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PubMed2001

The pdx genetic marker adjacent to the chloramphenicol biosynthesis gene cluster in Streptomyces venezuelae ISP5230: functional characterization.

The pdx-4 mutation in Streptomyces venezuelae ISP5230 confers a growth requirement for pyridoxal (pdx) and is a marker for the genetically mapped cluster of genes associated with chloramphenicol biosynthesis. A gene regulating salvage synthesis of vitamin B6 cofactors in S. venezuelae was cloned by transforming a pdx-4 mutant host with the plasmid vector pDQ101 carrying a library of wild-type genomic DNA fragments, and by selecting for complementation of the host's pdx requirement. However, the corresponding replicative plasmid could not be isolated. Southern hybridizations and transduction analysis indicated that the complementing plasmid had integrated into the chromosome; after excision by a second crossover, the plasmid failed to propagate. To avoid loss of the recombinant vector, a pdx-dependent Streptomyces lividans mutant, KAA1, with a phenotype matching that of S. venezuelae pdx-4, was isolated for use as the cloning host. Introduction of pIJ702 carrying an S. venezuelae genomic library into S. lividans KAA1, and selection of prototrophic transformants, led to the isolation of a stable recombinant vector containing a 2.5 kb S. venezuelae DNA fragment that complemented requirements for pdx in both S. venezuelae and S. lividans mutants. Sequence analysis of the cloned DNA located an intact ORF with a deduced amino acid sequence that, in its central and C-terminal regions resembled type-I aminotransferases. The N-terminal region of the cloned DNA fragment aligned closely with distinctive helix-turn-helix motifs found near the N termini of GntR family transcriptional regulators. The overall deduced amino acid sequence of the cloned DNA showed 73% end-to-end identity to a putative GntR-type regulator cloned in cosmid 6D7 from the Streptomyces coelicolor A3(2) genome. This location is close to that of pdxA, the first pdx marker in S. coelicolor A3(2) identified and mapped genetically in Sir David Hopwood's laboratory. The S. venezuelae gene and S. coelicolor pdxA are postulated to be homologues regulating vitamin B6 coenzyme synthesis from pdx.

Amino Acid Sequence↗

PubMed1980

Tumbling chemotaxis mutants of Escherichia coli: possible gene-dependent effect of methionine starvation.

Some mutants defective in chemotaxis show incessant tumbling behavior and are called tumbling mutants. Previously described tumbling mutations lie in two genes, cheB and cheZ (41.5 min on Escherichia coli map). Genetic analysis of various tumbling mutants, however, revealed that two more genetic loci, cheC (43 min) and cheE (99.2 min), could also mutate to produce tumbling mutants. The genetic map around cheC was revised: his flaP flaQ flaR flbD flaA (= cheC) flaE. flbD is a new gene. When cells were starved for methionine, the tumbling mutants changed their swimming behavior depending on the che gene mutated. cheZ mutants, like wild-type bacteria, ceased tumbling shortly after removal of methionine. The tumbling of cheB or cheE mutants was depressed after prolonged methionine starvation in the presence of a constant level of an attractant. cheC tumbling mutants appeared unique in that they did not cease tumbling even when cells were deprived of methionine. By contrast, arsenate treatment of the tumbling mutants resulted in smooth swimming of the cells in every case. These results suggest that two different processes are involved in regulation of tumbling; one requiring methionine and the other requiring some phosphorylated compound.

Arsenates↗

PubMed1987

Genetic linkage: sampling issues and multipoint mapping.

Genetic linkage is an important tool in determining the genetic contribution to the etiology of behavior disorders and psychiatric disease. Successful linkage studies employ large sample sizes. It is of particular relevance in psychiatric diseases, where the clinical workup is so extensive, to evaluate sample requirements critically. Recent studies indicate that extensive sampling, out to second-degree relatives, will not assist in identifying linkages although it may inflate the sample size considerably. The impact of the assumption about the mode of inheritance of the psychiatric trait and the effect of reduced penetrance are discussed. Multipoint mapping has the added advantage of using information from many markers simultaneously. This is helpful both in identifying individuals at risk to develop disease and in locating a gene with sufficient precision to determine the gene product. There are complications in applying multipoint mapping but these are generally of a technical nature and soluble. Recent suggestions for handling complications for multipoint mapping are evaluated. The correct design of the sampling procedure for selecting families and for selecting marker loci to use will greatly reduce the volume of work required for linkage studies and enhance the chances for success.

