and suitable cre transgenic mouse lines, etc. The Pearson's χ(2) test can be used to assess the significance of the observed frequencies of genotypes/phenotypes in relation to the expected values, in order to determine whether the observed cases fit the expected distribution. Here, I describe a simple Excel workbook to compare the observed and expected distributions of genotypes/phenotypes in transgenic and knockout mouse crosses involving up to three unlinked loci by means of a χ(2) test. The file is freely available for download from my laboratory's web page at: http://www.cnb.csic.es/~montoliu/Mendel.xls .

Deletion of long-range sequences at Sox10 compromises developmental expression in a mouse model of Waardenburg-Shah (WS4) syndrome

The transcription factor SOX10 is mutated in the human neurocristopathy Waardenburg-Shah syndrome (WS4), which is characterized by enteric aganglionosis and pigmentation defects. SOX10 directly regulates genes expressed in neural crest lineages, including the enteric ganglia and melanocytes. Although some SOX10 target genes have been reported, the mechanisms by which SOX10 expression is regulated remain elusive. Here, we describe a transgene-insertion mutant mouse line (Hry) that displays partial enteric aganglionosis, a loss of melanocytes, and decreased Sox10 expression in homozygous embryos. Mutation analysis of Sox10 coding sequences was negative, suggesting that non-coding regulatory sequences are disrupted. To isolate the Hry molecular defect, Sox10 genomic sequences were collected from multiple species, comparative sequence analysis was performed and software was designed (ExactPlus) to identify identical sequences shared among species. Mutation analysis of conserved sequences revealed a 15.9 kb deletion located 47.3 kb upstream of Sox10 in Hry mice. ExactPlus revealed three clusters of highly conserved sequences within the deletion, one of which shows strong enhancer potential in cultured melanocytes. These studies: (i) present a novel hypomorphic Sox10 mutation that results in a WS4-like phenotype in mice; (ii) demonstrate that a 15.9 kb deletion underlies the observed phenotype and likely removes sequences essential for Sox10 expression; (iii) combine a novel in silico method for comparative sequence analysis with in vitro functional assays to identify candidate regulatory sequences deleted in this strain. These studies will direct further analyses of Sox10 regulation and provide candidate sequences for mutation detection in WS4 patients lacking a SOX10-coding mutation.

Characterization of a centromeric marker on mouse Chromosome 11 and its introgression in a domesticus/musculus hybrid zone

It has been proposed that the distribution of Robertsonian chromosome fusions and the Chromosome 11 Nucleolar Organizer Region (NOR) in the Danish hybrid zone between M. m. musculus and M. m. domesticus stems from centromeric incompatibilities between the two subspecies. To test this hypothesis, we identified and characterized a diagnostic subspecific marker closely linked to the centromere on mouse Chromosome 11. Using an allele-specific PCR assay, we investigated the introgression pattern of this centromere in a large sample of mice from a North-South transect of the hybrid zone in Jutland. Domesticus alleles were found to introgress far away from the center of the zone on the musculus side. These results suggest there is no incompatibility between the domesticus centromere of Chromosome 11 in the musculus genomic background.

The ichq mutant mouse, a model for the human skin disorder harlequin ichthyosis: mapping, keratinocyte culture, and consideration of candidate genes involved in epidermal growth regulation

Harlequin ichthyosis (HI) is a rare and usually fatal scaling skin disorder. The HI mutant mouse (ichq/ichq) has many similarities to the human disorder and provides an important model to identify candidate genes. In this study, we report refined mapping of the mouse ichq locus and consideration of the candidate genes: calpain 1 (Capn1), phospholipase C beta 3 (Plcb3), and Rela and Ikka/Chuk that encode components of the nuclear factor-kappa B (NF-kappaB) pathway. Each are strong candidates because of epidermal expression and/or changes in expression in human HI. All candidates are linked to the ichq locus on mouse Chromosome 19, although Ikka is located more distally. Genetic mapping in mouse has narrowed the ichq critical region to 4 cM. Keratinocytes from skin of +/+, +/ichq and ichq/ichq mice were cultured; all genotypes had similar expression of epidermal differentiation markers. RT-PCR amplification and sequence analysis of each candidate gene did not reveal any mutations in the ichq mouse. Mutational screening of CAPN1 cDNA from different human HI cases revealed a R433P change, but analysis of 50 normal samples demonstrated that this was an apparent polymorphism. Sequence of RELA in five unrelated human HI cases was normal. The results provide compelling evidence that none of these genes are the primary defect in the ichq mouse and that CAPN1 and RELA are not mutated in the human disorder.

