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At least 577 records · Page 32Linked to original sources
PubMed1988

A primary genetic map of the pericentromeric region of the human X chromosome.

We report a genetic linkage map of the pericentromeric region of the human X chromosome, extending from Xp11 to Xq13. Genetic analysis with five polymorphic markers, including centromeric alpha satellite DNA, spanned a distance of approximately 38 cM. Significant lod scores were obtained with linkage analysis in 26 families from the Centre d'Etude du Polymorphisme Humain, establishing estimates of genetic distances between these markers and across the centromere. Physical mapping experiments, using a panel of somatic cell hybrids segregating portions of the X chromosome due to translocations or deletions, are in agreement with the multilocus linkage analysis and indicate the order Xp11 . . . DXS7(L1.28)-TIMP- DXZ1(alpha satellite, cen)- DXS159(cpX73)-PGK1 . . . Xq13. The frequency of recombination in the two approximately 20-cM intervals flanking alpha satellite on either chromosome arm was roughly proportional to the estimated physical distance between markers; no evidence for a reduced crossover frequency was found in the intervals adjacent to the centromere. However, significant interfamilial variations in recombination rates were noted in this region. This primary map should be useful both as a foundation for a higher resolution centromere-based linkage map of the X chromosome and in the localization of genes to the pericentromeric region.

Alleles↗
PubMed1999

Identification and genetic mapping of bovine chemokine genes expressed in epithelial cells.

RNA fingerprinting by arbitrarily primed (RAP)-PCR was used to identify two bovine genes that were differentially expressed in epithelial cells during an inflammatory response. RNA fingerprints revealed two differentially amplified transcripts when monolayers of Madin-Darby bovine kidney (MDBK) cells were stimulated with Escherichia coli O157:H7 lipopolysaccharide (LPS) in combination with cycloheximide (CX). Sequence analysis showed that both transcripts encoded members of the alpha C-X-C chemokine family; one was interleukin 8 (IL-8), and the other was a protein closely related to bovine growth-regulated protein (GRO)-gamma (89% identical). The latter putative epithelial cell inflammatory protein was designated ECIP-1. IL-8 and ECIP-1 genes were placed on the cattle genetic map with single-nucleotide polymorphism (SNP) markers amplified from genomic DNA. Multi-point linkage analysis indicated that the gene locations were indistinguishable from those of serum albumin (ALB) and vitamin D-binding protein (GC) on bovine Chromosome (BTA) 6. In humans, ALB and GC are located near IL-8, GRO-gamma, and seven other alpha chemokines on Chr 4 (HSA 4q11-4q13), suggesting that this gene cluster has been conserved on BTA6. These results provide a starting point for characterizing allelic variation in chemokine genes and their role in the pathogenesis of bacterial infections in cattle.

Amino Acid Sequence↗
PubMed1998

Sequencing and phylogenetic analysis of the protease gene, and genetic mapping of bovine adenovirus type 10 define its relatedness to other bovine adenoviruses.

The complete genome of a bovine adenovirus (BAV) type 10 isolate was molecularly cloned and partially sequenced. The encoded proteins were predicted by computer analysis of the DNA sequences of the ends or the entire length of the cloned viral fragments, and thus a rough genetic map was constructed. The protease gene of BAV-10 was completely sequenced and used in phylogenetic analysis. Based on the results of the phylogenetic analysis, and the location and presence of certain genes thought to be specifically characteristic of subgroup 1 or subgroup 2 BAVs, it could be concluded that, in spite of the striking similarity in certain biological properties, BAV-10 is not related to subgroup 2 BAVs as originally described. It does not however fit clearly into subgroup 1 either, the members of which show closer relationship with human adenoviruses. BAV-10 therefore should best be considered as the first member of a third subgroup of BAVs.

Adenoviruses, Canine↗
PubMed1998

Genetic mapping refines DFNB3 to 17p11.2, suggests multiple alleles of DFNB3, and supports homology to the mouse model shaker-2.

