[Complete genetic map of the left half of the genome of phage phi80].
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Bacteriophage lambda↗
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Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivum L.).
The broad-spectrum stem rust resistance gene Sr2 has provided protection in wheat against Puccinia graminis Pers. f. sp. tritici for over 80 years. The Sr2 gene and an associated dark pigmentation trait, pseudo-black chaff (PBC), have previously been localized to the short arm of chromosome 3B. In a first step towards the positional-based cloning of Sr2, we constructed a high-resolution map of this region. The wheat EST (wEST) deletion bin mapping project provided tightly linked cDNA markers. The rice genome sequence was used to infer the putative gene order for orthologous wheat genes and provide additional markers once the syntenic interval in rice was identified. We used this approach to map six wESTs that were collinear with the physical order of the corresponding genes on rice chromosome 1 suggesting there are no major re-arrangements between wheat and rice in this region. We were unable to separate by recombination the tightly linked morphological trait, PBC from the stem rust resistance gene suggesting that either a single gene or two tightly linked genes control both traits.
Basidiomycota↗
Genetic mapping of the beta 1- and gamma-subunits of the human skeletal muscle L-type voltage-dependent calcium channel on chromosome 17q and exclusion as candidate genes for malignant hyperthermia susceptibility.
Malignant hyperthermia susceptibility (MHS) is an autosomal dominant disorder of skeletal muscle which manifests as a life-threatening hypermetabolic crisis triggered by commonly-used inhalation anaesthetics and depolarizing muscle relaxants. Defects in the ryanodine receptor (RYR1) protein have been proposed to underly MHS, but significant genetic heterogeneity in MHS has recently been demonstrated. In order to investigate the potential roles played by other skeletal muscle calcium channels in MHS, we isolated cosmids containing the gene encoding the beta 1-subunit of skeletal muscle L-type voltage-dependent calcium channel (CACNLB1). We identified a new, highly polymorphic dinucleotide repeat motif close to this gene, and linkage analysis placed the marker proximal to the HOX2B locus, previously localized to chromosome segment 17q21-q22. We recently identified a novel marker within the gamma-subunit locus (CACNLG) at band 17q24, and since both markers are within the 17q11.2-q24 region reported to contain the MHS2 locus, we tested them for linkage in MHS families whose disease trait has been shown not to co-segregate with markers for the RYR1 region on chromosome 19q13.1. Our results exclude CACNLB1 and CACNLG as candidate genes for MHS2, and do not support the reported chromosome 17q localization for the MHS2 locus in our families.
Base Sequence↗
Identification and genetic mapping of RAPD markers linked to the densonucleosis refractoriness gene, nsd-2, in the silkworm, Bombyx mori.
In the silkworm, Bombyx mori, nonsusceptibility to B. mori densonucleosis virus type-2 (BmDNV-2) is controlled by a recessive gene, nsd-2 (nonsusceptibility to DNV-2). We investigated the genetic linkage between two random-amplified polymorphic DNA (RAPD) markers and the +nsd-2 gene. Initially, we constructed the JSD-2 strain (nsd-2/+), which is congenic to strain J137 (nsd-2/nsd-2) with respect to the chromosome containing the +nsd-2 gene, starting with a female of strain J137 and a male of strain C137 (+nsd-2/+nsd-2). Genomic DNAs were compared between infected individuals of the JSD-2 strain and J137 by a polymerase chain reaction (PCR) with 700 arbitrary 10-mer primers. Two RAPD markers (OPH19R and OPP01R) linked to the +nsd-2 gene were found. For the crossing-over experiment, a female of J137 was crossed with a male (nsd-2/+) of JSD-2. Segregation analysis showed that the most closely linked RAPD marker (OPP01R) was mapped 4.7 cM distant from +nsd-2.
Animals↗
Molecular cloning of restriction fragments and construction of a physical and genetic map of the Escherichia coli plasmid R538-1.
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DNA Restriction Enzymes↗
Cloning, sequencing and genetic mapping of a Bacillus subtilis cell wall hydrolase gene.
