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At least 127 records · Page 7Linked to original sources
PubMed1997

Rice molecular genetic map using RFLPs and its applications.

In the past decade, notable progress has been made in rice molecular genetic mapping using genomic or cDNA clones. A total of over 3000 DNA markers, mainly with RFLPs, have been mapped on the rice genome. In addition, many studies related to tagging of genes of interest, gene isolation by map-based cloning and comparative mapping between cereal genomes have advanced along with the development of a high-density molecular genetic map. Thus rice is considered a pivotal plant among cereal crops and, in addition to Arabidopsis, is a model plant in genome analysis. In this article, the current status of the construction of rice molecular genetic maps and their applications are reviewed.

Genetic Markers↗
PubMed1992

A physical and genetic map of the Spiroplasma citri genome.

A physical and genetic map of the Spiroplasma citri genome has been constructed using several restriction enzymes and pulsed field gel electrophoresis. A number of genes were subsequently localized on the map by the use of appropriate probes. The genome size of the spiroplasma estimated from restriction fragments is close to 1780 kbp, the largest of all Mollicutes studied so far. It contains multisite insertions of Spiroplasma virus 1 (SpV1) sequences. The physical and genetic map of the S. citri genome shares several features with that of other Mollicutes, especially those in the Mycoplasma mycoides cluster. This supports the finding that S. citri and these Mycoplasma spp. are phylogenetically related.

Bacteriophages↗
PubMed1993

Microdissection and microcloning of mid-chromosome 4: genetic mapping of 41 microdissection clones.

Available genetic information places the mouse db gene approximately 5 cM distal to Ifa on mid/distal mouse chromosome 4. These data have indicated that there is a relevant paucity of genetic markers that map to this region of chromosome 4. To increase the density of the genetic map on mid-chromosome 4, we have applied the techniques of microdissection and microcloning of the mid-portion of mouse chromosome 4. A total of 47 RFLPs from the microdissection library were used to type the progeny of three C57BL/6J Mus spretus backcrosses. The resulting composite genetic map positions seven known genes, 41 microclones, and three other anonymous markers to a region of approximately 21 cM on mid-chromosome 4 extending from b to Lck. The density of markers in this region of chromosome 4 should be sufficient to initiate the physical mapping of this subchromosomal segment, facilitating efforts to clone the db gene, as well as other uncloned mutant loci in this region of chromosome 4.

Animals↗
PubMed2002

Use of the Caulobacter crescentus genome sequence to develop a method for systematic genetic mapping.

The functional analysis of sequenced genomes will be facilitated by the development of tools for the rapid mapping of mutations. We have developed a systematic approach to genetic mapping in Caulobacter crescentus that is based on bacteriophage-mediated transduction of strategically placed antibiotic resistance markers. The genomic DNA sequence was used to identify sites distributed evenly around the chromosome at which plasmids could be nondisruptively integrated. DNA fragments from these sites were amplified by PCR and cloned into a kanamycin-resistant (Kan(r)) suicide vector. Delivery of these plasmids into C. crescentus resulted in integration via homologous recombination. A set of 41 strains containing Kan(r) markers at 100-kb intervals was thereby generated. These strains serve as donors for generalized transduction using bacteriophage phiCr30, which can transduce at least 120 kb of DNA. Transductants are selected with kanamycin and screened for loss of the mutant phenotype to assess linkage between the marker and the site of the mutation. The dependence of cotransduction frequency on sequence distance was evaluated using several markers and mutant strains. With these data as a standard, previously unmapped mutations were readily localized to DNA sequence intervals equivalent to less than 1% of the genome. Candidate genes within the interval were then examined further by subcloning and complementation analysis. Mutations resulting in sensitivity to ampicillin, in nutritional auxotrophies, or temperature-sensitive growth were mapped. This approach to genetic mapping should be applicable to other bacteria with sequenced genomes for which generalized transducing phage are available.

Amino Acid Sequence↗
PubMed2003

Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping.

