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PubMed2003

Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers.

Genetic maps for individual Pinus elliottii var. elliottii and P. caribaea var. hondurensis trees were generated using a pseudo-testcross mapping strategy. A total of 329 amplified fragment length polymorphic (AFLP) and 12 microsatellite markers were found to segregate in a sample of 93 interspecfic F(1) progeny. The male P. caribaea var. hondurensis parent was more heterozygous than the female P. elliottii var. elliottii parent with 19% more markers segregating on the male side. Framework maps were constructed using a LOD 5 threshold for grouping and interval support threshold of LOD 2. The framework map length for the P. elliottii var. elliottii megagametophyte parent (1,170 cM Kosambi; 23 linkage groups) was notably smaller than the P. caribaea var. hondurensis pollen parent (1,658 cM Kosambi; 27 linkage groups). The difference in map lengths was assumed to be due to sex-related recombination variation, which has been previously reported for pines, as the difference in map lengths not be accounted for by the larger number of markers mapping to the P. caribaea var. hondurensis parent - 109 compared with 78 in P. elliottii var. elliottii parent. Based on estimated genome sizes for these species, the framework maps for P. elliottii var. elliottii and P. caribaea var. hondurensis covered 82% and 88% of their respective genomes. The pseudo-testcross strategy was extended to include AFLP and microsatellite markers in an intercross configuration. These comprehensive maps provided further genome coverage, 1,548 and 1,828 cM Kosambi for P. elliottii var. elliottii and P. caribaea var. hondurensis, respectively, and enabled homologous linkage groups to be identified in the two parental maps. Homologous linkage groups were identified for 11 out of 24 P. elliottii var. elliottii and 10 out of 25 P. caribaea var. hondurensis groups. A higher than expected level of segregation distortion was found for both AFLP and microsatellite markers. An explanation for this segregation distortion was not clear, but it may be at least in part due to genetic mechanisms for species isolation in this wide cross.

Genetic Markers↗

PubMed1982

Antigen-specific soluble helper activity for murine major histocompatibility complex-encoded molecules. I. Kinetics of factor production after skin transplantation and genetic mapping of the H-2 region specificity.

Antigen-specific soluble helper molecules are produced during major histocompatibility complex-disparate allograft priming. Genetic mapping studies with appropriate recombinant and mutant lines of mice have defined the antigen specificities of the soluble helper molecules described here as being directed against the H-2Dd molecules. The production of antigen-specific helper molecules is a relatively early event after H-2Dd-region allograft priming. A later phase of factor production near the time of graft rejection also contains nonspecific helper factors and IL-2.

Animals↗

PubMed1984

Genetic mapping of Vibrio cholerae enterotoxin structural genes.

The structural genes which constitute the cholera toxin operon, ctxAB, were genetically mapped in the Vibrio cholerae El Tor strain RV79. This strain of V. cholerae contains two copies of the ctx operon located on a 7-kilobase-pair tandemly duplicated region. We began by isolating a vibriophage VcA1 insertion mutation in one of the two ctxA genes located in this region. The mutant carrying this ctxA::VcA1 insertion, DC24, was converted to a VcA1-facilitated donor by introduction of the conjugal plasmid pSJ15, which carries an inserted copy of a defective VcA1-like prophage. The donor characteristics of DC24(pSJ15) indicated that the ctxA::VcA1 insertion mutation was near the trp region of the V. cholerae chromosome. Subsequent RV79 three-factor crosses were performed between VcA1-facilitated donors and recipient strains carrying one of two structural gene mutations in ctx, either delta ctxA23P Kmr or delta ctx-7922. The former was constructed by an in vivo marker exchange procedure and could be scored either by its kanamycin resistance phenotype or by its lack of DNA sequences homologous to the ctxA region. The delta ctx-7922 mutation is a total deletion of both ctx copies of strain RV79. The three-factor cross data strongly suggest that the two ctx loci of RV79 map between the nal and his genes of V. cholerae in the trp nal his linkage group. Physical analysis and heterologous crosses between an RV79 El Tor donor and a 569B classical recipient indicates that one of the two 569B ctx operon copies maps in the same region as the RV79 ctx loci (i.e., linked to nal). Together with previously published observations, these data show that the ctx structural genes are not closely linked to other genes known to affect toxin production in V. cholerae.

Cholera Toxin↗

PubMed1993

Construction of a genetic map telomeric to HLA-A by microsatellite analysis.

Allele and genotype frequencies of five microsatellites on the short arm of chromosome 6 have been determined in 158 subjects from 14 large Italian families, using polymerase chain reaction amplification and a non-radioactive method of detection. The markers studied were: D6S89, D6S109, D6S105, pLR12 and HLA-F; their heterozygosity ranged from 0.65 to 0.78. Two point and three point linkage analysis among these markers and HLA-A serological types--available for all the studied samples--allowed construction of a partial genetic map telomeric to HLA-A. Our results may be useful for linkage analysis of genetic disorders mapping on this region of 6p.