The nonsyndromic congenital recessive deafness gene, DFNB3, first identified in Bengkala, Bali, was mapped to a approximately 12-cM interval on chromosome 17. New short tandem repeats (STRs) and additional DNA samples were used to identify recombinants that constrain the DFNB3 interval to less, similar6 cM on 17p11.2. Affected individuals from Bengkala and affected members of a family with hereditary deafness who were from Bila, a village neighboring Bengkala, were homozygous for the same alleles for six adjacent STRs in the DFNB3 region and were heterozygous for other distal markers, thus limiting DFNB3 to an approximately 3-cM interval. Nonsyndromic deafness segregating in two unrelated consanguineous Indian families, M21 and I-1924, were also linked to the DFNB3 region. Haplotype analysis indicates that the DFNB3 mutations in the three pedigrees most likely arose independently and suggests that DFNB3 makes a significant contribution to hereditary deafness worldwide. On the basis of conserved synteny, mouse deafness mutations shaker-2 (sh2) and sh2J are proposed as models of DFNB3. Genetic mapping has refined sh2 to a 0.6-cM interval of chromosome 11. Three homologous genes map within the sh2 and DFNB3 intervals, suggesting that sh2 is the homologue of DFNB3.

Alleles↗
PubMed1992

Gene isolation by complementation in Candida albicans and applications to physical and genetic mapping.

We have isolated three genes, ARG57, SER57, and LYS1, on the basis of their function in Candida albicans. A C. albicans transformation vector containing the C. albicans URA3 gene, a Candida ARS sequence, and a portion of the Saccharomyces cerevisiae 2 microns circle containing the replication origin was constructed. Clones from genomic libraries in this vector were isolated by direct complementation of the auxotrophies in strain 1006 (arg57 ser57 lys1 ura3 MPA1). Transformants typically contain two to four plasmids in a mixed tandem multimer. A scheme to resolve mixed multimers into monomers in vivo by transformation of S. cerevisiae with Candida transformant DNA selecting Ura+ transformants was devised. Monomeric plasmids were then isolated by transformation of Escherichia coli with the S. cerevisiae transformant DNA. These were retested by transformation of strain 1006 to identify the specific plasmid that complemented the auxotrophy. The chromosomal locations of the genes were determined by hybridization to C. albicans chromosomes separated on contour-clamped homogenous electric field gels. We used these locations to assess the stability of individual C. albicans chromosomes in parasexual genetic analysis. The Lys(+)-complementing clone was shown to be LYS1 by complementation of S. cerevisiae lys1 mutants. These cloned genes help to align the Candida physical and genetic maps and provide additional markers for the transformation system.

Candida albicans↗
PubMed1971

Genetic mapping of genes concerned with glutamyl polypeptide production by Bacillus licheniformis and a study of their relationship to the development of competence for transformation.

By transduction with SP-15, we have mapped some of the genetic sites involved in glutamyl polypeptide (Pep) production by Bacillus licheniformis 9945A. Eleven peptide mutations were assigned to group 1 which lies between the gly-42 and his-6 markers. Three other mutations were assigned to group 2 which lies between the ade-2 and str-1 sites. A series of 28 additional Pep(-) mutants did not belong to either group 1 or 2; the chromosomal location of those peptide mutations is unknown. All three mutants of group 2 were highly transformable, but only two of group 1 transformed well under the conditions employed. Knowing the chromosomal markers that were linked to peptide mutations made it possible to investigate the effect peptide mutations might have on the development of competence for transformation. Nontransformable organisms were rendered transformable upon the introduction, by transduction, of Pep(-) mutations from transformable strains. These results supported the conclusion that the ability of cells to develop competence for transformation when grown under appropriate conditions was related to the physiological effects of particular peptide mutations.

Bacillus↗
PubMed2003

Characterization of a radish introgression carrying the Ogura fertility restorer gene Rfo in rapeseed, using the Arabidopsis genome sequence and radish genetic mapping.