A nonsense mutation in the gene encoding 2'-5'-oligoadenylate synthetase/L1 isoform is associated with West Nile virus susceptibility in laboratory mice

A mouse model has been established to investigate the genetic determinism of host susceptibility to West Nile (WN) virus, a member of the genus flavivirus and family Flaviviridae. Whereas WN virus causes encephalitis and death in most laboratory inbred mouse strains after peripheral inoculation, most strains derived from recently trapped wild mice are completely resistant. The phenotype of resistance/susceptibility is determined by a major locus, Wnv, mapping to chromosome 5 within the 0.4-cM-wide interval defined by markers D5Mit408 and D5Mit242. We constructed a high resolution composite/consensus map of the interval by merging the data from the mouse T31 Radiation Hybrid map and those from the homologous region of human chromosome 12q, and found the cluster of genes encoding 2'-5'-oligoadenylate synthetases (2'-5'-OAS) to be the most prominent candidate. This cluster encodes a multimember family of IFN-inducible proteins that is known to play an important role in the established endogenous antiviral pathway. Comparing the cDNA sequences of 2'-5'-OAS L1, L2, and L3 isoforms, between susceptible and resistant strains, we identified a STOP codon in exon 4 of the gene encoding the L1 isoform in susceptible strains that can lead to a truncated form with amputation of one domain, whereas all resistant mice tested so far have a normal copy of this gene. The observation that WN virus sensitivity of susceptible mice was completely correlated with the occurrence of a point mutation in 2'-5'-OAS L1 suggests that this isoform may play a critical role in WN pathogenesis.

Linkage mapping of the mouse nephrosis (nep) gene to chromosome 15

ICGN is a partially inbred strain of mice with nephrotic syndrome caused by spontaneous glomerular lesion. It has been reported that the albuminuria in ICGN mouse was controlled by at least a single autosomal recessive gene (nep). In this study, we mapped the nep locus by linkage analysis of backcross progeny between ICGN and MSM mice using DNA pooling method. The linkage analysis revealed that the nep locus was localized on the distal part of chromosome 15.

Genetic and environmental factors modify bovine spongiform encephalopathy incubation period in mice

The incubation period (IP) and the neuropathology of transmissible spongiform encephalopathies (TSEs) have been extensively used to distinguish prion isolates (or strains) inoculated into panels of inbred mouse strains. Such studies have shown that the bovine spongiform encephalopathy (BSE) agent is indistinguishable from the agent causing variant Creutzfeldt-Jakob disease (vCJD), but differs from isolates of sporadic CJD, reinforcing the idea that the vCJD epidemic in Britain results from consumption of contaminated beef products. We present a mouse model for genetic and environmental factors that modify the incubation period of BSE cross-species transmission. We have used two mouse strains that carry the same prion protein (PrP) allele, but display a 100-day difference in their mean IP following intracerebral inoculation with primary BSE isolate. We report genetic effects on IP that map to four chromosomal regions, and in addition we find significant factors of host environment, namely the age of the host's mother, the age of the host at infection, and an X-cytoplasm interaction in the host.

A new family of genes and pseudogenes potentially expressing testis- and brain-specific leucine zipper proteins in man and mouse

We have characterized a new mouse gene highly transcribed in the testis, and a derived intronless gene expressed in the embryo. The latter gene is present in Mus musculus domesticus and in Mus musculus castaneus but is absent in Mus spretus. The sequencing of different clones from a testis cDNA library reveals a complex transcriptional regulation for the intron-containing gene. The use of several promoters, alternative splicing and trans-splicing, and of two different polyadenylation sites account for the diversity. The different cDNAs encode proteins with features of basic helix-loop-helix leucine zipper (bHLH-ZIP) DNA-binding factors with homology to a new brain-specific factor. The presence of multiple CK2 and PKC phosphorylation sites suggests that their activity may be regulated by phosphorylation. In man, a pseudogene, apparently derived from the same transcript as in mouse and showing 90% homology in the coding region, is present within an intron of another gene. Interestingly, although the human pseudogene is highly mutated in human, in the mouse it has only four nucleotide changes compared with the cDNA of origin, and is still capable of encoding a protein.

Characterization of otoconin-95, the major protein of murine otoconia, provides insights into the formation of these inner ear biominerals

During the course of a study aimed at identifying inner ear-specific transcripts, a 1,906-bp murine cDNA predicted to encode a secreted 469-aa protein with two domains of homology with the secreted phospholipases A2 was isolated. This transcript is specifically expressed in the inner ear from embryonic day 9.5. The encoded 95-kDa glycoprotein is the major protein of the utricular and saccular otoconia and thus was named otoconin-95. By immunohistofluorescence, otoconin-95 also was detected in the cupulae of the semicircular canals and in previously undescribed transient granular structures of the cochlea. Otoconin-95 was found to be synthesized by various nonsensory cell types, but not by the supporting cells of the sensory epithelia, which produce the otoconial precursor vesicles. In addition, multiple isoforms generated by differential splicing were observed in different combinations during development. Based on the present results, we propose a model for the formation of the otoconia.

