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At least 541 records · Page 30Linked to original sources
PubMed2001

[Construction of genetic map in sorghum and fine mapping of the germination stimulant production gene response to Striga asiatica].

Sorghum is the fifth important crop in the world. It is also the major food resource in African countries. Striga asiatica is a parasitism weed on sorghum and some other important crops. In this report, two sorghum lines with the difference in response to Striga asiatica, SRN39 (lower Germination Stimulant-GermStim production) and Shanguihong (high GermStim production), were selected as the parents for the construction of a recombinant inbred (RI) population. Ninety-four RI lines were collected for the molecular analysis and GermStim production evaluation. A genetic map was constructed with 251 molecular markers that distributed on 10 different linkage groups. The map covers sorghum genome of 1,779 cm with an average map distance of 7.1 cm between linked markers. It is one of the complete sorghum molecular map in the world. Co-segregation analysis indicated that the germination stimulant gene (GermStim) was located on linkage group J, which was at a distance of 13 cm from the closed marker. Further RAPD analysis between two parents and two DNA pools different in the amount of germination stimulant production, several polymorphic DNA fragments were identified and cloned. Mapping results showed two of them flanked with the GermStim gene at a distance of 1.6 cm and 2.1 cm respectively.

Chromosome Mapping↗
PubMed1994

Genetic mapping of the BRCA1 region on chromosome 17q21.

Chromosome 17q21 harbors a gene (BRCA1) associated with a hereditary form of breast cancer. As a step toward identification of this gene itself we developed a number of simple-sequence-repeat (SSR) markers for chromosome 17 and constructed a high-resolution genetic map of a 40-cM region around 17q21. As part of this effort we captured genotypes from five of the markers by using an ABI sequencing instrument and stored them in a locally developed database, as a step toward automated genotyping. In addition, YACs that physically link some of the SSR markers were identified. The results provided by this study should facilitate physical mapping of the BRCA1 region and isolation of the BRCA1 gene.

Base Sequence↗
PubMed2005

Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes.

BACKGROUND: Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an approximately 5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS has a transgenic insertion-deletion (TgPWS/TgAS) of chromosome 7B/C subsequent to paternal or maternal inheritance, respectively. In this study, we define the deletion endpoints and examine the impact on expression of flanking genes. RESULTS: Using molecular and cytological methods we demonstrate that 13 imprinted and 11 non-imprinted genes are included in the TgPWS/TgAS deletion. Normal expression levels were found in TgPWS brain for genes extending 9.1- or 5.6-Mb centromeric or telomeric of the deletion, respectively. Our molecular cytological studies map the proximal deletion breakpoint between the Luzp2 and Siglec-H loci, and we show that overall mRNA levels of Luzp2 in TgPWS and TgAS brain are significantly reduced by 17%. Intriguingly, 5' Chrna7 shows 1.7-fold decreased levels in TgPWS and TgAS brain whereas there is a > or =15-fold increase in expression in neonatal liver and spleen of these mouse models. By isolating a Chrna7-Tg fusion transcript from TgAS mice, we mapped the telomeric deletion breakpoint in Chrna7 intron 4. CONCLUSION: Based on the extent of the deletion, TgPWS/TgAS mice are models for PWS/AS class I deletions. Other than for the first gene promoters immediately outside the deletion, since genes extending 5.6-9.1 Mb away from each end of the deletion show normal expression levels in TgPWS brain, this indicates that the transgene array does not induce silencing and there are no additional linked rearrangements. Using gene expression, non-coding conserved sequence (NCCS) and synteny data, we have genetically mapped a putative Luzp2 neuronal enhancer responsible for approximately 33% of allelic transcriptional activity. The Chrna7 results are explained by hypothesizing loss of an essential neuronal transcriptional enhancer required for approximately 80% of allelic Chrna7 promoter activity, while the Chrna7 promoter is upregulated in B lymphocytes by the transgene immunoglobulin enhancer. The mapping of a putative Chrna7 neuronal enhancer inside the deletion has significant implications for understanding the transcriptional regulation of this schizophrenia-susceptibility candidate gene.

Alleles↗
PubMed1980

Genetic mapping of an H-2-associated antigen expressed on regulatory T cells.