We have cloned DNA fragments from Bacillus subtilis 168S into Escherichia coli, which produced a lytic zone on an agar medium containing B. subtilis cell wall. Sequencing of the fragments showed the presence of an open reading frame (ORF) which encodes a polypeptide of 272 amino acids with a molecular mass of 29919 Da. The deduced amino acid sequence showed considerable homology with that of the cell wall hydrolase gene of Bacillus sp. (Potvin, C., Leclerc, D., Tremblay, G., Asselin, A. & Bellemare, G. (1988). Molecular and General Genetics 214, 241-248). Accordingly, the gene was designated cwlA, for cell wall lysis. The N-terminal amino acid sequence of cwlA gene product prepared from a E. coli clone was AIKVVKNLVSKSKYGLKCPN, which is consistent with that of the deduced sequence starting from Ala at second position from the initiation codon of the cwlA gene. A presumed sigma A promoter and a rho-independent terminator were found upstream and downstream of the ORF, respectively. A chloramphenicol-resistance determinant integrated into the ORF was mapped by PBS1 transduction, which indicated the gene sequence dnaE-aroD-cwlA.
Amino Acid Sequence↗
Molecular structure and genetic mapping of the mouse gastrin gene.
The mouse gastrin gene has three exons totalling 460 bp and a deduced preprogastrin of 101 amino acids. The sequence of murine gastrin-34 is 94% identical to rat gastrin-34 and 76% identical to human gastrin-34. At Arg79, mouse progastrin has a unique cleavage site that might allow species-specific synthesis of gastrin-13. Northern analysis and RT-PCR demonstrated that gastrin gene transcripts are abundant in mouse stomach and duodenum and present at low levels in brain, ovary and pancreas, similar to the pattern described for other mammals. The gastrin gene was mapped to the distal region of mouse chromosome 11.
Amino Acid Sequence↗
Molecular analysis of mouse alcohol dehydrogenase: nucleotide sequence of the Adh-1 gene and genetic mapping of a related nucleotide sequence to chromosome 3.
The mouse has three genes (Adh) encoding alcohol dehydrogenase (ADH) enzymes of different tissue specificity and catalytic properties. Identified regulatory loci are known to affect the expression of Adh-1 and Adh-3, which are closely linked on chromosome 3. The Adh-1 gene product is expressed predominantly in liver, and its mRNA product is androgen-inducible in kidney. In this study, genomic clones of Adh-1 were obtained from a Balb/cJ DNA library. The nucleotide sequences of all exons, intron/exon boundaries and 5'- and 3'-flanking regions were obtained. The gene spans nearly 13 kb and is divided into nine exons and eight introns. The transcription start point of this gene was determined by S1 nuclease mapping studies and presumptive regulatory regions in the 5'-flanking regions were identified, including a TATA box and a glucocorticoid-responsive element. A restriction fragment length polymorphism in the Adh-1 gene was identified among inbred strains and mapped at the [Adh-1, Adh-3] complex on chromosome 3. An additional 'Adh-like' sequence in the genome was also mapped to chromosome 3 approx. 9 centiMorgans from Adh-1.
Alcohol Dehydrogenase↗
Thirty-one polymorphic microsatellite markers for genetic mapping in rainbow trout (Oncorhynchus mykiss).
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Animals↗
Recovery of DNA amplification products from silver-stained polyacrylamide gels. Applications in nucleic acid fingerprinting and genetic mapping.
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Base Sequence↗
Genetic mapping using microcell-mediated chromosome transfer suggests a locus for Nijmegen breakage syndrome at chromosome 8q21-24.
Nijmegen breakage syndrome (NBS) is an autosomal recessive disorder characterized by microcephaly, short stature, immunodeficiency, and a high incidence of cancer. Cultured cells from NBS show chromosome instability, an increased sensitivity to radiation-induced cell killing, and an abnormal cell-cycle regulation after irradiation. Hitherto, patients with NBS have been divided into the two complementation groups V1 and V2, on the basis of restoration of radioresistant DNA synthesis, suggesting that each group arises from a different gene. However, the presence of genetic heterogeneity in NBS has been considered to be controversial. To localize the NBS gene, we have performed functional complementation assays using somatic cell fusion between NBS-V1 and NBS-V2 cells, on the basis of hyper-radiosensitivity, and then have performed a genomewide search for the NBS locus, using microcell-mediated chromosome transfer followed by complementation assays based on radiosensitivity. We found that radiation resistance was not restored in the fused NBS-V1 and NBS-V2 cells and that only human chromosome 8 complements the sensitivity to ionizing radiation, in NBS cell lines. In complementation assays performed after the transfer of a reduced chromosome, merely the long arm of chromosome 8 was sufficient for restoring the defect. Our results strongly suggest that NBS is a homogeneous disorder and that the gene for NBS is located at 8q21-24.