Structure and expression of Wnt13, a novel mouse Wnt2 related gene

We have identified a novel mouse member of the Wnt family, Wnt13. Among mouse Wnt genes, Wnt13 is most closely related to Wnt2. Sequence comparisons and chromosomal localization strongly suggest that Wnt13, rather than Wnt2, is the mouse orthologue of both the human WNT13 and Xenopus XWnt2 genes. Wnt13 is expressed in the embryonic mesoderm during gastrulation. At later stages, transcripts are detected in the dorsal midline of the diencephalon and mesencephalon, the heart primordia, the periphery of the lung bud and the otic and optic vesicles. These data suggest that Wnt13 function might partially overlap with those of other Wnt genes in the cell signaling mechanisms controlling mesoderm specification during gastrulation and some aspects of brain, heart and lung formation.

The protein kinase N (PKN) gene PRKCL1/Prkcl1 maps to human chromosome 19p12-p13.1 and mouse chromosome 8 with close linkage to the myodystrophy (myd) mutation

Protein kinase N (PKN) is a fatty acid- and Rho-activated serine/threonine protein kinase involved in the regulation of cell motility by association with cytoskeletal components such as neurofilament and alpha-actinin. We determined the chromosomal location of the human PKN gene PRKCL1 by fluorescence in situ hybridization and by radiation hybrid mapping. The corresponding mouse gene Prkcl1 was mapped by segregation analysis. We found by FISH that PRKCL1 is localized to chromosome 19p12-p13.1 and, more precisely, by radiation hybrid mapping, about 11 cR from EST WI-6344 in subband 19p12. Prkcl1 maps to mouse chromosome 8 between D8Mit6 and junb. This region of mouse Chr 8 shows a scrambled syntenic conservation to human chromosomes 4q, 8p, and 19p. As the mouse mutation myodystrophy myd has been mapped to the same region, Prkcl1 is a candidate gene for myd.

Genes of the immune system cosegregate with the age at onset of diabetes in the BB/OK rat

The knowledge of genetic factors determining the age at onset of diabetes may help to delay the development of diabetes and its complications. This prompted us to use our well-characterized BB/OK rat whose age at onset of diabetes can change from 50 to more than 400 days for crossing studies to search for loci cosegregating with the age at onset. Fifty-nine diabetic first backcross hybrids resulting from crosses between diabetic BB/OK and diabetes-resistant DA and SHR rats were genotyped with PCR-analyzed microsatellite markers located on 21 chromosomes. Loci on chromosomes 6 (Ighe -D6Mgh2) and 8 (D8Mit2- Apoc3) were linked with the age at onset. Hybrids which were homozygous for the BB alleles developed significantly earlier diabetes than hybrids which were heterozygous The difference between the age at onset of heterozygous and homozygous hybrids reached a maximum at the loci Ighe on chromosome 6 (+ 32 days, p = 0.0018) and D8Mit2 on chromosome 8 (+ 28 days, p = 0.007). Candidate genes around the loci linked with the age at onset of diabetes are involved in the humoral and cellular immune response. For the first time, this study provides evidence that genetic factors can affect the age at onset of diabetes in the rat.

Analysis of expression of lymphocyte homing-related adhesion molecules in ALY mice deficient in lymph nodes and Peyer's patches

The aly, alymphoplasia, is an autosomal recessive mutation in mice of an unknown etiology, which induces total aplasia of lymph nodes and Peyer's patches. We hypothesized that the lack of lymphoid tissue may be due to abnormalities of lymphocyte traffic into these tissues. Therefore, we analyzed the expression of various adhesion molecules associated with lymphocyte homing. Among the adhesion molecules examined, all were normally expressed except the mucosal addressin MAdCAM-1. In aly/aly mice MAdCAM-1 was absent in the spleen at mRNA and protein levels, but was normally expressed in the intestinal venules. The FISH analysis and linkage analysis using microsatellite markers demonstrated that the MAdCAM-1 gene is located on chromosome 10, indicating that MAdCAM-1 is not encoded by the aly gene, which is located on chromosome 11. Our results indicate that the aberrant expression of MAdCAM-1 is not the direct cause of aly mutation but rather a secondary defect.