Chromosome Aberrations↗

PubMed2003

Fine scale mapping of a genetic locus for conditioned fear.

Fear conditioning is one of a number of models for investigating the genetic basis of individual variation in emotion and learning. Genetic mapping using crosses between strains of laboratory mice has identified a locus on chromosome one that appears to influence not only variation in conditioned fear, but also in other validated tests of fear-related behaviour, (including the open-field and the elevated-plus maze), suggesting that the rodent locus may act in ways consistent with how a locus influencing susceptibility to anxiety in humans is believed to operate. Here we use high-resolution mapping in genetically heterogeneous mice to show that a quantitative trait locus influencing conditioned fear can be separated from loci influencing open-field activity. Mapping in two different heterogeneous stocks, the Boulder and Northport HS, gave similar map locations for open-field activity at two positions on the current mouse physical map, one at 162 Mb on chromosome one (negative log P-value 5.4) the other at 173 Mb (negative log P-value 4.8), while mapping of contextual conditioned fear in the Boulder HS identified a locus at 170 Mb (negative log P-value 5.4). Estimates of the 95% confidence intervals show that the locations do not overlap. The region containing a gene or genes that influence variation in conditioned fear is approximately 1 megabase in size and contains only one gene of known function, a pre-B cell leukaemia factor.

Animals↗

PubMed1991

Chromosomal mapping of two genetic loci associated with blood-pressure regulation in hereditary hypertensive rats.

The spontaneously hypertensive rat and the stroke-prone spontaneously hypertensive rat are useful models for human hypertension. In these strains hypertension is a polygenic trait, in which both autosomal and sex-linked genes can influence blood pressure. Linkage studies in crosses between the stroke-prone spontaneously hypertensive rat and the normotensive control strain Wistar-Kyoto have led to the localization of two genes, BP/SP-1 and BP/SP-2, that contribute significantly to blood pressure variation in the F2 population. BP/SP-1 and BP/SP-2 were assigned to rat chromosomes 10 and X, respectively. Comparison of the human and rat genetic maps indicates that BP/SP-1 could reside on human chromosome 17q in a region that also contains the angiotensin I-converting enzyme gene (ACE). This encodes a key enzyme of the renin-angiotensin system, and is therefore a candidate gene in primary hypertension. A rat microsatellite marker of ACE was mapped to rat chromosome 10 within the region containing BP/SP-1.

Animals↗

PubMed2004

Duplicate marker loci can result in incorrect locus orders on linkage maps.

Genetic linkage maps, constructed from multi-locus recombination data, are the basis for many applications of molecular markers. For the successful employment of a linkage map, it is essential that the linear order of loci on a chromosome is correct. The objectives of this theoretical study were to (1) investigate the occurrence of incorrect locus orders caused by duplicate marker loci, (2) develop a statistical test for the detection of duplicate markers, and (3) discuss the implications for practical applications of linkage maps. We derived conditions, under which incorrect locus orders do or do not occur with duplicate marker loci for the general case of n markers on a chromosome in a BC(1) mapping population. We further illustrated these conditions numerically for the special case of four markers. On the basis of the extent of segregation distortion, an exact test for the presence of duplicate marker loci was suggested and its power was investigated numerically. Incorrect locus orders caused by duplicate marker loci can (1) negatively affect the assignment of target genes to chromosome regions in a map-based cloning experiment, (2) hinder indirect selection for a favorable allele at a quantitative trait locus, and (3) decrease the efficiency of reducing the length of the chromosome segment attached to a target gene in marker-assisted backcrossing.

Chromosome Mapping↗

PubMed1987

A primary genetic linkage map for human chromosome 12.

A primary genetic map for human chromosome 12 has been constructed from data on 23 restriction fragment length polymorphic systems collected in 38 normal families with large sibships. Linkage analysis of the genotypic data has ordered 16 loci into a continuous genetic map of 111 cM in males and 258 cM in females. Although most of the genetic map reflects a higher rate of recombination in females relative to males, significantly more frequent recombination was observed in males than in females in intervals between loci on the distal portion of the short arm of the chromosome. The mapping data shown here will serve as a first step toward a high-resolution genetic map for human chromosome 12.