Efforts to build a comprehensive genetic linkage map for the turkey (Meleagris gallopavo) have focused on development of genetic markers and experimental resource families. In this study, PCR amplification was attempted for 772 microsatellite markers that had been previously developed for three avian species (chicken, quail and turkey). Allelic polymorphism at 410 markers (53.1% of total examined) was determined by genotyping ten individuals (six F1 parents and four grandparents) in a new resource population specifically developed for genetic linkage mapping. Of these 410 markers, 109 (26.6%) were polymorphic in the tested individuals, with an average of 2.3 alleles per marker. Higher levels of polymorphism were found for the turkey-specific markers (61.1%) than for the chicken (22.7%) or quail-specific markers (33.3%). To test the fidelity of the matings, demonstrate the power of these families for linkage analysis, and determine genetic linkage relationships, 86 polymorphic markers were genotyped for up to 224 birds including founder grandparents, parents and F2 progeny. Linkage relationships for many of the chicken markers elucidated in the turkey were comparable to those observed in the chicken. These data demonstrate that the new UMN/NTBF resource population will provide a solid foundation for constructing a comparative genetic map of the turkey.

Alleles↗
PubMed2006

Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden.

We mapped the genetic influences for type 1 diabetes (T1D), using 2,360 single-nucleotide polymorphism (SNP) markers in the 4.4-Mb human major histocompatibility complex (MHC) locus and the adjacent 493 kb centromeric to the MHC, initially in a survey of 363 Swedish T1D cases and controls. We confirmed prior studies showing association with T1D in the MHC, most significantly near HLA-DR/DQ. In the region centromeric to the MHC, we identified a peak of association within the inositol 1,4,5-triphosphate receptor 3 gene (ITPR3; formerly IP3R3). The most significant single SNP in this region was at the center of the ITPR3 peak of association (P=1.7 x 10(-4) for the survey study). For validation, we typed an additional 761 Swedish individuals. The P value for association computed from all 1,124 individuals was 1.30 x 10(-6) (recessive odds ratio 2.5; 95% confidence interval [CI] 1.7-3.9). The estimated population-attributable risk of 21.6% (95% CI 10.0%-31.0%) suggests that variation within ITPR3 reflects an important contribution to T1D in Sweden. Two-locus regression analysis supports an influence of ITPR3 variation on T1D that is distinct from that of any MHC class II gene.

Adolescent↗
PubMed1995

[A circular genetic map of chromosomes from Erwinia carotovora subsp. Atroseptica 3-2].

A circular genetic map of the bacterium Erwinia carotovora subsp. atroseptica 3-2 was constructed on the basis of the R471a plasmid and Tn5 and Tn9 using Hfr-like donors. Forty-six genes, including phytopathogenicity genes, were located on the basis of interrupted mating experiment results and analysis of coinheritance of markers on a map of 183 min in length. The similarity and differences of chromosomal genetic maps of Erwinia genus bacteria are discussed.

Chromosome Mapping↗
PubMed1988

A primary genetic map of markers of human chromosome 10.

We have constructed a primary genetic map for human chromosome 10 from 13 polymorphic marker systems defining 11 loci, using a new gene mapping algorithm implemented in the computer program GMS. The loci form a continuous genetic map that spans approximately 116 cM in males and 170 cM in females. These loci provide regularly spaced anchor points for linkage studies, except for one interval that is 28 cM in males and 64 cM in females.

Algorithms↗
PubMed1979

Structure of the malB region in Escherichia coli K12. III. Correlation of the genetic map with the restriction map.

A correlation between the genetic and physical maps of the malB region was obtained by performing a restriction cleavage analysis of DNA's carrying various genetically characterized malB deletions. This also allowed to localize the boundaries between malF and malE, malE and malK, mal K and lamB on the restriction map. The genetic map is not grossly distorted with respect to the physical map.

Chromosome Mapping↗
PubMed2002

Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations.