The human gene ZFP161 on 18p11.21-pter encodes a putative c-myc repressor and is homologous to murine Zfp161 (Chr 17) and Zfp161-rs1 (X Chr)

A clone from a lambda gt11 cDNA expression library of HeLa cells was isolated, sequenced, and shown to encode a new human zinc finger protein. The cDNA of the gene termed ZFP161 has an open reading frame of 1347 bp. The predicted protein comprises 449 amino acid residues and contains five zinc finger motifs of the Krüppel type near the C-terminus and a BTB/POZ domain in the N-terminal region. The protein is 98% homologous to a murine zinc finger protein, ZF5 (M. Numoto et al., 1993, Nucleic Acids Res. 21: 3767-3775), which is a putative transcriptional repressor of c-myc and exhibits growth-suppressive activity in mouse cell lines. Through the use of a panel of somatic cell hybrids for chromosomal assignment and DNAs of somatic cell hybrids containing a deleted chromosome 18 for fine mapping, the human gene ZFP161 was localized to 18p11.21-pter. Therefore, ZFP161 is a candidate gene by position for the holoprosencephaly type 4 gene, HPE4, which is involved in congenital malformations. With DNAs from an interspecific backcross, two homologous mouse genes, Zfp161 and Zfp161-rs1, were mapped to chromosome 17 and the X chromosome, respectively. Mapping of Zfp161 confirms and extends a region of homology between distal mouse chromosome 17 and human 18p.

Dynamin genes Dnm1 and Dnm2 are located on proximal mouse chromosomes 2 and 9, respectively

Dynamins, microtubule-binding GTPases, are encoded by at least three genes in mammals. Two distinct gene-specific cDNAs were used to analyze the segregation of dynamin genes Dnm1 and Dnm2 in a mouse interspecies backcross. The nervous system-expressed gene Dnm1 was localized to Chr 2 between the genes for vimentin and nebulin, within a chromosomal region of conserved synteny to human chromosome 9q, consistent with the localization of the human dynamin-1 gene by FISH (see accompanying paper by Newman-Smith et al., 1997, Genomics 41:286-289). The ubiquitously expressed Dnm2 gene was found to be closely linked to the intercellular adhesion molecule-1 gene, Icam1, in a region with homologies to human chromosomes 19p, 8q, and 11q. Potential relations of both loci to disease genes are discussed.

cDNA isolation, expression, and chromosomal localization of the mouse survival motor neuron gene (Smn)

Spinal muscular atrophy (SMA) is a frequent autosomal recessive disease in human characterized by degeneration of motor neurons of the spinal cord. The genomic region containing the defective gene (5q13) is particularly unstable and prone to large-scale deletions whose characterization led to the identification of the survival motor neuron (SMN) gene, the SMA determining gene encoding a hitherto unknown protein. As an initial step toward the generation of a murine model for SMA, we identified and characterized a full-length murine Smn cDNA. The coding sequence of the mouse Smn gene was found to be 82% identical, at the amino acid level, with the human SMN coding sequence. The Smn locus was mapped to the segment of mouse chromosome 13 exhibiting conservation of synteny with human chromosome 5q11-q23, which contains the SMN gene. However, no evidence for a duplication of the Smn gene was found in the mouse, suggesting that the duplication reported in human is a recent evolutionary event.

Isolation of markers for chondro-osteogenic differentiation using cDNA library subtraction. Molecular cloning and characterization of a gene belonging to a novel multigene family of integral membrane proteins

To identify novel marker molecules associated with chondro-osteogenic differentiation, we have set up a differential screening system based on a cDNA library subtraction in organ cultures of prenatal mouse mandibular condyles. Differential screening of a cDNA library constructed from in vitro cultured condyles allowed the isolation of a novel gene, named E25. Full-length E25 cDNA is predicted to encode a type II integral membrane protein of 263 amino acid residues. In situ hybridization experiments show that E25 is expressed in the outer perichondrial rim of the postnatal mandibular condyle, which contains the proliferating progenitor cells, but not in the deeper layers of the condyle containing the more differentiated chondroblasts and chondrocytes. Other cartilagenous tissues and their perichondrium were negative. Strong in situ hybridization signals were also detected on bone trabeculae of mature bone in tooth germs and in hair follicles. Northern blot analysis showed strong expression in osteogenic tissues, such as neonatal mouse calvaria, paws, tail, and in skin. This expression profile suggests that E25 could be a useful marker for chondro-osteogenic differentiation. Homology searches of DNA databanks showed that E25 belongs to a novel multigene family, containing three members both in man and mouse. The mouse E25 gene locus (Itm2) was mapped to the X chromosome.

Lanceolate hair (lah): a recessive mouse mutation with alopecia and abnormal hair

A new autosomal recessive mutation of the house mouse developed generalized alopecia associated with breakage of abnormal hair shafts. This mutation, named 'lanceolate hair' (symbol: lah), arose in a mutagenesis experiment using ethylnitrosourea. Hair shafts were short with a focal degeneration at the breakpoint characterized by a pronounced enlargement at the apex, resembling a lance head. Plucked hair fibers were 2.0 to 3.5 mm in length with a normal base, suggesting that there was a synchronized developmental defect. Histologic examination of anagen follicles revealed abnormal cornification of the matrix region with degeneration resulting in the focal hair shaft deformity. Catagen follicles showed pronounced follicular dystrophy but telogen follicles were almost normal. There was a marked, persistent thickening of the epidermis associated with a non-scarring, relatively non-inflammatory ichthyosiform dermatitis. These features are found in the Netherton's syndrome of the human, for which this mouse mutation may represent a model. The lah mutation has been localized to the centromeric end of mouse Chromosome 18.

