Relevant bibliographies by topics / Agriculture, Plant Pathology. Biology, Bioinformatics

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters

Academic literature on the topic 'Agriculture, Plant Pathology. Biology, Bioinformatics'

Author: Grafiati
Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "Agriculture, Plant Pathology. Biology, Bioinformatics"

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Harborne, Jeffrey B. "Plant Pathology in Agriculture:." Phytochemistry 30, no. 4 (1991): 1355. http://dx.doi.org/10.1016/s0031-9422(00)95241-5.

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Yarden, O., D. J. Ebbole, S. Freeman, R. J. Rodriguez, and M. B. Dickman. "Fungal Biology and Agriculture: Revisiting the Field." Molecular Plant-Microbe Interactions® 16, no. 10 (October 2003): 859–66. http://dx.doi.org/10.1094/mpmi.2003.16.10.859.

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Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.
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Turner, R. Steven. "Potato Agriculture, Late Blight Science, and the Molecularization of Plant Pathology." Historical Studies in the Natural Sciences 38, no. 2 (2008): 223–57. http://dx.doi.org/10.1525/hsns.2008.38.2.223.

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By the mid-1980s nucleic-acid based methods were penetrating the farthest reaches of biological science, triggering rivalries among practitioners, altering relationships among subfields, and transforming the research front. This article delivers a "bottom up" analysis of that transformation at work in one important area of biological science, plant pathology, by tracing the "molecularization" of efforts to understand and control one notorious plant disease——the late blight of potatoes. It mobilizes the research literature of late blight science as a tool through which to trace the changing typography of the research front from 1983 to 2003. During these years molecularization intensified the traditional fragmentation of the late blight research community, even as it dramatically integrated study of the causal organism into broader areas of biology. In these decades the pathogen responsible for late blight, the oomycete Phytophthora infestans, was discovered to be undergoing massive, frightening, and still largely unexplained genetic diversification——a circumstance that lends the episode examined here an urgency that reinforces its historiographical significance as a casestudy in the molecularization of the biological sciences.
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Tello, Daniel, Juanita Gil, Cristian D. Loaiza, John J. Riascos, Nicolás Cardozo, and Jorge Duitama. "NGSEP3: accurate variant calling across species and sequencing protocols." Bioinformatics 35, no. 22 (April 25, 2019): 4716–23. http://dx.doi.org/10.1093/bioinformatics/btz275.

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Abstract Motivation Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features. Results Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using real data from three sequencing protocols and four species with different distributions of repetitive elements. NGSEP consistently shows comparative accuracy and better efficiency compared to the existing solutions. We expect that this work will contribute to the continuous improvement of quality in variant calling needed for modern applications in medicine and agriculture. Availability and implementation NGSEP is available as open source software at http://ngsep.sf.net. Supplementary information Supplementary data are available at Bioinformatics online.
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Jeyasri, Rajendran, Pandiyan Muthuramalingam, Lakkakula Satish, Shunmugiah Karutha Pandian, Jen-Tsung Chen, Sunny Ahmar, Xiukang Wang, Freddy Mora-Poblete, and Manikandan Ramesh. "An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics." Plants 10, no. 7 (July 19, 2021): 1472. http://dx.doi.org/10.3390/plants10071472.

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Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.
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Stewart, C. Neal, Patrick J. Tranel, David P. Horvath, James V. Anderson, Loren H. Rieseberg, James H. Westwood, Carol A. Mallory-Smith, Maria L. Zapiola, and Katrina M. Dlugosch. "Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics." Weed Science 57, no. 5 (October 2009): 451–62. http://dx.doi.org/10.1614/ws-09-011.1.

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The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but noArabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.
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Derevnina, Lida, Benjamin Petre, Ronny Kellner, Yasin F. Dagdas, Mohammad Nasif Sarowar, Artemis Giannakopoulou, Juan Carlos De la Concepcion, et al. "Emerging oomycete threats to plants and animals." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1709 (December 5, 2016): 20150459. http://dx.doi.org/10.1098/rstb.2015.0459.

