The Experts below are selected from a list of 1956 Experts worldwide ranked by ideXlab platform

Takayuki Kohchi - One of the best experts on this subject based on the ideXlab platform.

  • The Arabidopsis Photomorphogenic Mutant hy1 Is Deficient in Phytochrome Chromophore Biosynthesis as a Result of a
    2013
    Co-Authors: Mutation Plastid, Takuya Muramoto, Akiho Yokota, Takayuki Kohchi, Heme Oxygenase, Inhwan A Hwang, Howard Goodman M. B
    Abstract:

    The HY1 locus of Arabidopsis is necessary for phytochrome chromophore biosynthesis and is defined by mutants that show a long hypocotyl phenotype when grown in the light. We describe here the molecular cloning of the HY1 gene by using Chromosome Walking and mutant complementation. The product of the HY1 gene shows significant similarity to animal heme oxygenases and contains a possible transit peptide for transport to plastids. Heme oxygenase activity was detected in the HY1 protein expressed in Escherichia coli. Heme oxygenase catalyzes the oxygenation of heme to biliverdin, an activity that is necessary for phytochrome chromophore biosynthesis. The predicted transit peptide is sufficient to transport the green fluorescent protein into chloroplasts. The accumulation of the HY1 protein in plastids was detected by using immunoblot analysis with an anti-HY1 antiserum. These results indicate that the Arabidopsis HY1 gene encodes a plastid heme oxygenase necessary for phytochrome chromophore biosynthesis

  • the arabidopsis photomorphogenic mutant hy1 is deficient in phytochrome chromophore biosynthesis as a result of a mutation in a plastid heme oxygenase
    The Plant Cell, 1999
    Co-Authors: Takuya Muramoto, Akiho Yokota, Takayuki Kohchi, Inhwan Hwang, Howard M Goodman
    Abstract:

    The HY1 locus of Arabidopsis is necessary for phytochrome chromophore biosynthesis and is defined by mutants that show a long hypocotyl phenotype when grown in the light. We describe here the molecular cloning of the HY1 gene by using Chromosome Walking and mutant complementation. The product of the HY1 gene shows significant similarity to animal heme oxygenases and contains a possible transit peptide for transport to plastids. Heme oxygenase activity was detected in the HY1 protein expressed in Escherichia coli. Heme oxygenase catalyzes the oxygenation of heme to biliverdin, an activity that is necessary for phytochrome chromophore biosynthesis. The predicted transit peptide is sufficient to transport the green fluorescent protein into chloroplasts. The accumulation of the HY1 protein in plastids was detected by using immunoblot analysis with an anti-HY1 antiserum. These results indicate that the Arabidopsis HY1 gene encodes a plastid heme oxygenase necessary for phytochrome chromophore biosynthesis.

Howard M Goodman - One of the best experts on this subject based on the ideXlab platform.

  • the arabidopsis photomorphogenic mutant hy1 is deficient in phytochrome chromophore biosynthesis as a result of a mutation in a plastid heme oxygenase
    The Plant Cell, 1999
    Co-Authors: Takuya Muramoto, Akiho Yokota, Takayuki Kohchi, Inhwan Hwang, Howard M Goodman
    Abstract:

    The HY1 locus of Arabidopsis is necessary for phytochrome chromophore biosynthesis and is defined by mutants that show a long hypocotyl phenotype when grown in the light. We describe here the molecular cloning of the HY1 gene by using Chromosome Walking and mutant complementation. The product of the HY1 gene shows significant similarity to animal heme oxygenases and contains a possible transit peptide for transport to plastids. Heme oxygenase activity was detected in the HY1 protein expressed in Escherichia coli. Heme oxygenase catalyzes the oxygenation of heme to biliverdin, an activity that is necessary for phytochrome chromophore biosynthesis. The predicted transit peptide is sufficient to transport the green fluorescent protein into chloroplasts. The accumulation of the HY1 protein in plastids was detected by using immunoblot analysis with an anti-HY1 antiserum. These results indicate that the Arabidopsis HY1 gene encodes a plastid heme oxygenase necessary for phytochrome chromophore biosynthesis.

Charles-eric Durel - One of the best experts on this subject based on the ideXlab platform.