Cardiac and skeletal muscle troponin I isoforms are encoded by a dispersed gene family on mouse chromosomes 1 and 7

We mapped the locations of the genes encoding the slow skeletal muscle, fast skeletal muscle, and cardiac isoforms of troponin I (Tnni) in the mouse genome by interspecific hybrid backcross analysis of species-specific (C57BL/6 vs Mus spretus) restriction fragment length polymorphisms (RFLPs). The slow skeletal muscle troponin I locus (Tnni1) mapped to Chromosome (Chr) 1. The fast skeletal muscle troponin I locus (Tnni2), mapped to Chr 7, approximately 70 cM from the centromere. The cardiac troponin I locus (Tnni3) also mapped to Chr 7, approximately 5-10 cM from the centromere and unlinked to the fast skeletal muscle troponin I locus. Thus, the troponin I gene family is dispersed in the mouse genome.

A high-resolution genetic map of mouse chromosome 15 encompassing the Dominant megacolon (Dom) locus

Dominant megacolon (Dom) is one of four mutations in the mouse that can produce a phenotype similar to Hirschsprung disease in human. The Dom gene product is not known, and no candidate region has been defined for a possible human homolog. In this publication we report mapping the Dom locus with high definition, using several intra-and interspecific crosses and a set of 16 Chr 15-specific microsatellites flanking this locus.

Genetic and physical mapping of the natural resistance-associated macrophage protein 1 (NRAMP1) in chicken

The chicken natural resistance-associated macrophage protein 1 (NRAMP1) gene has been mapped by linkage analysis by use of a reference panel to develop the chicken molecular genetic linkage map and by fluorescence in situ hybridization. The chicken homolog of the murine Nramp 1 gene was mapped to a linkage group located on Chromosome (Chr) 7q13, which includes three genes (CD28, NDUSF1, and EF1B) that have previously been mapped either to mouse Chr 1 or to human Chr 2q. Physical mapping by pulsed-field gel electrophoresis revealed that NRAMP1 is tightly linked to the villin gene and that the genomic organization (gene order and presence of CpG islands) of the chromosomal region carrying NRAMP1 is well conserved between the chicken and mammalian genomes. The regions on mouse Chr 1, human Chr 2q, and chicken Chr 7q that encompass NRAMP1 represent large conserved chromosomal segments between the mammalian and avian genomes. The chromosome mapping of the chicken NRAMP1 gene is a first step in determining its possible role in differential susceptibility to salmonellosis in this species.

Genetic analysis of three loci homologous to human G9a: evidence for linkage of a class III gene with the chicken MHC

The cDNA clones of two newly discovered genes in the class III region of the human major histocompatibility complex (MHC) were hybridized to chicken DNA. One of these cDNA clones (pG9a-4C7), which detects the single-copy human G9a (BAT8) gene, gave a repeatable restriction pattern. This heterologous cDNA clone was used to detect and map three different PstI restriction fragment length polymorphisms among the two internationally recognized chicken reference populations. Two of the loci were unlinked to previously mapped markers, but one polymorphism cosegregated with the EaB locus in the Compton mapping population. These results provide evidence that some genes of the mammalian class III region, such as G9a, may be linked to the MHC in chickens.

Fourteen anonymous DNA markers of laboratory rats identified with arbitrarily primed polymerase chain reaction (AP-PCR)

In order to develop genetic markers in rats, arbitrarily primed polymerase chain reaction (AP-PCR) was performed with single primers originally designed for microsatellite loci, instead of primers with short-sized and arbitrary nucleotide sequences. Each primer generated reliable and reproducible segments under optimal conditions. The fourteen amplification products have been successfully mapped to rat chromosomes by either linkage analysis using backcross progeny or chromosomal assignment with somatic cell hybrids. All of the loci were located on different chromosomes from those of the microsatellite loci, suggesting that sequence-specifically designed single primers can produce anonymous segments of genomic DNA showing polymorphisms. These markers should contribute to finding linkages for traits of interest in rats.

Functional genes mapped on the chicken genome

Microsatellite polymorphisms are finding increasing use in genetics. In addition to the random isolation of microsatellite markers, such markers can also be developed from sequences already present in public domain databases. An advantage of public domain databases is that these microsatellites are known to be located within or close to identified functional genes. In this study the GenBank and EMBL databases were screened for microsatellite markers and primers were defined for amplification. Subsequently, these markers were tested on a panel of five different birds from layer and broiler stocks and on the international reference families: the East Lansing reference family and the Compton reference family. Of the 33 loci tested, 25 were polymorphic on the test panel and from these 25, 14 were polymorphic in one or both reference families. Twelve of the 14 loci that could be mapped fell into previously defined linkage groups. The other two markers were not linked. Because three of the loci had previously been mapped to specific chromosomes by in situ hybridization, linkage groups E6 and C3 could be assigned to chromosome 6, E5 and C17 to chromosome 4 and E21 to one of the microchromosomes.