Animals↗

PubMed2006

Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo).

The efficacy of employing the chicken genome sequence in developing genetic markers and in mapping the turkey genome was studied. Eighty previously uncharacterized microsatellite markers were identified for the turkey using BLAST alignment to the chicken genome. The chicken sequence was then used to develop primers for polymerase chain reaction where the turkey sequence was either unavailable or insufficient. A total of 78 primer sets were tested for amplification and polymorphism in the turkey, and informative markers were genetically mapped. Sixty-five (83%) amplified turkey genomic DNA, and 33 (42%) were polymorphic in the University of Minnesota/Nicholas Turkey Breeding Farms mapping families. All but one marker genetically mapped to the position predicted from the chicken genome sequence. These results demonstrate the usefulness of the chicken sequence for the development of genomic resources in other avian species.

Alleles↗

PubMed1988

Mapping of Escherichia coli chromosomal Tn5 and F insertions by pulsed field gel electrophoresis.

A low resolution Not I physical map of Escherichia coli was recently constructed. In this report we demonstrated that this map can be used to map Tn5 and F insertions physically. The transposon, Tn5, contains Not I recognition sequences in its IS50 sequences. F plasmid contains an unmapped Not I site. Hence, the location of Tn5 and F in the chromosome can be mapped by identifying the location of the introduced Not I sites using pulsed field gel electrophoresis. The physical mapping of genetically mapped Tn5 insertions confirm the previously constructed Not I map and helps align the E. coli physical and genetic maps. The use of Tn5 can assist the construction of both physical and genetic maps for microorganisms lacking such maps. Variations on this approach will facilitate physical mapping with a wide variety of organisms, enzymes, and genetic elements.

Alleles↗

PubMed1992

A comprehensive genetic linkage map of the human genome. NIH/CEPH Collaborative Mapping Group.

A genetic linkage map of the human genome was constructed that consists of 1416 loci, including 279 genes and expressed sequences. The loci are represented by 1676 polymorphic systems genotyped with the CEPH reference pedigree resource. A total of 339 microsatellite repeat markers assayed by PCR are contained within the map, and of the 351 markers with heterozygosities of at least 70%, 205 are microsatellites. Seven telomere loci define physical and genetic endpoints for 2q, 4p, 7q, 8p, 14q, 16p, and 16q, and in other cases distal markers on the maps have been localized to terminal cytogenetic bands. Therefore, at least 92% of the autosomal length of the genome and 95% of the X chromosome is estimated to be spanned by the map. Since the maps have relatively high marker density and numerous highly informative loci, they can be used to map disease phenotypes, even for those with limited pedigree resources. The baseline map provides a foundation for achieving continuity of clone-based physical maps and for the development of a truly integrated physical, genetic, and cytogenetic map of the human.

Chromosome Mapping↗

PubMedDate not supplied

Genetics of Drosophila subobscura populations. VIII. Allozyme loci and their chromosome maps.

Genetic information on 25 enzyme polymorphisms in Drosophila subobscura, the location of corresponding genes, and cytological and genetic maps of the chromosomes are presented, as well as photographic maps of the salivary gland chromosomes in the third instar larva and white-case early pupal stages. Biochemical markers were used to establish chromosomal homologies among D. subobscura, D. pseudoobscura, D. melanogaster, and D. willistoni.

Acid Phosphatase↗

PubMed1998

A high-density rice genetic linkage map with 2275 markers using a single F2 population.

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.

Chromosome Mapping↗

PubMed1988

A mapped set of genetic markers for human chromosome 9.

A genetic map of markers for human chromosome 9, spanning a genetic distance of 147 cM in males and 231 cM in females, has been constructed from linkage studies with 19 loci in a large panel of reference families. The markers included four classical systems previously assigned to chromosome 9, and restriction fragment length polymorphisms of two cloned genes, ABL oncogene and argininosuccinase synthetase pseudogene 3 (ASSP3). The remaining 13 marker loci, with an average heterozygosity of 42%, were defined by arbitrary DNA probes newly ascertained from genomic libraries; seven of them were variable number of tandem repeat (VNTR) loci. A subset of 7 of the 19 linked markers is proposed for a primary map that could detect linkage with a genetic defect within the covered region of chromosome 9, provided that at least 45 phase-known meioses were available for study in an affected family.