The radish Rfo gene restores male fertility in radish or rapeseed plants carrying Ogura cytoplasmic male-sterility. This system was first discovered in radish and was transferred to rapeseed for the production of F1 hybrid seeds. We aimed to identify the region of the Arabidopsis genome syntenic to the Rfo locus and to characterize the radish introgression in restored rapeseed. We used two methods: amplified consensus genetic markers (ACGMs) in restored rapeseed plants and construction of a precise genetic map around the Rfo gene in a segregating radish population. The use of ACGMs made it possible to detect radish orthologs of Arabidopsis genes in the restored rapeseed genome. We identified radish genes, linked to Rfo in rapeseed and whose orthologs in Arabidopsis are carried by chromosomes 1, 4 and 5. This indicates several breaks in colinearity between radish and Arabidopsis genomes in this region. We determined the positions of markers relative to each other and to the Rfo gene, using the progeny of a rapeseed plant with unstable meiotic transmission of the radish introgression. This enabled us to produce a schematic diagram of the radish introgression in rapeseed. Markers which could be mapped both on radish and restored rapeseed indicate that at least 50 cM of the radish genome is integrated in restored rapeseed. Using markers closely linked to the Rfo gene in rapeseed and radish, we identified a contig spanning six bacterial artificial chromosome (BAC) clones on Arabidopsis chromosome 1, which is likely to carry the orthologous Rfo gene.

Arabidopsis↗
PubMed2001

Genetic mapping and allelic loss analysis in mouse thymic lymphomas of Helios and Aiolos belonging to the Ikaros gene family.

The Ikaros gene undergoes bi-allelic changes at a high frequency in gamma-ray-induced mouse thymic lymphomas, suggesting the relevance of Ikaros to the lymphoma development. Here we test whether Helios and Aiolos, two other members of the Ikaros gene family, are also involved in lymphomagenesis. Genetic mapping showed that Helios is located between D1Mit531 and D1Mit19 on chromosome 1 and Aiolos is between D11Mit222 and D11Mit332 on chromosome 11. Analysis using polymorphic markers around the two regions revealed that neither locus exhibited allelic loss in the 78 lymphomas that were induced in p53 wild-type mice, whereas in 102 p53(KO / + ) mouse-derived lymphomas Helios and Aiolos loci showed allelic loss in 8% (8 / 102) and 33% (34 / 102), respectively. However, 33 of the 34 lymphomas showing allelic loss at Aiolos were p53(KO / - ) and were accompanied by loss of the p53 wild-type allele on the same chromosome. Homozygous deletion and mutation analyses failed to detect bi-allelic alterations. These results do not suggest any obvious contribution of Helios or Aiolos to oncogenesis of the mouse thymic lymphomas.

Animals↗
PubMed2003

Genetic mapping and molecular characterization of the self-incompatibility (S) locus in Petunia inflata.

Gametophytic self-incompatibility (SI) possessed by the Solanaceae is controlled by a highly polymorphic locus called the S locus. The S locus contains two linked genes, S-RNase, which determines female specificity, and the as yet unidentified pollen S gene, which determines male specificity in SI interactions. To identify the pollen S gene of Petunia inflata, we had previously used mRNA differential display and subtractive hybridization to identify 13 pollen-expressed genes that showed S -haplotype-specific RFLP. Here, we carried out recombination analysis of 1205 F2 plants to determine the genetic distance between each of these S -linked genes and S-RNase. Recombination was observed between four of the genes (3.16, G211, G212, and G221) and S-RNase, whereas no recombination was observed for the other nine genes (3.2, 3.15, A113, A134, A181, A301, G261, X9, and X11). A genetic map of the S locus was constructed, with 3.16 and G221 delimiting the outer limits. None of the observed crossovers disrupted SI, suggesting that all the genes required for SI are contained in the chromosomal region defined by 3.16 and G221. These results and our preliminary chromosome walking results suggest that the S locus is a huge multi-gene complex. Allelic sequence diversity of G221 and 3.16, as well as of 3.2, 3.15, A113, A134 and G261, was determined by comparing two or three alleles of their cDNA and/or genomic sequences. In contrast to S-RNase, all these genes showed very low degrees of allelic sequence diversity in the coding regions, introns, and flanking regions.