T lymphomagenesis is determined by a dominant host gene thymic lymphoma susceptible mouse-1 (TLSM-1) in mouse models

Susceptibility to T lymphomas in mice is determined by a number of viral and host genetic factors. We analyzed the types and latent period of lymphomas spontaneously occurring in crosses between AKR/Ms, a T lymphoma-prone mouse strain, and SL/Kh, a pre-B lymphoma-prone strain. The incidence of T lymphomas in the F1 hybrids backcross to SL/Kh as well as F2 generation mice indicated that a dominant host gene thymic lymphoma susceptible mouse-1 (Tlsm-1) of AKR/Ms determined the type of lymphomas to be thymic. Linkage analysis with microsatellite markers assigned Tlsm-1 to the map position 61 cM from centromere of the chromosome 7. Close scrutiny of this region of AKXD recombinant inbred strains for spontaneous T lymphomas revealed the presence of Tlsm-1-like gene most likely between D7MIT71 (map position 62) and D7MIT13 (map position 70). On the other hand, a SL/Kh-derived recessive allele at a major histocompatibility complex (MHC)-linked locus accelerated development of both T and B lymphomas.

Linkage mapping and partial sequencing of 10 cDNA loci in the chicken

Ten cDNA clones derived from chicken spleen cell mRNA have been partially sequenced and the genes which encode the mRNAs have been located within the linkage map of the chicken genome. The sequences of five of these clones show strong homology to known mammalian genes, the remainder show little homology to sequence present in the current databases. Interestingly, one of these clones appears to be the chicken homologue of the mammalian peptide transporter gene TAP2 and is located within the major histocompatibility complex. Two other clones are homologous to genes involved in protein synthesis and these are tightly linked in chickens, as in mice. These results suggest that partial sequencing and mapping of clones from selective cDNA libraries may be an efficient way of adding candidate genes to the chicken linkage map and that on a local scale there may be some conservation of grouping of genes between chickens and mammalian species.

The spastic mouse: aberrant splicing of glycine receptor beta subunit mRNA caused by intronic insertion of L1 element

Mice homozygous for the spastic mutation (spa) suffer from a complex motor disorder resulting from reduced CNS levels of the adult glycine receptor isoform GlyRA, which is composed of ligand-binding alpha 1 and structural beta polypeptides. The beta subunit-encoding gene (Glyrb) was mapped near the spa locus on mouse chromosome 3. In spa/spa mice, aberrant splicing of the beta subunit pre-mRNA strikingly diminishes the CNS contents of full-length transcripts, whereas truncated beta subunit mRNAs accumulate. This is a result of exon skipping, which causes translational frameshifts and premature stop codons. Intron 5 of the spa Glyrb gene contains an L1 transposable element that apparently is causal for the aberrant splicing of beta subunit transcripts.

Chromosomal mapping in the mouse of eight K(+)-channel genes representing the four Shaker-like subfamilies Shaker, Shab, Shaw, and Shal

The four Shaker-like subfamilies of Shaker-, Shab-, Shaw-, and Shal-related K+ channels in mammals have been defined on the basis of their sequence homologies to the corresponding Drosophila genes. Using interspecific backcrosses between Mus musculus and Mus spretus, we have chromosomally mapped in the mouse the Shaker-related K(+)-channel genes Kcna1, Kcna2, Kcna4, Kcna5, and Kcna6; the Shab-related gene Kcnb1; the Shaw-related gene Kcnc4; and the Shal-related gene Kcnd2. The following localizations were determined: Chr 2, cen-Acra-Kcna4-Pax-6-a-Pck-1-Kras-3-Kcn b1 (corresponding human Chrs 11p and 20q, respectively); Chr 3, cen-Hao-2-(Kcna2, Kcnc4)-Amy-1 (human Chr 1); and Chr 6, cen-Cola-2-Met-Kcnd2-Cpa-Tcrb-adr/Clc-1-Hox-1.1-Myk - 103-Raf-1-(Tpi-1, Kcna1, Kcna5, Kcna6) (human Chrs 7q and 12p, respectively). Thus, there is a cluster of at least three Shaker-related K(+)-channel genes on distal mouse Chr 6 and a cluster on Chr 2 that at least consists of one Shaker-related and one Shaw-related gene. The three other K(+)-channel genes are not linked to each other. The map positions of the different types of K(+)-channel genes in the mouse are discussed in relation to those of their homologs in man and to hereditary diseases of mouse and man that might involve K+ channels.