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Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans , Phytophthora palmivora , Phytophthora ramorum , Plasmopara obducens , and the animal pathogens Aphanomyces invadans , Saprolegnia parasitica and Halioticida noduliformans . For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
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Kaufmane, Edīte, Māra Skrīvele, Edgars Rubauskis, Sarmīte Strautiņa, Laila Ikase, Gunārs Lācis, Dalija Segliņa, Inga Moročko-Bičevska, Silvija Ruisa, and Ilze Priekule. "Development of Fruit Science in Latvia." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences 67, no. 2 (August 1, 2013): 71–83. http://dx.doi.org/10.2478/prolas-2013-0013.

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Development of fruit growing and fruit science in Latvia has always been closely linked to the development of the whole country. After the founding of the independent Latvia state in 1918, fruit growing developed rapidly. Although in the Soviet times the situation was not favourable for quality fruit growing, research and breeding continued with good results. After Latvia regained independence, private land property rights were restored, and interest in intensive orchard establishment and growing technologies increased rapidly, which demanded change in the research focus. At present, the Latvia State Institute of Fruit-Growing is the leading institution in this field, working in cooperation with Pūre Horticultural Research Centre, Latvian Plant Protection Research Centre, Institute of Agrobiotechology, and Faculty of Food Technology, Latvia University of Agriculture, Laboratory of Plant Mineral Nutrition, Institute of Biology, University of Latvia. Research is carried out in the following directions: breeding and cultivar evaluation; genetics and molecular biology; plant pathology and entomology; orchard management; experimental processing and storage.
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Saad, Mohd Faiz Mat, Aziz Ramlee Sau, Muhamad Afiq Akbar, Syarul Nataqain Baharum, Ahmad Bazli Ramzi, Noraini Talip, and Hamidun Bunawan. "Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications." Biology 10, no. 7 (June 29, 2021): 604. http://dx.doi.org/10.3390/biology10070604.

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Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.
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Lee, Joan. "Reviewer Acknowledgements for Journal of Plant Studies, Vol. 6, No. 1." Journal of Plant Studies 6, no. 1 (February 26, 2017): 103. http://dx.doi.org/10.5539/jps.v6n1p103.

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Journal of Plant Studies wishes to acknowledge the following individuals for their assistance with peer review of manuscripts for this issue. Their help and contributions in maintaining the quality of the journal are greatly appreciated.Journal of Plant Studies is recruiting reviewers for the journal. If you are interested in becoming a reviewer, we welcome you to join us. Please find the application form and details at http://www.ccsenet.org/reviewer and e-mail the completed application form to jps@ccsenet.org.Reviewers for Volume 6, Number 1Adriana F. Sestras, University of Agricultural Sciences and Veterinary Medicine, RomaniaAna Simonovic, Institute for Biological Research "Sinisa Stankovic", SerbiaArthur T. O. Melo, College of Life Sciences and Agriculture, University of New Hampshire, United StatesBing Wang, Iowa State University, United StatesChrystian Iezid Maia e Almeida Feres, Tocantins Federal University, BrazilHoma Mahmoodzadeh, Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, IranKinga Kostrakiewicz-Gieralt, Institute of Botany, Jagiellonian University, PolandKirandeep Kaur Mani, California seed and Plant Labs, Pleasant Grove, CA, United States of AmericaMalgorzata Pietrowska-Borek, Poznan University of Life Sciences, PolandMartina Pollastrini, University of Florence, ItalyMassimo Zacchini, National Research Council of Italy (CNR), ItalyMelekber Sulusoglu, Arslanbey Vocational School Kocaeli University, TurkeyMontaser Fawzy Abdel-Monaim, Plant Pathology Res. Instatute, Agric. Res. Center, EgyptPanagiotis Madesis, Institiute of Applied Biosciences (CE.R.T.H.)/INAB, GreecePeter R. Greene, BGKT Consulting Ltd. Huntington, New York 11743, United StatesRosana Noemi Malpassi, Universidad Nacional de Rio Cuarto, ArgentinaSaid Laarabi, University Mohammed V/Ministry of National Education, MoroccoSlawomir Borek, Adam Mickiewicz University, PolandSuheb Mohammed, University of Virginia, United StatesVikas Mishra, Paher University, IndiaXiaomin Wu, Loyola University Chicago, United StatesYa-Yi Huang, Institution of Plant and Microbial Biology, Academia Sinica, Taiwan
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Dissertations / Theses on the topic "Agriculture, Plant Pathology. Biology, Bioinformatics"

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Deblais, Loic. "Understanding of Salmonella-phytopathogen-environment-plant interactions and development of novel antimicrobial to reduce the Salmonella burden in fresh tomato production." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1534437638478448.