T lymphocytes that serve regulatory functions in the generation of effector T cells to alloantigen and to altered syngeneic cells express a distinguishing H-2-associated cell surface marker that we have termed Ha. Genetic mapping studies with the B10.A(2R), B10.A(4R), B10.A(5R), and LG/Ckc lines of mice have delineated the locus determining the expression of Ha to the right of H-2K and left of H-2IB or within the I-A region. Thus these regulatory T lymphocytes express Ia antigens.

Absorption↗
PubMed1998

Molecular cloning, genetic mapping, and developmental expression of a bovine transforming growth factor beta (TGF-beta) type I receptor.

A full-length cDNA encoding the bovine transforming growth factor beta (TGF-beta) receptor type I (bT beta R-I) was isolated from a placenta cDNA library. The deduced protein sequence of 499 residues contains a single transmembrane domain, a cysteinerich extracellular domain, and an intracellular kinase domain with predicted serine/threonine specificity. The amino acid sequence is 96% and 95% identical with its human and mouse homologues, respectively. Genetic mapping assigned the TGFBR1 gene to bovine chromosome 8 at a male genetic distance of 2 centimorgan from D8S28. Assuming conservation of gene order, the linkage data define a breakpoint in mammalian chromosome evolution. Both TGF-beta receptor type I and II mRNAs were found to be expressed in bovine oocytes and preimplantation two-cell, four-cell, eight-cell, morula-, and blastocyst-stage embryos, as determined by heminested reverse transcription polymerase chain reaction (RT-PCR). The mRNA expression patterns of TGF-beta receptor types I, II, and III in a variety of bovine organ tissues were examined by Northern blot hybridization, and highest levels were detected in lung and ovary.

Amino Acid Sequence↗
PubMed1989

Physical and genetic maps of the genome of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120.

A restriction map of the chromosome of the cyanobacterium Anabaena sp. strain PCC 7120 was generated by the determination of the order of restriction fragments of the infrequently cleaving restriction endonucleases AvrII, SalI, and PstI. These restriction fragments were resolved by the pulsed homogeneous orthogonal field gel electrophoresis system of pulsed-field gel electrophoresis (I. Bancroft and C. P. Wolk, Nucleic Acids Res. 16:7405-7418, 1988). Other infrequently cutting restriction endonucleases (AhaII, Asp718, AsuII, BanII, BglII, BssHII, FspI, NcoI, NruI, SphI, SplI, SstII, and StuI) were identified that could prove useful for higher-resolution mapping. The chromosome was found to be 6.4 megabases in size and circular. Three apparently circular large plasmids (410, 190, and 110 kilobases) were also identified. A genetic map was constructed by hybridization with gene-specific probes. Genes encoding components of the photosynthetic electron transport chain were not within a single tight cluster.

Chromosome Mapping↗
PubMed1989

Autosomal dominant congenital cataract. Morphology and genetic mapping.

We studied a large Danish pedigree with autosomal dominant congenital cataracts (ADCC) in 9 generations. Morphological characteristics of the cataracts are described and documented by photos. In contrast with several other types of ADCC the cataracts studied were progressive during infancy and childhood. Linkage analysis with 14 marker systems revealed close linkage between this Marner cataract locus (CAM) and the locus of Haptoglobin (HP) on chromosome 16. Genetic heterogeneity in ADCC has now established with the genetic mapping of cataract loci to chromosome 1, chromosome 2, and chromosome 16.

Adolescent↗
PubMed1985

Molecular characterization and genetic mapping of two clusters of genes encoding chlorophyll a/b-binding proteins in Lycopersicon esculentum (tomato).

We have constructed a tomato genomic library in the gamma Charon 4 phage vector. The library was screened with a pea cDNA probe encoding a chlorophyll a/b-binding protein (CAB), and several recombinant phages containing tomato CAB genes were isolated and characterized by restriction mapping, heteroduplex analysis and nucleotide sequencing. Two phages with overlapping segments of the tomato genome contain a total of four CAB genes, all arranged in tandem. A third phase contains three CAB genes, two arranged in tandem and one in opposite orientation, and an additional, truncated CAB gene. Genetic mapping experiments showed that the four CAb genes on the first two phages belong to a locus, previously designated Cab-1, on chromosome 2. The CAB genes from the third phage belong to the Cab-3 locus on chromosome 3. Complete sequence determination of two CAB genes, one from each locus, and additional sequence determination of about 50% of each of the other five CAB genes showed that each gene within a CAB locus is more similar to other CAB genes in the same locus than it is to the CAB genes from the second locus. Furthermore, the polypeptides encoded by Cab-1 genes diverge significantly from those encoded by Cab-3 genes in the domains of transit peptide and the N terminus of the mature polypeptide but are essentially identical in the rest of the sequence.