Alleles↗
PubMed2001

A physical and genetic map of the Mycoplasma flocculare ATCC 27716 chromosome reveals large genomic inversions when compared with that of Mycoplasma hyopneumoniae strain J(T).

Pulsed-field gel electrophoresis and DNA hybridization data were used to construct a chromosomal map of Mycoplasma flocculare ATCC 27716, a non-pathogenic inhabitant of porcine respiratory tracts. Twenty-one genetic markers were placed on the map. Comparison of the genetic map with that of the closely related Mycoplasma hyopneumoniae strain J(T), the type strain of the causative agent of enzootic pneumonia in pigs, identified three chromosomal inversions that differentiate these genomes. One of these inversions involves genes that possibly may be involved in M. hyopneumoniae pathogenicity.

Animals↗
PubMed1995

Molecular cloning and physical and genetic mapping of a novel human Na+/H+ exchanger (NHE5/SLC9A5) to chromosome 16q22.1.

A human genomic clone for a novel fifth member of the Na+/H+ exchanger (NHE) family, NHE5 (gene symbol SLC9A5), has been isolated and partially sequenced. The deduced amino acid sequence of two exons, containing 154 codons, exhibits 59-73% identity to the other members of the NHE family, with closest similarity to NHE3. Northern blot analysis demonstrated that the NHE5 gene is expressed in brain, testis, spleen, and skeletal muscle. Fluorescence in situ hybridization analysis of a cosmid containing NHE5 to human metaphase chromosomes localized the NHE5 gene to the cytogenetic interval 16q21-q22. A panel of somatic cell hybrids containing various portions of chromosome 16 was used to refine further the placement of NHE5 within band 16q22.1. A polymorphic dinucleotide (GT/CA)n repeat contained in the NHE5 cosmid was identified and developed into a microsatellite PCR marker. This was typed in a subset of the CEPH (Centre d'Etude du Polymorphisme Humain) families to place it on a genetic map of the human genome. Pairwise linkage analysis of this marker showed that it was linked to marker D16S421 with a maximal lod score of 35.21 at a recombination fraction (theta) of 0.000, in complete concordance with its chromosomal localization by physical mapping. Multipoint linkage analysis placed NHE5 between the flanking markers D16S421 and D16S512. The cloning of this new member of the sodium hydrogen exchanger family, its chromosomal localization, and the discovery of a polymorphic marker for it now make it feasible to study the possible involvement of this gene in disorders of Na+/H+ transport.

Amino Acid Sequence↗
PubMed2006

Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor.

Wheat prolamin-box binding factor (WPBF) was shown to be an activator of Triticum aestivum L. storage protein genes. Three homoeologous genes encoding this transcription factor were isolated from a bacterial artificial chromosome genomic library and sequenced. The genes all have two exons separated by an intron of approximately 1,000 bp where the second exon contains the entire coding sequence. Many differences were found between homoeologous sequences, but none of them is predicted to significantly alter the sequence of the putative encoded protein. The three homoeologous genes are specifically expressed in grain from 3 to 39 days after anthesis. The allelic variation of a genetically diverse collection of 27 bread wheat lines was assessed. One, five, and one single-nucleotide polymorphisms (SNPs) were detected in the wPbf genes for the A, B, and D genomes, respectively. Physical and genetic mapping utilizing some of the SNPs identified confirmed that wPbf genes are located close to the centromeres on the homoeologous group 5 chromosomes. The low level of allelic diversity found in wPbf genes may suggest that these genes play a key role and are thus constrained by selection.

Amino Acid Sequence↗
PubMed1994

Mouse cellular nucleic acid binding proteins: a highly conserved family identified by genetic mapping and sequencing.