Cell Line↗

PubMedDate not supplied

Methods of analysis and resources available for genetic trait mapping.

Methods of genetic linkage analysis are reviewed and put in context with other mapping techniques. Sources of information are outlined (books, web sites, computer programs). Special consideration is given to statistical problems in canine genetic mapping (heterozygosity, inbreeding, marker maps).

Animals↗

PubMed2004

[Current status and future perspective of genetic linkage mapping in aquaculture species].

Constructing genetic linkage map is an essential tool to acknowledge genome in aquaculture species. This paper has reviewed the current status of genetic linkage map research, including mapping population, mapping method and molecular markers used to construct linkage map. Linkage map has great potential in marker assisted selection (MAS), gene locating and cloning, and comparative genome mapping. Genetic linkage map with high density and wide coverage of genome will allow cloning the genes which contribute to economically important traits. The ultimate aim of the constructing linkage map is the development of fast-growing, disease-resistant strains of the major aquaculture species.

Animals↗

PubMed1991

Genetic and physical mapping of the patatin genes in potato and tomato.

Genes for the major storage protein of potato, patatin, have been mapped genetically and physically in both the potato and tomato genomes. In potato, all patatin genes detected by the cDNA clone pGM01 map to a single locus at the end of the long arm of chromosome 8. By means of pulsed field gel electrophoresis (PFGE) it was possible further to delimit this locus, containing 10-15 copies of the gene, to a maximum size of 1.4 million base pairs. Hybridizations with class-specific clones suggest that the locus is at least partially divided into domains containing the two major types of patatin genes, class I and II. In tomato, patatin-homologous sequences were found to reside at the orthologous locus at the end of chromosome 8. The approximately three copies in tomato were localized by PFGE to a single fragment of 300 kilobases. Whereas the class II-specific 5' promoter sequences reside in tomato at the same locus as the coding sequences, the single class I-specific copy of the 5' promoter sequences was localized on chromosome 3 with no coding sequence attached to it. A clone from this chromosome 3 locus of tomato was isolated and by restriction fragment length polymorphism mapping it could be further shown that a similar class I-specific sequence also exists on chromosome 3 of potato. As in tomato, this copy on chromosome 3 is not linked to a coding sequence for patatin. The results are discussed with respect to genome evolution and PFGE analysis of complex gene families.

Carboxylic Ester Hydrolases↗

PubMed1983

[Mapping of the genetic determinant controlling Salmonella K-antigen synthesis. I. Localization of the determinant in conjugation experiments].

The preliminary data on the localization of the gene responsible for the synthesis of K-antigen in salmonellae were obtained. Using Salmonella Hfr donors with different onset of the transfer of chromosomal markers and with phenotype K+, the authors selected different classes of recombinants in the process of their crossing with K- recipients. The positive result of the agglutination test with specific K-antiserum indicated that the transconjugate thus obtained possessed phenotype K+. The gene responsible for the synthesis of K-antigen was shown to be localized between minutes 46 and 41 of the genetic map of S. typhimurium. This gene was not cotransduced with the histidine marker localized on minute 44 of the map.

Antigens↗

PubMed2003

Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a wheat background.

Three rye-specific repeated sequences, pSc10C, pSc20H and R173-1, were used to design sequence-specific anchored primers. These primers and 16 restriction site-specific adaptor primers were used in all possible combinations to establish sequence-specific amplified polymorphic (SSAP) markers for the 1RS chromosome arm of rye in a wheat background. Thirty 1RS-specific SSAP markers were detected in 19 primer combinations. Along with six markers localised previously on 1RS, 26 of the SSAP markers were mapped genetically in wheat genotypes carrying recombinant 1BL.1RS translocations. A clear decrease in recombination frequency from distal to proximal regions was observed. Wheat-rye addition lines for the 1R chromosome with different-sized deletions of the short arm were used to physically localise these markers. Physical mapping suggested an even distribution of the SSAP markers along the total length of the 1RS chromosome arm.

Chromosome Mapping↗