Amino Acid Sequence↗
PubMed2002

Histologic-genetic mapping by allele-specific PCR reveals intraurothelial spread of p53 mutant tumor clones.

Common and clinically important features of urothelial carcinomas are multifocality and a high rate of recurrence. Molecular studies demonstrated that multifocal tumors are frequently composed of one tumor clone spreading throughout the urothelial tract. A combination of histologic and genetic mapping of cystectomy specimens from bladder cancer patients is a valuable tool to study bladder carcinogenesis and tumor cell spread by correlating urothelial morphologic features and defined genetic alterations. In the present study, the primary tumors of 14 cystectomy specimens were investigated for p53 protein overexpression by immunohistochemistry and p53 gene mutation by genomic sequencing. Seven tumors showed a strong nuclear staining for the p53 protein. In six of seven tumors, a p53 gene mutation was detected. Allele-specific PCR of defined p53 mutations was established in five of six cases with a p53 mutation. Subsequent screening of the entire urothelial lining of each cystectomy specimen by allele-specific PCR revealed p53-mutant cell clones in urothelial patches with carcinoma in situ and dysplasia, but also frequently in histomorphologically normal urothelium adjacent to the tumor. The pattern of tumor cell spread indicated a continuous intraurothelial growth of the p53-mutant clone. P53 immunohistochemistry visually confirmed the presence of mutant cells in most of these samples. We conclude that allele-specific PCR is a highly sensitive and reliable method for tracking specific p53 mutant clones in the urothelium. Moreover, the detection of p53-mutant cells in histologically normal or preneoplastic urothelial areas in four patients with invasive bladder cancer indicates an extensive intraurothelial tumor cell spread. The excellent correlation of immunohistochemically positive urothelial patches with the presence of a specific mutation highlights the biologic significance of p53-positive cells in the urothelium of tumor patients.

Aged↗
PubMed1991

Virulence patterns and long-range genetic mapping of extraintestinal Escherichia coli K1, K5, and K100 isolates: use of pulsed-field gel electrophoresis.

A total of 127 extraintestinal Escherichia coli strains of the capsule serotypes K1, K5, and K100 from human and animal sources were analyzed for DNA sequences specific for the genes for various adhesins (P fimbriae [pap] and P-related sequences [prs], S fimbriae [sfa]/F1C fimbriae [foc], and type I fimbriae [fim]), aerobactin (aer), and hemolysin (hly). The expression of corresponding virulence factors was also tested. Twenty-four selected strains were analyzed by long-range DNA mapping to evaluate their genetic relationships. DNA sequences for the adhesins were often found in strains not expressing them, while strains with hemolysin and aerobactin genes usually did express them. Different isolates of the same serotype often expressed different virulence patterns. The use of virulence-associated gene probes for Southern hybridization with genomic DNA fragments separated by pulsed-field gel electrophoresis revealed that a highly heterogeneous restriction fragment length and hybridization pattern existed even within strains of the same serotype. Long-range DNA mapping is therefore useful for the evaluation of genetic relatedness among individual isolates and facilitates the performance of precise molecular epidemiology.

Adhesins, Escherichia coli↗
PubMed2002

The development of a genetic map for meadowfoam comprised of amplified fragment length polymorphisms.

Limnanthes alba Benth. (meadowfoam), a diploid ( x=5) winter annual, produces novel very long-chain seed oils (C(20) and C(22)) with less than 2% saturated fatty acids. The first genetic map of meadowfoam, a recently domesticated species, is described herein. Two phenotypically diverse inbred lines, OMF40-11 ( L. alba ssp. alba) and OMF64 ( L. alba ssp. versicolor), were screened for amplified fragment length polymorphisms (AFLPs) using 16 primer combinations. Twenty three percent of the AFLP bands (415 out of 1,801) were polymorphic between OMF40-11 and OMF64. One hundred (OMF40-11xOMF64)xOMF64 BC(1) progeny were genotyped for 107 polymorphic AFLP markers produced by nine AFLP primer combinations. One hundred and three AFLP loci amalgamated into five linkage groups with 14 to 28 loci per linkage group (four loci segregated independently). The map was 698.5-cM long with a mean interlocus spacing of 6.7 cM and no dense clustering of loci. The segregation ratios for 25 loci (23.2%) were significantly distorted. Twenty one of the distorted loci (84%) had an excess of L. alba ssp. versicolor (recurrent parent) alleles. The distorted loci, apart from one locus on linkage group 4, were distally clustered on both ends of linkage groups 1, 4 and 5. The development of the map was facilitated by the small chromosome number, an abundance of restriction site polymorphisms between the two subspecies (23%), and a high multiplex ratio of the AFLP markers (112 per primer combination).

