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Methods in Molecular Biology (Clifton,... 2021Reliable methods of phenotype prediction from genomic data play an increasingly important role in many areas of plant and animal breeding. Thus, developing methods that...
Reliable methods of phenotype prediction from genomic data play an increasingly important role in many areas of plant and animal breeding. Thus, developing methods that enhance prediction accuracy is of major interest. Here, we provide three methods for this purpose: (1) Genomic Best Linear Unbiased Prediction (GBLUP) as a model just accounting for additive SNP effects; (2) Epistatic Random Regression BLUP (ERRBLUP) as a full epistatic model which incorporates all pairwise SNP interactions, and (3) selective Epistatic Random Regression BLUP (sERRBLUP) as an epistatic model which incorporates a subset of pairwise SNP interactions selected based on their absolute effect sizes or the effect variances, which is computed based on solutions from the ERRBLUP model. We compared the predictive ability obtained from GBLUP, ERRBLUP, and sERRBLUP with genotypes from a publicly available wheat dataset and respective simulated phenotypes. Results showed that sERRBLUP provides a substantial increase in prediction accuracy compared to the other methods when the optimal proportion of SNP interactions is kept in the model, especially when an optimal proportion of SNP interactions is selected based on the SNP interaction effect sizes. All methods described here are implemented in the R-package EpiGP, which is able to process large-scale genomic data in a computationally efficient way.
Topics: Datasets as Topic; Epistasis, Genetic; Genetic Association Studies; Genotype; Heterozygote; Models, Genetic; Models, Statistical; Phenotype; Plant Breeding; Plant Tumors; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Quantitative Trait, Heritable; Triticum
PubMed: 33733353
DOI: 10.1007/978-1-0716-0947-7_8 -
Journal of Experimental Botany Dec 2000Solid-tumour growth in animals as in humans depends on angiogenesis. Tumours that fail to induce the formation of new blood vessels do not enlarge beyond a few... (Review)
Review
Solid-tumour growth in animals as in humans depends on angiogenesis. Tumours that fail to induce the formation of new blood vessels do not enlarge beyond a few millimetres in diameter. Plant tumours induced by Agrobacterium tumefaciens can reach diameters of more than 100 mm, thus raising the question of how they are sufficiently supplied with nutrients and water. Until recently, these rapidly growing tumours were considered unorganized or partly organized masses. However, in analogy to animal and human tumours, growth of leaf and stem tumours depends on neovascularization. Plant tumour cells induce the formation of a sophisticated vascular network consisting of water-conducting vessels and assimilate-transporting sieve elements. Similar to animal and human tumours that overexpress angiogenic growth factors, plant tumours overexpress the T-DNA-encoded vascularization-promoting growth factors auxin and cytokinin upon AGROBACTERIUM: infection. High auxin levels induce ethylene emission from the tumours, which has a strong impact on tumour and host stem, as well as on root structure and function. Ethylene apparently stimulates abscisic acid synthesis in the leaves above the tumour, which reduces transpiration and thus protects the host plant from rapid wilting. Hence, for the elucidation of phytohormone-dependent vascular development in plants, such tumours are regarded as an excellent model system. The comparison of analogous requirement of neovascularization for tumour growth in plants, as in animals and humans, is discussed in terms of interdisciplinary strategies of possible prevention and therapy.
Topics: Animals; Biological Transport; Humans; Neoplasms; Neovascularization, Pathologic; Plant Growth Regulators; Plant Tumors; Species Specificity; Water
PubMed: 11141169
DOI: 10.1093/jexbot/51.353.1951 -
Current Biology : CB Aug 2018We report evidence of a new trophic interaction in nature whereby a parasitic plant attacks multiple species of insects that manipulate plant tissue when the two...
We report evidence of a new trophic interaction in nature whereby a parasitic plant attacks multiple species of insects that manipulate plant tissue when the two co-occur on a shared primary host plant. Most plant species are attacked by a great diversity of external and internal herbivores [1]. One common herbivore guild, gall-forming insects, induce tumor-like structures of nutrient-rich plant tissue within which immature insects feed and develop [2,3]. While the gall is made of plant tissue, its growth and development are controlled by the insect and it therefore represents an extended phenotype of the gall former [4]. Typically, parasitic plants attack other plants to gain nutritional requirements by connecting directly to the vascular system of their hosts using modified root structures called haustoria[5]. Here, we document the first observation of a parasitic plant attacking the insect-induced galls of multiple gall-forming species and provide evidence that this interaction negatively affects gall former fitness.