Alleles↗

PubMed1992

High-resolution genetic map around the spinal muscular atrophy (SMA) locus on chromosome 5.

Although autosomal recessive spinal muscular atrophy (SMA) has been mapped to chromosome 5q12-q13, there is for this region no genetic map based on highly informative markers. In this study we present the mapping of two previously reported microsatellite markers in 40 CEPH and 31 SMA pedigrees. We also describe the isolation of a new microsatellite marker at the D5S112 locus. The most likely order of markers (with recombination fractions given in parentheses) is 5cen-D5S6-(.02)-D5S125-(.04)-(JK53CA1/2,D5S11 2)-(.04)-D5S39-qter. The relative order of D5S6, D5S112, and D5S39 was confirmed by in situ hybridization. Multipoint linkage analysis in 31 SMA families indicates that the SMA locus lies in the 6-cM interval between D5S6 and JK53CA1/2, D5S112.

Base Sequence↗

PubMed1993

A detailed genetic map for the X chromosome of the malaria vector, Anopheles gambiae.

Anopheles gambiae, the primary vector of human malaria in Africa, is responsible for approximately a million deaths per year, mostly of children. Despite its significance in disease transmission, this mosquito has not been studied extensively by genetic or molecular techniques. To facilitate studies on this vector, a genetic map has been developed that covers the X chromosome at an average resolution of 2 centimorgans. This map has been integrated with the chromosome banding pattern and used to localize a recessive, sex-linked mutation (white eye) to within 1 centimorgan of flanking markers.

Alleles↗

PubMed1995

Genetic map of the region surrounding the retrovirus restriction locus, Fv1, on mouse chromosome 4.

The Friend virus susceptibility-1 (Fv1) gene maps to mouse Chromosome (Chr) 4 close to a cluster of four endogenous murine leukemia viruses (MLVs). To investigate the feasibility of cloning Fv1 by a positional approach, we have performed an extensive genetic analysis of this region of Chr 4. We have typed 368 backcross mice for the four proviruses, Nppa, Lck, and D4Smh6b. Recombinant animals were screened in a hierarchical fashion with a variety of other markers, including Fv1 and the isozyme marker Gpd1. A detailed genetic map of the region surrounding Fv1 was derived. Three markers, Xmv9, Nppa, and Iap3rc11, were identified that showed no recombination with Fv1. By combining backcross and recombinant inbred strain data, we estimated that Xmv9 and Nppa must lie within 0.6 cM of one another and Fv1.

Animals↗

PubMed1990

Genetic map of Rhizobium meliloti megaplasmid pRmeSU47b.

A circular linkage map of the Rhizobium meliloti megaplasmid pRmeSU47b was constructed. The map consists of transposon insertions carrying alternating antibiotic resistance markers linked by phi M12 transduction. Data from conjugation experiments utilizing donor strains carrying Tn5-oriT insertions in the megaplasmid supported the proposed genetic map. In addition, the positions of previously identified Fix, exopolysaccharide synthetic, thiamine synthetic, and C4-dicarboxylate transport loci on the megaplasmid map were determined. By converting cotransduction frequencies to physical distance, we calculated the replicon to be 1,600 kilobases in size, which compares favorably with previous physical estimates.

Chromosome Mapping↗

PubMed1986

Meiotic segregation analysis of restriction site polymorphisms allows rapid genetic mapping.

The white rot fungus Phanerochaete chrysosporium is an efficient degrader of lignin. Development of classical genetics in this organism would require several years of work, so an alternative strategy was devised. As in the mapping of human genetic diseases, the approach depends on the presence of interallelic restriction site polymorphism, but differs in following their meiotic segregation into the haploid state. Using a set of 20 cloned sequences as probes we were able to demonstrate meiotic segregation of 14 restriction site polymorphisms from fruiting of a single dikaryotic culture and obtained evidence of genetic linkage within two groups of three and two of two. The method could be used to obtain a genetic map of this fungus and should be applicable to genetic analysis of any other organism for which haploid material is available.

Alleles↗

PubMed1990

Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes.