Abnormalities, Multiple↗
Genetic mapping of a mouse chromosomal locus required for mink cell focus-forming virus replication.
Mouse-hamster somatic cell hybrids were used to show that the recombinant mink cell focus-forming murine leukemia viruses and their ecotropic virus progenitors require different mouse chromosomes for replication. Mouse chromosome 1 was shown to carry the genetic information necessary for the replication of six different mink cell focus-forming isolates, and this gene, designated Rmc-1, was tentatively positioned at the distal end of the chromosome.
Animals↗
Olfactory fingerprints for major histocompatibility complex-determined body odors II: relationship among odor maps, genetics, odor composition, and behavior.
The olfactory system detects small differences in the composition of natural odorants, made up of hundreds of molecules. Odorous quality is hypothetically represented by a combinatorial code: activation of distinct but overlapping subsets of olfactory receptors resulting in activation of a distinct subset of glomeruli in the main olfactory bulb (MOB). Here we show that modification of a single gene (the K gene of the major histocompatibility locus), which results in a subtle change in the odiferous quality of urine, causes a small but significant change in the composition of urine volatiles and consequently the evoked glomerular activation pattern in the MOB. The magnitude of disparity between urine-evoked glomerular activation patterns is predictive of the extent of (1) the genetic difference among the urine donors, (2) the difference in the chemical composition of urine, and (3) the odor detector's ability to discriminate. These data on natural odors are consistent with the combinatorial code hypothesis and identify subsets of glomeruli that are apt to play a significant role in mediating individual recognition.
Animals↗
Characterization and genetic mapping of simple sequence repeats in the rice genome.
We searched partial sequences of over 22,706 rice cDNA and 1220 genomic DNA clones to find and characterize simple sequence repeats (SSRs) in the rice genome. The most frequently found repeated SSR motif in both cDNA and genomic DNA sequences was d(CCG/CGG)n. The second most frequently found SSR was d(AG/CT)n. In contrast with mammalian genomes, in which d(AC/GT)n sequences are the most abundant, d(AG/GT)n sequences were not frequently observed in rice. Sequences containing d(CCG/CGG)n, d(AG/CT)n repeats, and other SSRs were chosen for polymorphism detection. It was predicted that 17 of 20 SSRs in cDNA sequences were located in 5'-untranslated regions near initiation codons. Twenty-two loci can be mapped on our RFLP linkage map by these SSRs. Six markers were tested with 16 japonica rice varieties as templates for PCR. Two markers exhibited amplified fragment length polymorphism among these rice varieties, implying that SSRs are polymorphic among rice varieties which have similar genetic backgrounds. Even these polymorphic SSRs are located within or around genes which code ubiquitous proteins.
Base Sequence↗
A detailed genetic map of the chromosome 7 bronchial hyper-responsiveness locus.
Non-specific bronchial hyper-responsiveness to various inhaled stimuli is a characteristic of asthma. We have previously shown linkage of bronchial responsiveness to methacholine (measured as dose-response slope (DRS)) and the peripheral blood eosinophil count (EOS) to chromosome 7. We have now further investigated these linkages by genotyping 49 microsatellite markers across the DRS locus on chromosome 7. The markers were spaced on average 2.6 cM apart and spanned a sex averaged cumulative genetic distance of 129 cM. Multipoint linkage to DRS was bimodal and dipped at the centromere. The two peaks of linkage were close to markers D7S484 (P=0.0003) and D7S669 (P=0.006) respectively. Separate testing for linkage to paternally and maternally derived alleles showed that the linkage near D7S484 was paternally derived (P<0.00001): maternally derived alleles did not exhibit significant linkage. The results indicate that two disparate loci may be influencing asthma from chromosome 7.