Topics: Animals; Herbivory; Insecta; Parasites; Plant Tumors; Plants
PubMed: 30130501
DOI: 10.1016/j.cub.2018.06.024 -
Cell Cycle (Georgetown, Tex.) Jan 2011
Topics: Animals; Biomarkers, Tumor; Gene Expression Regulation, Plant; Humans; Medical Laboratory Personnel; Plant Proteins; Plant Tumors; Plants; Tumor Protein, Translationally-Controlled 1
PubMed: 21191187
DOI: 10.4161/cc.10.1.14288 -
The New Phytologist May 2016In the tumor-inducing (Ti) Agrobacterium tumefaciens, quorum sensing activates the horizontal transfer of the virulent Ti plasmid. In pure culture, this process can be...
In the tumor-inducing (Ti) Agrobacterium tumefaciens, quorum sensing activates the horizontal transfer of the virulent Ti plasmid. In pure culture, this process can be impaired by the A. tumefaciens BlcC lactonase, whose expression is induced by gamma-aminobutyrate (GABA). It was therefore hypothesized that host GABA content might modulate quorum sensing and virulence gene dissemination during A. tumefaciens infection. We examined GABA metabolism and transport in Arabidopsis thaliana tumors combining transcriptomic, metabolomic and histological approaches. In addition, using genetically modified plants and bacteria, we evaluated the impact of plant host GABA content on Ti plasmid dissemination. The results showed that GABA and free proline, which acts as an antagonist of GABA uptake in A. tumefaciens, accumulated in wild-type tumors relative to uninfected plant tissues. Moreover, comparisons of tumors induced on Col-0 and her1 plants showed that the increase in the plant GABA : proline ratio was associated with both the upregulated expression of the blcC gene and the decreased dissemination of Ti plasmid in tumor-colonizing A. tumefaciens populations. This work demonstrates experimentally that the variation in the GABA content in plant tumors can interfere with the dissemination of A. tumefaciens Ti plasmids, and therefore highlights plant GABA content as an important trait in the struggle against pathogenic bacteria.
Topics: Agrobacterium tumefaciens; Arabidopsis; Biological Transport; Down-Regulation; Gene Expression Regulation, Plant; Gene Transfer Techniques; Genes, Plant; Metabolome; Plant Tumors; Plasmids; Signal Transduction; Transcriptome; Virulence; gamma-Aminobutyric Acid
PubMed: 26714842
DOI: 10.1111/nph.13813 -
Plant Physiology Nov 2003
Review
Topics: Agrobacterium tumefaciens; Arabidopsis; DNA, Bacterial; Plant Tumors; Plants; Plants, Genetically Modified; Transformation, Genetic
PubMed: 14612581
DOI: 10.1104/pp.103.032243 -
Plant Signaling & Behavior May 2016Accumulation of amino acids is a common plant response to several biotic and abiotic stresses, even if the roles of these accumulations remain often poorly understood....
Accumulation of amino acids is a common plant response to several biotic and abiotic stresses, even if the roles of these accumulations remain often poorly understood. In a recent study we measured the levels of different amino acids in tumors of Arabidopsis thaliana induced by the phytopathogen Agrobacterium tumefaciens and correlated these data with changes of gene expressions in both organisms. This led to the demonstration that the non-protein amino acid GABA plays an important role for the adaptation of the bacteria to the plant tumor environment, and especially in the control of the virulent Ti plasmid dissemination. Here we present a model that describes how different GABA:proline ratios in the A. thaliana host may have different impacts on the conjugation of A. tumefaciens Ti plasmid, and advance the view that the amino acid metabolism of plant hosts could be critical for the propagation of the virulence genes in A. tumefaciens populations.
Topics: Agrobacterium tumefaciens; Arabidopsis; Bacterial Proteins; Biological Transport; Glutamic Acid; Models, Biological; Plant Tumor-Inducing Plasmids; Plant Tumors; Polyamines; Proline; Quorum Sensing; Signal Transduction; Virulence; gamma-Aminobutyric Acid
PubMed: 27110651
DOI: 10.1080/15592324.2016.1178440 -
Plant Physiology Apr 1995Agrobacterium tumefaciens is the causative agent of crown gall, a disease of dicotyledonous plants characterized by a tumorous phenotype. Earlier in this century,... (Review)
Review
Agrobacterium tumefaciens is the causative agent of crown gall, a disease of dicotyledonous plants characterized by a tumorous phenotype. Earlier in this century, scientific interest in A. tumefaciens was based on the possibility that the study of plant tumors might reveal mechanisms that were also operating in animal neoplasia. In the recent past, the tumorous growth was shown to result from the expression of genes coded for by a DNA segment of bacterial origin that was transferred and became stably integrated into the plant genome. This initial molecular characterization of the infection process suggested that Agrobacterium might be used to deliver genetic material into plants. The potential to genetically engineer plants generated renewed interest in the study of A. tumefaciens. In this review, we concentrate on the most recent advances in the study of Agrobacterium-mediated gene transfer, its relationship to conjugation, DNA processing and transport, and nuclear targeting. In the following discussion, references for earlier work can be found in more comprehensive reviews (Hooykaas and Schilperoort, 1992; Zambryski, 1992; Hooykaas and Beijersbergen, 1994).