DNA segments mapped by reciprocal use of microsatellite primers between mouse and rat

Rat microsatellite primers were used for detection of homologous DNA segments in the mouse species (Mus laboratorius, Mus musculus musculus, and Mus spretus). Twenty five (16.3%) of 153 rat primer pairs amplified specific DNA segments, when genomic DNA of mice was used as a template in the polymerase chain reaction (PCR). Size variation among inbred strains of mice was found for 13 DNA segments (8.5%). Eight out of the 13 polymorphic DNA segments were mapped to a particular chromosome with two sets of recombinant inbred strains, AKXL or BXD. Similarly, mouse microsatellite primers were used for detection of homologous DNA segments in rats (Rattus norvegicus). Twenty (12.0%) of 166 primer pairs amplified specific DNA segments from rat genome. Size variation among inbred strains of rats was found for seven DNA segments (4.2%). Eleven of these 20 DNA segments were mapped with a rat x mouse somatic cell hybrid clone panel and/or linkage analysis by use of backcross progeny. Our results suggest that the mapped DNA segments are really homologs between mouse and rat. These polymorphic DNA segments are useful genetic markers.

Sequence-tagged microsatellite sites as markers in chicken reference and resource populations

Two chicken genomic libraries were screened for the presence of poly(TG/AC) microsatellite tracts. The number of positive clones was low, confirming the low frequency of such microsatellites in the chicken genome relative to mammalian genomes. Polymorphism of 29 microsatellite tracts, comprising 11 from the library screening and 18 obtained from GenBank, was examined in the East Lansing and Compton reference families, in a resource population formed by a cross between a single White Rock broiler and inbred Leghorn females, and in a panel of birds from five layer stocks. Twenty microsatellites, primarily of the poly(TG/AC) type, were polymorphic in at least one of the populations. Thirteen of the microsatellites were polymorphic in the East Lansing reference family and 13 were also polymorphic in the resource population, confirming that the genetic distance between White Rock and White Leghorn is about as great as between Jungle fowl and White Leghorn. Only six microsatellites were polymorphic in the Compton reference family, formed by a cross between two White Leghorn strains. Twelve of the microsatellites were mapped in the East Lansing and/or Compton reference families. These were well dispersed among the various linkage groups and did not show any indications of terminal clustering.

Mapping loci influencing the persistence of Theiler's virus in the murine central nervous system

Inbred strains of mice differ greatly in their susceptibility to the demyelinating disease caused by Theiler's Murine Encephalomyelitis Virus. In this murine disease, which is an animal model for the study of multiple sclerosis, demyelination depends on the persistent infection of the central nervous system. Previous studies identified a locus in the H-2D region of the major histocompatibility complex which controls susceptibility to the persistent infection, and also showed that other loci are involved. In order to identify these loci, we screened the genome of a set of backcross animals with a combination of polymorphic microsatellites and restriction enzymes sites. We now show that viral persistence is also controlled by a locus close to Ifg on chromosome 10 and possibly by a locus near Mbp on chromosome 18.

Fine genetic mapping of the proximal part of mouse chromosome 2 excludes Pax-8 as a candidate gene for Danforth's short tail (Sd)

Danforth's short tail (Sd) is a semidominant mutation of the mouse with effects on the skeleton and the urogenital system. In view of its phenotype and its position in the proximal part of Chromosome (Chr) 2, three genes qualified as possible candidates: Pax-8, a paired box-containing gene; Midkine (Mdk), a retinoic acid-responsive gene; and a new locus (Etl-4) identified by enhancer trapping with a lacZ reporter gene which showed expression in the notochord, the mesonephric mesenchyme, and the apical ectodermal ridge. Three different backcrosses involving all three genes in different combinations were set up and analyzed. From our results we conclude that Sd, Etl-4, Pax-8, and Mdk are independent loci, with Etl-4 being the closest genetic marker (1.1 +/- 1.4 cM) to the Danforth's short tail (Sd) gene.

Re-localization of Actsk-1 to mouse chromosome 8, a new region of homology with human chromosome 1

We present here the genetic mapping of the alpha-skeletal actin locus (Actsk-1) on mouse Chromosome (Chr) 8, on the basis of the PCR analysis of a microsatellite in an interspecific backcross. Linkage and genetic distances were established for four loci by analysis of 192 (or 222) meiotic events and indicated the following gene order: (centromere)-Es-1-11.7 cM-Tat-8.3 cM-Actsk-1-0.5 cM-Aprt. Mapping of ACTSK to human Chr 1 and of TAT and APRT to human Chr 16 demonstrates the existence of a new short region of homology between mouse Chr 8 and human Chr 1. Intermingling on this scale between human and mouse chromosomal homologies that occurred during evolution creates disorders in comparative linkage studies.