Several plant genetic maps presented in the literature are longer than expected from cytogenetic data. Here we compare F(2) and RI maps derived from a cross between the same two parental lines and show that excess heterozygosity contributes to map inflation. These maps have been constructed using a common set of dominant markers. Although not generally regarded as informative for F(2) mapping, these allowed rapid map construction, and the resulting data analysis has provided information not otherwise obvious when examining a population from only one generation. Segregation distortion, a common feature of most populations and marker systems, found in the F(2) but not the RI, has identified excess heterozygosity. A few markers with a deficiency of heterozygotes were found to map to linkage group V (chromosome 3), which is known to form rod bivalents in this cross. Although the final map length was longer for the F(2) population, the mapped order of markers was generally the same in the F(2) and RI maps. The data presented in this analysis reconcile much of the inconsistency between map length estimates from chiasma counts and genetic data.

Chromosome Mapping↗
PubMed1997

The mouse formin (Fmn) gene: genomic structure, novel exons, and genetic mapping.

Mutations in the mouse formin (Fmn) gene, formerly known as the limb deformity (ld) gene, give rise to recessively inherited limb deformities and renal malformations or aplasia. The Fmn gene encodes many differentially processed transcripts that are expressed in both adult and embryonic tissues. To study the genomic organization of the Fmn locus, we have used Fmn probes to isolate and characterize genomic clones spanning 500 kb. Our analysis of these clones shows that the Fmn gene is composed of at least 24 exons and spans 400 kb. We have identified two novel exons that are expressed in the developing embryonic limb bud as well as adult tissues such as brain and kidney. We have also used a microsatellite polymorphism from within the Fmn gene to map it genetically to a 2.2-cM interval between D2Mit58 and D2Mit103.

Amino Acid Sequence↗
PubMed1997

Physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome.

A physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome was constructed. The macrorestriction map for CeuI, EagI, and SstII was created by ordering the 38 restriction sites by one- and two-dimensional pulsed-field gel electrophoresis (PFGE) and by using an original strategy based on the CeuI enzyme and indirect end labelling by hybridization on both sides of the CeuI sites with rrs (16S RNA) and 3' rrl (23S RNA) probes. The circular chromosome was estimated to be 4.15 Mb in size, and the average resolution of the physical map is 110 kb. The chromosome contains 11 rrn loci, which are localized on 44% of the chromosome in a divergent transcriptional orientation regarding the presumed location of the replication origin. In addition to these 11 rrn operons, a total of 40 identified genes were mapped by hybridization experiments with genes from C. acetobutylicum and from various other clostridia as probes. The genetic map of C. acetobutylicum was compared to that of the three other endospore-forming bacteria characterized so far: Bacillus subtilis, Clostridium beijerinckii, and Clostridium perfringens. Parodoxically, the chromosomal backbone of C. acetobutylicum showed more similarity to that of B. subtilis than to those of the clostridia.

Chromosomes, Bacterial↗
PubMed1997

The use of a genetic map of biallelic markers in linkage studies.

Improvements in genetic mapping techniques have driven recent progress in human genetics. The use of single nucleotide polymorphisms (SNPs) as biallelic genetic markers offers the promise of rapid, highly automated genotyping. As maps of SNPs and the techniques for genotyping them are being developed, it is important to consider what properties such maps must have in order for them to be useful for linkage studies. I examine how polymorphic and densely spaced biallelic markers need to be for extraction of most of the inheritance information from human pedigrees, and compare maps of biallelics with today's genome-scanning sets of microsatellite markers. I conclude that a map of 700-900 moderately polymorphic biallelic markers is equivalent--and a map of 1,500-3,000 superior--to the current 300-400 microsatellite marker sets.

Alleles↗
PubMed1994

A 300 kilobase interval genetic map of rice including 883 expressed sequences.

We have constructed a high resolution rice genetic map containing 1,383 DNA markers at an average interval of 300 kilobases (kb). The markers, distributed along 1,575 cM on 12 linkage groups, comprise 883 cDNAs, 265 genomic DNAs, 147 randomly amplified polymorphic DNAs (RAPD) and 88 other DNAs. cDNAs were derived from rice root and callus, analysed by single-run sequencing and searched for similarities with known proteins. Nearly 260 rice genes are newly identified and mapped, and genomic DNA and cloned RAPD fragments were also sequenced to generate STSs. Our map is the first significant gene expression map in plants. It is also the densest genetic map available in plants and the first to be backed up comprehensively by clone sequence data.