Topics: Agrobacterium tumefaciens; Base Sequence; Cell Nucleus; Conjugation, Genetic; DNA, Bacterial; DNA, Single-Stranded; Gene Transfer Techniques; Molecular Sequence Data; Plant Tumors; Plants
PubMed: 7770515
DOI: 10.1104/pp.107.4.1041 -
The New Phytologist Jul 2021Ustilago maydis is a biotrophic fungus causing smut disease in corn. The infectious forms are dikaryotic hyphae. Here we analyze mutants lacking the nlt1 transcription...
Ustilago maydis is a biotrophic fungus causing smut disease in corn. The infectious forms are dikaryotic hyphae. Here we analyze mutants lacking the nlt1 transcription factor and investigate why these mutants are unable to induce leaf tumors. The study involved reverse genetics, complementation, epistasis analysis, microscopy, gene expression analysis by quantitative reverse transcriptase PCR and virulence assays. We show that nlt1 mutants colonize maize leaves efficiently but fail to undergo karyogamy and are attenuated in late proliferation. Nlt1 activates transcription of ros1, a transcription factor controlling karyogamy, and represses see1, an effector previously shown to contribute to leaf tumor induction. In mononuclate solopathogenic strains, nlt1 mutants cause attenuated leaf tumor formation. In actively dividing maize organs, nlt1 mutants undergo karyogamy and induce tumor formation. Sporisorium reilianum, a smut fungus unable to induce leaf tumors, possesses an ortholog of nlt1 that controls the fusion of dikaryotic nuclei late in infection during cob colonization. Our results have established a regulatory connection between nlt1, ros1 and see1 and suggest the existence of two stages contributing to leaf tumor formation, one before nuclear fusion and involving nlt1 and one after karyogamy that is nlt1 independent.
Topics: Basidiomycota; Fungal Proteins; Plant Diseases; Plant Leaves; Plant Tumors; Protein-Tyrosine Kinases; Proto-Oncogene Proteins; Ustilago; Zea mays
PubMed: 33786841
DOI: 10.1111/nph.17377 -
Plant Physiology and Biochemistry : PPB May 2016Ustilago maydis is a biotrophic plant pathogenic fungus that leads to tumor development in the aerial tissues of its host, Zea mays. These tumors are the result of cell...
Ustilago maydis is a biotrophic plant pathogenic fungus that leads to tumor development in the aerial tissues of its host, Zea mays. These tumors are the result of cell hypertrophy and hyperplasia, and are accompanied by the reprograming of primary and secondary metabolism of infected plants. Up to now, little is known regarding key plant actors and their role in tumor development during the interaction with U. maydis. Polyamines are small aliphatic amines that regulate plant growth, development and stress responses. In a previous study, we found substantial increases of polyamine levels in tumors. In the present work, we describe the maize polyamine oxidase (PAO) gene family, its contribution to hydrogen peroxide (H2O2) production and its possible role in tumor development induced by U. maydis. Histochemical analysis revealed that chlorotic lesions and maize tumors induced by U. maydis accumulate H2O2 to significant levels. Maize plants inoculated with U. maydis and treated with the PAO inhibitor 1,8-diaminooctane exhibit a notable reduction of H2O2 accumulation in infected tissues and a significant drop in PAO activity. This treatment also reduced disease symptoms in infected plants. Finally, among six maize PAO genes only the ZmPAO1, which encodes an extracellular enzyme, is up-regulated in tumors. Our data suggest that H2O2 produced through PA catabolism by ZmPAO1 plays an important role in tumor development during the maize-U. maydis interaction.
Topics: Host-Pathogen Interactions; Oxidoreductases Acting on CH-NH Group Donors; Plant Proteins; Plant Tumors; Ustilago; Zea mays; Polyamine Oxidase
PubMed: 26926794
DOI: 10.1016/j.plaphy.2016.02.019