Cloned DNA fragments from 14 characterized maize genes and 91 random fragments used for genetic mapping in maize were tested for their ability to hybridize and detect restriction fragment length polymorphisms in sorghum and other related crop species. Most DNA fragments tested hybridized strongly to DNA from sorghum, foxtail millet, Johnsongrass, and sugarcane. Hybridization to pearl millet DNA was generally weaker, and only a few probes hybridized to barley DNA under the conditions used. Patterns of hybridization of low-copy sequences to maize and sorghum DNA indicated that the two genomes are very similar. Most probes detected two loci in maize; these usually detected two loci in sorghum. Probes that detected one locus in maize generally detected a single locus in sorghum. However, maize repetitive DNA sequences present on some of the genomic clones did not hybridize to sorghum DNA. Most of the probes tested detected polymorphisms among a group of seven diverse sorghum lines tested; over one-third of the probes detected polymorphism in a single F2 population from two of these lines. Cosegregation analysis of 55 F2 individuals enabled several linkage groups to be constructed and compared with the linkage relationships of the same loci in maize. The linkage relationships of the polymorphic loci in the two species were usually conserved, but several rearrangements were detected.

Blotting, Southern↗

PubMed2000

Multipoint genetic mapping with uniparental disomy data.

Uniparental disomy (UPD) refers to the presence of two copies of a chromosome from one parent and none from the other parent. In genetic studies of UPDs, many genetic markers are usually used to identify the stage of nondisjunction that leads to UPD and to uncover the associated unusual patterns of recombinations. However, genetic information in such data has not been fully utilized because of the limitations of the existing statistical methods for UPD data. In the present article, we develop a multilocus statistical approach that has the advantages of being able to simultaneously consider all genetic markers for all individuals in the same analysis and to allow general models for the crossover process to incorporate crossover interference. In particular, for a general crossover-process model that assumes only that there exists in each interval at most one crossover, we describe how to use the expectation-maximization algorithm to examine the probability distribution of the recombination events underlying meioses leading to UPD. We can also use this flexible approach to create genetic maps based on UPD data and to inspect recombination differences between meioses exhibiting UPD and normal meioses. The proposed method has been implemented in a computer program, and we illustrate the proposed approach through its application to a set of UPD15 data.

Algorithms↗

PubMed1999

Zebrafish genetic map with 2000 microsatellite markers.

The zebrafish is the first vertebrate organism used for large-scale genetic screens seeking genes critical to development. These screens have been quite successful, with more than 1800 recessive mutations discovered that speak to morphogenesis of the vertebrate embryo. The cloning of the mutant genes depends on a dense genetic map. The 2000 markers we present here, using microsatellite (CA) repeats, provides 1.2-cM average resolution. One centimorgan in zebrafish is about 0. 74 megabase, so, for many mutations, these markers are close enough to begin positional cloning by YAC walks.

Animals↗

PubMed1996

Genetic mapping in Xiphophorus hybrid fish: assignment of 43 AP-PCR/RAPD and isozyme markers to multipoint linkage groups.

The combined use of the arbitrarily primed polymerase chain reaction [AP-PCR, also known as random amplification of polymorphic DNA (RAPD)] and isozyme mapping resulted in the production of 87 potential marker loci, enabling an overall expansion within the genetic map of the fish genus Xiphophorus. Use of DNA sequencing-style acrylamide gels and carefully controlled conditions of amplification and silver staining allowed exceptional resolution and reproducibility of AP-PCR/RAPD generated markers. Linkage analysis of AP-PCR/RAPD and isozyme markers resulted in the addition of 16 new markers to Xiphophorus linkage groups (LGs) I, II, III, V, IX, X, XII, and XIV. Addition of 5 AP-PCR/RAPD markers to linkage group U6 containing the Tailspot pigment pattern locus (P) and designation of eight new unassigned linkage groups with 22 markers was also accomplished. Genetic linkage data allowed inference of the existence of a novel pigment pattern modifier locus. Expansion of the Xiphophorus gene map by linkage analysis of AP-PCR/RAPD markers in conjunction with isozyme polymorphisms should lead to the rapid saturation of genetic linkage groups such as LG V, which will probably be instrumental to cloning the Diff tumor suppressor gene locus.

Animals↗

PubMed2007

Physical and genetic map of the Staphylococcus xylosus C2a chromosome.

Staphylococcus xylosus is a ubiquitous bacterium frequently isolated from mammalian skin and occurring naturally on meat and dairy products. A physical and genetic map of the S. xylosus C2a chromosome was constructed by pulsed-field gel electrophoresis analysis after digestion with AscI, ApaI, I-CeuI, SfiI and SmaI enzymes and hybridization analysis. The chromosome size was estimated to be 2868+/-10 kb. Thirty-three genetic markers were mapped. The probable origin of replication (oriC) was positioned. Six rrn loci were located, and their orientation was determined. The chromosomes of six additional S. xylosus strains were also analysed by I-CeuI digestion, and an intraspecies diversity of the chromosome size and the number of rrn operons was shown.

Bacterial Proteins↗

PubMed1992

Physical and genetic mapping of the telomeric major histocompatibility complex region in man and relevance to the primary hemochromatosis gene (HFE).