  • Identification of candidate genes at the Dp-fl locus conferring resistance against the rosy apple aphid Dysaphis plantaginea
    Tree Genetics and Genomes, 2018
    Co-Authors: Michela Dall’agata, Giulia Pagliarani, S. Padmarasu, Michela Troggio, Luca Bianco, E. Dapena, M. Miñarro, Sébastien Aubourg, Yves Lespinasse, Charles-eric Durel
    Abstract:

    The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA; Dysaphis plantaginea Passerini), control of which is mainly based on chemical treatments. A few cases of resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar ‘Florina’ is resistant to RAA, and recently, the Dp-fl locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a Chromosome Walking approach was performed by using a ‘Florina’ bacterial artificial Chromosome (BAC) library. The Walking started from the available tightly linked molecular markers flanking the resistance region. Various Walking steps were performed in order to identify the minimum tiling path of BAC clones covering the Dp-fl region from both the “resistant” and “susceptible” Chromosomes of ‘Florina’. A genomic region of about 279 Kb encompassing the Dp-fl resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.

Steven D Tanksley - One of the best experts on this subject based on the ideXlab platform.

  • genetic mapping of a wide spectrum nematode resistance gene hero against globodera rostochiensis in tomato
    Molecular Plant-microbe Interactions, 1995
    Co-Authors: Martin W Ganal, Steven D Tanksley, M S Phillips, R Simon, S Brommonschenkel, M Arndt, Amar Kumar
    Abstract:

    The Hero gene confers resistance to a wide spectrum of pathotypes of the potato cyst nematode Globodera rostochiensis. This gene has been introgressed from the wild tomato species Lycopersicon pimpinellifolium into the cultivated tomato. We have used RFLP and RAPD analysis for the targeted search of the L. pimpinellifolium into the cultivated tomato. We have used RFLP and RAPD analysis for the targeted search of the L. pimpinellifolium segment. The resistant line LA 1792 contains a single introgressed segment on Chromosome 4, which is characterized by three RFLP markers from the high-density RFLP map of tomato. The map position of the Hero gene in large populations, four additional markers were identified in the introgressed region. After analyzing more than 800 gametes for recombination, we found that one marker is only 0.4 cM away from the Hero gene. YAC clones isolated from a region near the Hero gene indicate that in this area of the genome, the kb/cM ratio is relatively low (<450 kb/cM) and Chromosome Walking should be feasible in order to isolate this gene.

  • Chromosome landing a paradigm for map based gene cloning in plants with large genomes
    Trends in Genetics, 1995
    Co-Authors: Steven D Tanksley, Martin W Ganal, Gregory B. Martin
    Abstract:

    Abstract The original concept behind map-based or positional cloning was to find a DNA marker linked to a gene of interest, and then to ‘walk’ to the gene via overlapping clones (e.g. cosmids or YACs). While Chromosome Walking is straightforward in organisms with small genomes, it is difficult to apply in most plant species, which typically have large, complex genomes. The strategy of Chromosome Walking is based on the assumption that it is difficult and time consuming to find DNA markers that are physically close to a gene of interest. Recent technological developments invalidate this assumption for many species. As a result, the mapping paradigm has now changed such that one first isolates one or more DNA marker(s) at a physical distance from the targeted gene that is less than the average insert size of the genomic library being used for clone isolation. The DNA marker is then used to screen the library and isolate (or ‘land’ on) the clone containing the gene, without any need for Chromosome Walking and its associated problems. Chromosome landing, together with the technology that has made it possible, is likely to become the main strategy by which map-based cloning is applied to isolate both major genes and genes underlying quantitative traits in plant species.

  • construction of a yeast artificial Chromosome library of tomato and identification of cloned segments linked to two disease resistance loci
    Molecular Genetics and Genomics, 1992
    Co-Authors: Gregory B. Martin, Martin W Ganal, Steven D Tanksley
    Abstract:

    We have constructed a yeast artificial Chromosome (YAC) library of tomato for Chromosome Walking that contains the equivalent of three haploid genomes (22 000 clones). The source of high molecular weight DNA was leaf protoplasts from the tomato cultivars VFNT cherry and Rio Grande-PtoR, which together contain loci encoding resistance to six pathogens of tomato. Approximately 11 000 YACs have been screened with RFLP markers that cosegregate withTm-2a andPto — loci conferring resistance to tobacco mosaic virus andPseudomonas syringae pv.tomato, respectively. Five YACs were identified that hybridized to the markers and are therefore starting points for Chromosome walks to these genes. A subset of the library was characterized for the presence of various repetitive sequences and YACs were identified that carried TGRI, a repeat clustered near the telomeres of most tomato Chromosomes, TGRII, an interspersed repeat, and TGRIIl, a repeat that occurs primarily at centromeric sites. Evaluation of the library for organellar sequences revealed that approximately 10% of the clones contain chloroplast sequences. Many of these YAC clones appear to contain the entire 155 kb tomato chloroplast genome. The tomato cultivars used in the library construction, in addition to carrying various disease resistance genes, also contain the wild-type alleles corresponding to most recessive mutations that have been mapped by classical linkage analysis. Thus, in addition to its utility for physical mapping and genome studies, this library should be useful for Chromosome Walking to genes corresponding to virtually any phenotype that can be scored in a segregating population.

Beat Keller - One of the best experts on this subject based on the ideXlab platform.

  • a large rearrangement involving genes and low copy dna interrupts the microcollinearity between rice and barley at the rph7 locus
    Genetics, 2003
    Co-Authors: Susanne Brunner, Beat Keller, Catherine Feuillet
    Abstract:

    Grass genomes differ greatly in Chromosome number, ploidy level, and size. Despite these differences, very good conservation of the marker order (collinearity) was found at the genetic map level between the different grass genomes. Collinearity is particularly good between rice Chromosome 1 and the group 3 Chromosomes in the Triticeae. We have used this collinearity to saturate the leaf rust resistance locus Rph7 on Chromosome 3HS in barley with ESTs originating from rice Chromosome 1S. Chromosome Walking allowed the establishment of a contig of 212 kb spanning the Rph7 resistance gene. Sequencing of the contig showed an average gene density of one gene/20 kb with islands of higher density. Comparison with the orthologous rice sequence revealed the complete conservation of five members of the HGA gene family whereas intergenic regions differ greatly in size and composition. In rice, the five genes are closely associated whereas in barley intergenic regions are >38-fold larger. The size difference is due mainly to the presence of six additional genes as well as noncoding low-copy sequences. Our data suggest that a major rearrangement occurred in this region since the Triticeae and rice lineage diverged.

  • subgenome Chromosome Walking in wheat a 450 kb physical contig in triticum monococcum l spans the lr10 resistance locus in hexaploid wheat triticum aestivum l
    Proceedings of the National Academy of Sciences of the United States of America, 2000
    Co-Authors: Nils Stein, Catherine Feuillet, Thomas Wicker, Edith Schlagenhauf, Beat Keller
    Abstract:

    For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum, the genome is hexaploid, has a size of 1.6 × 1010 bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed Chromosome Walking and positional cloning. Here, we demonstrate that Chromosome Walking using bacterial artificial Chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (Am genome). BAC end sequences were mostly repetitive and could not be used for the first Walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two Walking steps resulted in a physical contig of 450 kb on Chromosome 1AmS. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on Chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome Chromosome Walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.

  • construction and characterization of a bacterial artificial Chromosome bac library for the a genome of wheat
    Genome, 1999
    Co-Authors: Diego Lijavetzky, Rod A. Wing, Thomas Wicker, Beat Keller, G Muzzi, Jorge Dubcovsky
    Abstract:

    A genomic bacterial artificial Chromosome (BAC) library of the A genome of wheat has been constructed. Triticum monococcum accession DV92 was selected for this purpose because it is a cultivated diploid wheat and one of the parental lines used in the construction of a saturated genetic map. Leaves from this accession were used to isolate high-molecular-weight DNA from nuclei. This DNA was partially digested with restriction enzyme Hind III, subjected to double size selection, electroeluted and cloned into the pINDIGO451 BAC vector. The library consists of 276,480 clones with an average insert size of 115 kb. Excluding the 1.33% of empty clones and 0.14% of clones with chloroplast DNA, the coverage of this library is 5.6 genome equivalents. With this genome coverage the probability of having any DNA sequence represented in this library is higher than 99.6%. Clones were sorted in 720,384-well plates and blotted onto 15 high-density filters. High-density filters were screened with several single or low-copy clones and five positive BAC clones were selected for further analysis. Since most of the T. monococcum BAC ends included repetitive sequences, a modification was introduced into the classical end-isolation procedure to select low copy sequences for Chromosome Walking.