Adolescent↗
Physical and genetic mapping of a human apical epithelial Na+/H+ exchanger (NHE3) isoform to chromosome 5p15.3.
A gene family of Na+/H+ exchanger isoforms has been identified. Characterization of rabbit NHE3 suggests that it is the apical epithelial Na+/H+ exchanger isoform responsible for transepithelial, electroneutral Na+ absorption in intestinal and renal epithelial cells. We have previously isolated from a human kidney cortex library a partial human NHE3 cDNA, clone HKC-3. Using HKC-3 to probe human/rodent somatic cell hybrid mapping panels, the human NHE3 gene was physically mapped to the distal portion of chromosome 5p15.3. Southern analysis of EcoRI-digested human genomic DNAs of CEPH pedigrees probed with HKC-3 detected three polymorphic sites containing a total of nine alleles that segregate in a Mendelian fashion. The observed heterozygosity for the NHE3 locus in unrelated individuals was 71%. Linkage analysis between NHE3 and other markers known to map at 5p15 confirmed the localization of NHE3 to chromosome 5p15.3, making NHE3 the most telomeric gene identified on the short arm of chromosome 5.
Animals↗
A high-resolution genetic map of the familial Mediterranean fever candidate region allows identification of haplotype-sharing among ethnic groups.
Familial Mediterranean fever (FMF) is a recessive disorder of inflammation caused by mutations in a gene (designated MEFV) on chromosome 16p13.3. We have recently constructed a 1-Mb cosmid contig that includes the FMF critical region. Here we show genotype data for 12 markers from our physical map, including 5 newly identified microsatellites, in FMF families. Intrafamilial recombinations placed MEFV in the approximately 285 kb between D16S468/D16S3070 and D16S3376. We observed significant linkage disequilibrium in the North African Jewish population, and historical recombinants in the founder haplotype placed MEFV between D16S3082 and D16S3373 (approximately 200 kb). In smaller panels of Iraqi Jewish, Arab, and Armenian families, there were significant allelic associations only for D16S3370 and D16S2617 among the Armenians. A sizable minority of Iraqi Jewish and Armenian carrier chromosomes appeared to be derived from the North African Jewish ancestral haplotype. We observed a unique FMF haplotype common to Iraqi Jews, Arabs, and Armenians and two other haplotypes restricted to either the Iraqi Jewish or the Armenian population. These data support the view that a few major mutations account for a large percentage of the cases of FMF and suggest that some of these mutations arose before the affected Middle Eastern populations diverged from one another.
Alleles↗
Genetic mapping of the amide response element(s) of the hsr omega locus of Drosophila melanogaster.
Small chromosomal deletions [Df(3R)eR-1 and Df(3R)eP] with intact hsromega transcription units but with variable deletions of the upstream region were used to map the upstream regions that regulate heat shock and amide responsivity of the 93D puff (hsromega locus) in salivary glands of late third instar larvae of Drosophila melanogaster. The Df(3R)eP deletion, generated by a P-element mobilization screen, removed the 93B6-7 to 93D3-5 cytogenetic region. [3H]uridine-labeled transcription autoradiograms revealed that normal developmental and heat shock-induced expression of the 93D puff remained unaffected in both the deficiency chromosomes. However, the amide responsivity of the 93D site was lost on the Df(3R)eP homolog while the Df(3R)eR-1 homolog responded normally to amides. Southern hybridizations with a series of upstream probes mapped the distal breakpoint of the Df(3R)eP deletion between -22 kb and -23 kb of the hsromega transcription unit. Since the distal breakpoint of Df(3R)eR-1 is at about -45 kb upstream of the hsromega gene it is inferred that the amide response element(s) that modulate the specific transcriptional activation of the 93D puff following treatment of salivary glands with a variety of amides is/are located in the -22 kb to about -45 kb upstream interval. The Df(3R)eP and Df(3R)eR-1 deletions also abolished dosage compensation at the 93D locus as well as the effect of beta-alanine levels on its heat shock inducibility.
5' Untranslated Regions↗