Chromosome Mapping↗
PubMedDate not supplied

[Comparative molecular-genetic mapping of genomes of rye (Secale cereale L.) and other cereals].

The genetic map of rye consisting of 149 RFLP, 20 isozyme and 12 microsatellite markers was developed. Using the collection of cross-hybridizing probes, the presence of multiple translocations in rye genome with respect to wheat and barley genomes was shown. However, within large regions of genome a strict collinearity of marker order was observed that allow us to use the method of comparative mapping for an introduction of new genes. In the developed genetic map 18 morphological and breeding-valuable genes mapped in different rye populations were integrated. The comparative analysis of homeological loci in genomes of Triticeae species as well as in genomes of rice and maize was carried out. The genes controlling a number of morphological traits, plant height, photoperiodic response and winter/spring growth habit were shown to be conserve among cereals and to form clear homoeologous rows.

Chromosome Mapping↗
PubMed1994

A genetic map of common bean to localize specific resistance genes against anthracnose.

A bean genetic map was developed to locate resistance genes against anthracnose and genes involved in plant defense mechanisms. One hundred and fifty-seven markers (51 restriction fragment length polymorphism, 100 random amplified polymorphic DNA, 2 sequence characterized amplified regions, and 4 morphological markers) were used to construct a genetic map covering 567.5 cM of the bean genome. Morphological markers consisted in two resistance genes towards anthracnose (Are and RVI), a dominant gene for nuclear male sterility (Ms8) and a pod-shape character (SGou). This map was established by using a backcross population (BC1) of 128 individuals, derived from a cross between two European bean genotypes: Ms8EO2 and Corel. Nine percent of the markers showed segregation distortions and mapped to three regions. Clusters of 2-10 markers were observed in every linkage group. The possible origin of these clusters is discussed. Nineteen markers shared with a previously published bean linkage map allowed us to establish a preliminary correspondence between the two maps. Finally, seven genes involved in plant defense mechanisms were located on this map.

Base Sequence↗
PubMed1975

Physical mapping of bacteriophage P2 mutations and their relation to the genetic map.

Three new deletion mutants and an insertion mutant of E. coli bacteriophage P2, del2, vir79, del4 and sig5, were mapped by the electron microscope heteroduplex method. The deletions were found to cover 45.5-51.6%, 75.6-76.7% and 92.3-99.3% respectively of P2 DNA while sig5 represented a 3.7% insertion at 78.6% from the left end. The region covering 75.9-76.7% of P2 DNA is also deleted in the two previously characterized immunity insensitive variants of P2, vir22 and Hy dis. This region may identify the portion of the genome responsible for immunity. The physical and genetic maps of P2 were previously found to be colinear with respect to the two mutations vir22 and vir37. This relationship is confirmed by the position of del2.

Bacteriophage P2↗
PubMed2004

A physically anchored genetic map and linkage to avirulence reveals recombination suppression over the proximal region of Hessian fly chromosome A2.

Resistance in wheat (Triticum aestivum) to the Hessian fly (Mayetiola destructor), a major insect pest of wheat, is based on a gene-for-gene interaction. Close linkage (3 +/- 2 cM) was discovered between Hessian fly avirulence genes vH3 and vH5. Bulked segregant analysis revealed two DNA markers (28-178 and 23-201) within 10 cM of these loci and only 3 +/- 2 cM apart. However, 28-178 was located in the middle of the short arm of Hessian fly chromosome A2 whereas 23-201 was located in the middle of the long arm of chromosome A2, suggesting the presence of severe recombination suppression over its proximal region. To further test that possibility, an AFLP-based genetic map of the Hessian fly genome was constructed. Fluorescence in situ hybridization of 20 markers on the genetic map to the polytene chromosomes of the Hessian fly indicated good correspondence between the linkage groups and the four Hessian fly chromosomes. The physically anchored genetic map is the first of any gall midge species. The proximal region of mitotic chromosome A2 makes up 30% of its length but corresponded to <3% of the chromosome A2 genetic map.

Animals↗