Homologous chromosomal locations of the four genes for inter-alpha-inhibitor and pre-alpha-inhibitor family in human and mouse: assignment of the ancestral gene for the lipocalin superfamily

The inter-alpha-inhibitor (I alpha I) and pre-alpha-inhibitor (P alpha I) family is composed of three plasma protease inhibitors, I alpha I, P alpha I, and bikunin, whose chains are encoded by a set of three evolutionarily related heavy (H) chain genes designated H1, H2, and H3 and a fourth gene, the so-called alpha 1-microglobulin/bikunin precursor (AMBP) gene. The latter codes for a precursor that splits into: (i) alpha 1-microglobulin, which belongs to the lipocalin superfamily; and (ii) bikunin, which is made up of two tandemly arranged protease inhibitor domains and belongs to the superfamily of Kunitz-type protease inhibitors. The bikunin chain is found in I alpha I and P alpha I molecules and it is also present as a free molecule in plasma. In human, the AMBP and H2 genes have been mapped to 9q32-q34 and 10p14-p15, respectively, while the H1 and H3 genes are tandemly located at 3p21.1-p21.2. In situ hybridization mappings indicate that the mouse AMBP gene (Intin-4) is located at 4C1----C4, and the H1 (Intin-1) and H3 (Intin-3) genes are colocated at 14A2----C1. In interspecific backcrosses (C57BL/6Pas x Mus spretus) a TaqI restriction variant in (and/or near) the H2 (Intin-2) gene identified a linkage of this gene with other polymorphic loci, which assigns Intin-2 to the centromeric area of chromosome 2. All such assignments are in conserved chromosomal regions between human and mouse. Therefore the genetic events that gave rise to the four I alpha I family genes took place prior to the divergence between human and mouse.(ABSTRACT TRUNCATED AT 250 WORDS)

A new strategy useful for rapid identification of microsatellites from DNA libraries with large size inserts

Microsatellites are new powerful polymorphic markers used for gene mapping. Their characterization requires that all the sequence surrounding the repeat be known in order to be able to design primers for PCR amplification. However, when using DNA libraries with large cloned inserts, this sequence characterization is not immediately practicable. In this paper, we describe a new strategy, based both on the use of a microsatellite specific probing and on the creation of nested deleted clones with the Exonuclease III, in order to position microsatellites in a range allowing direct sequencing. This method was applied to the screening of a mouse chromosome 19 DNA specific library. In this way, thirteen clones were identified by specific probing and seven were submitted to the nested deletion strategy. Five of them presented microsatellite sequences in specific deleted subclones which were selected and sequenced. Primers were designed for each of them and polymorphism between the genomes of several inbred strain of mouse have been determined. These microsatellites were mapped, three of them to chromosome 19 and two to chromosome 11.

Wobbler, a mutation affecting motoneuron survival and gonadal functions in the mouse, maps to proximal chromosome 11

The wobbler mouse (genotype wr/wr) has been considered as an animal model for human neurodegenerative disorders. In the homozygous condition, the autosomal mutation wobbler (wr) causes a motoneuron disease and gonadal dysfunction. We have genetically mapped the wr gene, using an interspecific backcross between the laboratory strain C57BL/6J (wr/+) and Mus spretus. The expected percentage of wobbler progeny were obtained, but heterogeneous expression of the wobbler phenotype indicated the existence of modifier genes in the M. spretus genetic background. The segregation of DNA markers of known chromosomal location among wobbler progeny and unaffected mice was scored. Close linkage of wr was obtained with Erbb and Rel on chromosome 11 and the gene order cen-Nfh-Erbb-wr-Rel-Hba-Il-3 was established. Closely linked markers like Erbb provide tools for a prognostic DNA diagnosis of the wobbler disease, and thereby for its analysis by descriptive and experimental embryology.

Polymorphisms revealed by PCR with single, short-sized, arbitrary primers are reliable markers for mouse and rat gene mapping

Ten single, arbitrarily designed oligodeoxynucleotide primers, with 50-70% (G+C) content, were used to amplify by polymerase chain reaction (PCR) sequences with DNA templates from several mouse species (Mus spretus, Mus musculus musculus, and Mus musculus domesticus), as well as DNA from the laboratory rat (Rattus norvegicus). Eight of these ten primers, used either individually or associated in pairs, generated a total of 13 polymorphic products which were used as genetic markers. All of these polymorphic sequences but one were mapped to a particular mouse chromosome, by use of DNA panels prepared either from interspecific backcross progeny of the type (C57BL/6 x Mus spretus)F1 x C57BL/6 or DNA samples prepared from two sets of recombinant inbred (RI) strains (AKXL and BXD). Six rat-specific DNA segments were also assigned to a particular chromosome with DNA panels prepared from 18 rat/mouse somatic cell hybrids segregating rat chromosomes. From these experiments we conclude that, under precisely standardized PCR conditions, the DNA molecules amplified with these arbitrarily designed primers are useful and reliable markers for genetic mapping in both mouse and rat.