Journal Article↗
PubMed1994

Genetic mapping of a susceptibility locus for insulin-dependent diabetes mellitus on chromosome 11q.

Loci in the major histocompatibility complex (MHC) on chromosome 6 and the insulin (INS) region on chromosome 11 have been implicated in susceptibility to insulin-dependent diabetes mellitus (IDDM) through candidate gene investigations, but they may account for less than 50% of genetic risk for the disease. Genome-wide linkage studies have led to localization of more than 10 susceptibility loci for insulin-dependent diabetes in the non-obese diabetic (NOD) mouse and the BB rat. Similar studies are now possible in humans through the development of dense genetic maps of highly informative microsatellite loci obtained using polymerase chain reaction analysis. We have applied microsatellite markers from recent Généthon maps, and other highly informative markers, in a genome-wide linkage study in IDDM. Here we report evidence for the localization of a previously undetected susceptibility locus for IDDM in the region of the FGF3 gene on chromosome 11q. Our results shows the potential of genome-wide linkage studies to detect susceptibility loci in IDDM and other multifactorial disorders.

Chromosome Mapping↗
PubMed1994

NotI linking clones as a tool for joining physical and genetic maps of the human genome.

To study the connection among NotI linking clones, CpG islands, and genes, the sequence surrounding 143 NotI sites was determined. These NotI linking clones were isolated from human chromosome 3-specific libraries and contain an average C + G content of 65%. These clones represent sequence-tagged sites that can be positioned onto chromosome maps and used for generating a long-range NotI map of the human genome. A majority (about 90%) of these clones contain transcribed sequences, as detected by Northern blot hybridization, providing an efficient link between physical and functional (genetic) maps. The GenBank nucleotide database was searched with sequences from these NotI linking clones. For many clones, homology was found to human and other vertebrate genes. About 20 clones contained various repeats in their sequences and may represent microsatellite loci. Most of these NotI linking clones therefore represent evolutionarily conserved DNA fragments and also can be used for comparative genome mapping of other mammalian species. In addition, approximately 20% of all sequenced human CpG island-containing genes and more than 12% of all well-characterized human genes were found to possess NotI restriction sites. This is at least 2-5 times more than has been previously estimated and suggests that NotI sites have a much stronger association with genes.

Animals↗
PubMed2002

Resistance gene analogues of chickpea ( Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster.

Resistance gene analogues (RGAs) of Cicer were isolated by different PCR approaches and mapped in an inter-specific cross segregating for fusarium wilt by RFLP and CAPS analysis. Initially, two pairs of degenerate primers targeting sequences encoded at nucleotide-binding sites (NBS), which are conserved in plant disease resistance genes such as RPS2, L6 and N, were selected for amplification. Cloning and sequence analysis of amplified products from C. arietinum DNA revealed eight different RGAs. Additionally, five RGAs were identified after characterisation of the presumptive RGA alleles from C. reticulatum. Therefore, a total of 13 different RGAs were isolated from Cicer and classified through pair-wise comparison into nine distinct classes with sequence similarities below a 68% amino acid identity threshold. Sequence comparison of seven RGA alleles of C. arietinum and C. reticulatum revealed polymorphisms in four RGAs with identical numbers of synonymous and non-synonymous substitutions. An NlaIII site, unique in the RGA-A allele of C. arietinum, was exploited for CAPS analysis. Genomic organisation and map position of the NBS-LRR candidate resistance genes was probed by RFLP analysis. Both single-copy as well as multi-copy sequence families were present for the selected RGAs, which represented eight different classes. Five RGAs were mapped in an inter-specific population segregating for three race-specific Fusarium resistances. All RGAs mapped to four of the previously established eight linkage groups for chickpea. Two NBS-LRR clusters were identified that could not be resolved in our mapping population. One of these clusters, which is characterised by RFLP probe CaRGA-D, mapped to the linkage group harbouring two of three Fusarium resistance genes characterised in the inter-specific population. Our study provides a starting point for the characterisation and genetic mapping of candidate resistance genes in Cicer that is useful for marker-assisted selection and as a pool for resistance genes of Cicer.