We performed pulsed-field gel electrophoresis (PFGE) on genomic DNA from a radiation hybrid (RH) cell line and constructed a high-resolution physical map of the major histocompatibility complex class I region in 6p21.3, where the gene for primary hemochromatosis (HFE) is believed to be located. Due to the intact microsegment of hemizygous human genomic DNA preserved in the RH cell line, simplified and distinct restriction fragment banding patterns were generated. Using the RH cell line, we were able to extend the physical map of the HLA class I region to about 3000 kb, order the known HLA class I genes from centromere to telomere: HLA-B, -C, -E, (-A, -H, -G), and -F, and orient the HLA-F gene along the chromosome. The proximity of HLA-F to HLA-A was confirmed by linkage and linkage disequilibrium analysis. This study shows that RH cell lines can be useful for constructing long-range physical maps in specific regions of the human genome with PFGE. Physical and genetic mapping studies of this region are consistent with a localization of the HFE gene proximal or distal to HLA-A.

Animals↗

PubMed1995

Refinement of the high-resolution physical and genetic map of Rhodobacter capsulatus and genome surveys using blots of the cosmid encyclopedia.

Cosmids from a library containing Rhodobacter capsulatus DNA fragments were previously ordered in two contigs: one corresponding to the chromosome and one to a 134 kb plasmid. This map contained 40 regions connected only by colony hybridization. To confirm the linkage and correct the map, the actual sizes of the overlaps were determined by blot-hybridization with Rhodobacter chromosomal DNA and by mapping of additional cosmids. Several revisions of the earlier map include single cosmid shifts and inversions. One additional gap in a cosmid contig was also found, raising the possibility that the chromosome is not a contiguous circle. About 2500 additional EcoRI,BamHI and HindIII restriction sites were added to the 560 EcoRV sites previously mapped onto the Rhodobacter chromosome, increasing the resolution of the physical map to the size of individual genes. Twenty-five new markers were located on the genetic map. The 48 markers now mapped represent nearly 300 genes and ORFs cloned from different species of Rhodobacter. The orientation of transcription of the four rrn operons was established using 16S rRNA- and 23S rRNA-specific probes and digestion with the rare-cutting enzyme, CeuI. Gel blots of 192 cosmids of the miniset of R.capsulatus digested with EcoRV were prepared. Such a hybridization template represents the whole genome cut into 560 DNA fragments varying in size from 0.4 to 25 kb. This template was used for high-resolution mapping of single genes, analysis of total genomic DNAs from related Rhodobacter strains and differentially expressed RNAs.

Chromosome Mapping↗

PubMed2002

Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat.

In hexaploid bread wheat ( Triticum aestivum L. em. Thell), ten members of the IWMMN ( International Wheat Microsatellites Mapping Network) collaborated in extending the microsatellite (SSR = simple sequence repeat) genetic map. Among a much larger number of microsatellite primer pairs developed as a part of the WMC ( Wheat Microsatellite Consortium), 58 out of 176 primer pairs tested were found to be polymorphic between the parents of the ITMI ( International Triticeae Mapping Initiative) mapping population W7984 x Opata 85 (ITMI pop). This population was used earlier for the construction of RFLP ( Restriction Fragment Length Polymorphism) maps in bread wheat (ITMI map). Using the ITMI pop and a framework map (having 266 anchor markers) prepared for this purpose, a total of 66 microsatellite loci were mapped, which were distributed on 20 of the 21 chromosomes (no marker on chromosome 6D). These 66 mapped microsatellite (SSR) loci add to the existing 384 microsatellite loci earlier mapped in bread wheat.

Journal Article↗

PubMed1984

Fine structure genetic map and complementation analysis of mutations in the dnaA gene of Escherichia coli.

A fine structure genetic map of several mutations in the dnaA gene of Escherichia coli was constructed by the use of recombinant lambda and M13 phages. The dnaA508 mutation was found to be the mutation most proximal to the promoter, while the dnaA203 mutation was found to be the most distal one. The order of mutations established in this analysis was: dnaA508, dnaA167, (dnaA5, dnaA46, dnaA211), dnaA205, dnaA204, dnaA203. The mutations dnaA601, dnaA602, dnaA603, dnaA604 and dnaA606 were found to map very close to each other and close to dnaA205 in the middle third of the dnaA gene. In analysing the dominance relationship all 13 dnaA mutations were found to be recessive to the wild type. Characteristic phenotypes of the dnaA(Ts) mutants, like reversibility of the temperature inactivation of the dnaA protein, cold sensitivity of haploid or of merodiploid strains and suppressibility by rpoB mutations, are found to correlate with clusters of mutations within the gene.

Bacterial Proteins↗