Human cellular nucleic acid binding protein (CNBP) is a zinc finger DNA binding protein of unknown function. The human CNBP cDNA was used as a probe to isolate four structurally distinct but highly homologous mouse liver cDNA clones. Each of the mouse clones exhibited extraordinary sequence conservation with human CNBP cDNA, and the predicted mouse amino acid sequence identities with human CNBP protein ranged from 99 to 100%. Genetic mapping of CNBP genes in interspecific and intersubspecific mouse backcrosses revealed two loci that hybridize to CNBP cDNA at high stringency, located on chromosomes 5 and 6. The subcellular distribution of the CNBP protein was characterized with a specific polyclonal antibody generated against a synthetic peptide from the carboxyl terminus. CNBP was found in the cytosol and the endoplasmic reticulum in subcellular fractions from mouse liver, but was undetectable in nuclear fractions. These data suggest that CNBP is a member of a highly conserved family of cytosolic proteins that may be encoded by multiple dispersed genes.

Amino Acid Sequence↗
PubMed1991

Physical and genetic map of the Neisseria gonorrhoeae strain MS11-N198 chromosome.

A macro-restriction map of the Neisseria gonorrhoeae chromosome was constructed using the enzymes Nhel and Spel. Combinations of one- and two-dimensional electrophoresis of completely or partially digested chromosomal DNA were performed to align the restriction fragments. The chromosome is circular, with an estimated size of 2.33 Mb +/- 35 kb. A genetic map was derived from the physical map; positions of over 60 defined loci were determined by Southern hybridization.

Blotting, Southern↗
PubMed1997

Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.

The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions of A. thaliana resemble human centromeres in size and genomic organization.

Alleles↗
PubMed1996

Genetic mapping of four mouse bHLH genes related to Drosophila proneural gene atonal.

It has been shown that mammalian neurogenesis is partly controlled by multiple basic helix-loop-helix (bHLH) genes, as in Drosophila. Recently, mouse homologs of Drosophila atonal, a proneural gene encoding a bHLH protein required for chordotonal organ and photoreceptor development, have been characterized to obtain further insights into the molecular nature of mammalian neurogenesis. Here, to assess their potential involvement in genetic neural disorders, we have determined genetic map positions for four mouse atonal-related genes, Atoh1, Atoh2, Atoh3, and Ndrf, which encode MATH-1, MATH-2, MATH-3, and NDRF, respectively. Interspecific backcross analysis indicated that Atoh1 and Atoh2 were located in separate positions of Chr 6 and that Atoh3 and Ndrf were mapped to Chr 10 and Chr 11, respectively. Thus, these structurally related genes are located separately on multiple chromosomes.

Amino Acid Sequence↗
PubMed2004

Chicken single nucleotide polymorphism identification and selection for genetic mapping.

Single nucleotide polymorphisms (SNP) are the ideal markers for high-density genome wide mapping. A total of 327,000 expressed sequence tag (EST) sequences, obtained from the ChickEST project, were examined for the presence of SNP. A total of 32,268 potential chicken SNP were identified and stored in a customized Microsoft Access database and evaluated in silico for their usability for a high-density genetic map. Based on a minimum of 3 for the minor allele occurrence and a minimum of 30% for the minor allele frequency, 5,332 reliable SNP were selected, of which both SNP alleles were present in the database at a high frequency. To test the usefulness of the in silico SNP identification, 24 SNP affecting a BglII site were used for a genotyping study. A functional PCR assay could be designed for 21 of the 24 SNP. It was possible to validate 90% of this marker subset (21 SNP) by BglII restriction analysis. The high percentage of validated markers demonstrates the reliability of the 5,332 chicken SNP markers. Furthermore, the limited number of genomic DNA samples necessary to validate 90% of the SNP markers confirmed the prediction of the high frequency at which both alleles of the selected SNP were present in the tested chicken populations.

Animals↗