Journal Article↗
PubMed2005

Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton.

Mapping of genes that play major roles in cotton fiber development is an important step toward their cloning and manipulation, and provides a test of their relationships (if any) to agriculturally-important QTLs. Seven previously identified fiber mutants, four dominant (Li (1), Li (2), N (1) and Fbl) and three recessive (n (2), sma-4(h (a)), and sma-4(fz)), were genetically mapped in six F(2) populations comprising 124 or more plants each. For those mutants previously assigned to chromosomes by using aneuploids or by linkage to other morphological markers, all map locations were concordant except n (2), which mapped to the homoeolog of the chromosome previously reported. Three mutations with primary effects on fuzz fibers (N (1), Fbl, n (2)) mapped near the likelihood peaks for QTLs that affected lint fiber productivity in the same populations, perhaps suggesting pleiotropic effects on both fiber types. However, only Li (1) mapped within the likelihood interval for 191 previously detected lint fiber QTLs discovered in non-mutant crosses, suggesting that these mutations may occur in genes that played early roles in cotton fiber evolution, and for which new allelic variants are quickly eliminated from improved germplasm. A close positional association between sma-4(h ( a )), two leaf and stem-borne trichome mutants (t (1) , t (2)), and a gene previously implicated in fiber development, sucrose synthase, raises questions about the possibility that these genes may be functionally related. Increasing knowledge of the correspondence of the cotton and Arabidopsis genomes provides several avenues by which genetic dissection of cotton fiber development may be accelerated.

Chromosome Mapping↗
PubMed1990

Isolation of high frequency of recombination donors from Tn5 chromosomal mutants of Pseudomonas putida PPN and recalibration of the genetic map.

A Tn5 loaded derivative of the IncP-10 plasmid R91-5 (pMO75) was used as a suicide vector to generate random chromosomal insertion mutations in Pseudomonas putida PPN. Reintroduction of pMO75 into such mutants resulted in integration of the plasmid at the site of Tn5 insertion, giving rise to two classes of high frequency of donors recombination (Hfr) donors, transferring chromosome at high frequency (greater than 10(-1) per donor cell) in opposite directions. Consequently, Tn5 induced auxotrophic mutations could be equated with or distinguished from previously mapped mutations, and closely linked markers ordered, on the basis of marker recovery using the two classes of Hfr donor. The isolation of many new transfer origins allowed more accurate time-of-entry analysis than previously possible and resulted in the reduction of the genetic map from 103 min to 88 min.

Blotting, Southern↗
PubMed1994

Microsatellite markers for genetic mapping in the chicken.

Microsatellite markers have been found to be abundant, evenly distributed, and highly polymorphic in a number of eukaryotic genomes. The objective of this study was to determine the utility of (TG)n microsatellites in the chicken. A chicken library enriched for (TG)n repeats was generated and 42 unique clones containing (TG)n microsatellites were identified and sequenced. The number of uninterrupted TG repeats ranged from 4 to 14 with an average of 7.8, which was considerably less than the number of repeats found in mammalian species. When primers designed to amplify across the (TG)n microsatellites were used in polymerase chain reactions (PCR) containing genomic chicken DNA, 19 of the 33 primer sets examined yielded polymorphisms in at least one of the three sets of chicken families: 15, 11, and 11 primer sets detected polymorphisms in the East Lansing (EL) reference population, the Compton (C) reference family, and between Line 63 and Line 72 chickens, respectively. The polymorphic microsatellite markers in the EL and C reference families were genetically mapped. Nine and seven mapped markers in the EL and C reference families, respectively, are polymorphic between Line 63 and Line 72, indicating that microsatellite markers will greatly enhance the ability to genotype specific loci of any chicken population.

Animals↗
PubMed1994

Genetic mapping of the amphotropic murine leukemia virus receptor on mouse chromosome 8.

Southern blotting with a molecular clone of the amphotropic murine leukemia virus receptor identified restriction enzyme length polymorphisms among different taxonomic groups of mice. Analysis of the progeny of two interspecies genetic crosses was used to establish the genetic map location of the mouse gene encoding this receptor, Ram1, within the proximal region of chromosome 8.

Animals↗