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Gunadi, Andika. "Characterization of Rps8 and Rps3 Resistance Genes to Phytophthora sojae through Genetic Fine Mapping and Physical Mapping of Soybean Chromosome 13." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354640151.

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Chen, Chenxi. "Analysis of the molecular basis of virulence in pathogenic fungi." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1374006951.

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Bigelow, Donna Marie 1954. "Biology and control of Coniophora eremophila on lemon in Arizona." Thesis, The University of Arizona, 1995. http://hdl.handle.net/10150/278499.

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A field survey of mature lemon trees showed an average of 30% of the trees with symptoms of brown heartwood rot caused by Coniophora sp. The temperature range of growth in culture for Coniophora is 15-40C with growth optimum at 30C. Vegetative incompatibility trials from one mature orchard show isolates from different trees are incompatible. In wood block decay studies, the average weight loss over 20 weeks was 5-20%. In comparison, decay studies comparing Coniophora with other brown or white rotting fungi, the other fungi decayed 4-8 times more in vitro. Cultural characteristics include simple septate hyphae, moderately growing mycelium that develop crustose brown to brownish-black patches as they mature, and negative for polyphenol oxidases. In vitro fungicide trials show that only NECTEC paste was effective in reducing decay on lemon blocks inoculated 15 weeks with Coniophora. SEM studies show mycelial fragments, pit enlargement, in radial plates, cracking and disintegration of wood.
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Meyn, Malcolm Anthony 1967. "A genetic, biochemical, and population analysis of MGL, a non-LTR retroelement from the plant pathogenic fungus Magnaporthe grisea." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/288755.

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This dissertation describes the characterization of a novel transposable element isolated from the plant pathogenic fungus Magnaporthe grisea. The sequence of MGR583, a previously reported repeated DNA fragment, was completed and shown to have features characteristic of non-LTR retroelements (LINEs). These include an element length of 5.9 kb, the lack of flanking long terminal repeats, the presence of short (6-13 bp) direct repeats flanking many element copies, and two principal open reading frames (ORFs). The first ORF is 570 amino acids in length and contains homology to the gag ORFs found in many retroelements. The second ORF is 1,295 amino acids in length and has strong homology to reverse transcriptases (RT) ORFs found in non-LTR retroelements (LINEs). In accordance with these results, the name of the repeat was changed to MGL for Magnaporthe grisea LINE. Analysis of the 3' terminus of MGL showed 90% homology to the 3' terminus of Mg-SINE, suggesting an evolutionary relationship between these two elements. A survey of the distribution of MGL in populations of M. grisea showed the element to be present in all isolates tested. Copy number was not uniform between isolates, with approximately fifty copies present in rice isolates and between less than 10 and up to 50 copies in the 17 non-rice isolates tested. A PCR-based assay was designed and used to screen M. grisea isolates for polymorphic MGL insertion loci. Thirteen polymorphic MGL insertions were scored and used to construct a phylogenetic tree that included 11 non-rice isolates and 20 rice isolates. The results strongly suggested that development of virulence on rice was a single event correlated with the acquisition of virulence on several other grass species. In addition, the observation that rearrangements occurred at one of the insertion loci in some rice isolate strains support the proposal that there is considerable plasticity in the genomes of these isolates. Finally, a yeast transposon ( Tyl) system was used to express and test the second ORF for RT activity. No activity was detected for any of the MGL RT constructs tested.
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Hu, Jinnan. "Exploring Genome Structure and Gene Regulation Related to Virulence in Fungal Phytopathogens Using Next Generation Sequencing Techniques." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366213390.

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Gupta, Chirag. "Transcriptome-based Gene Networks for Systems-level Analysis of Plant Gene Functions." Thesis, University of Arkansas, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10636543.

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Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of cellular activities with increasing breadth and depth. However, we know very little about how the genome functions and what the identified genes do. The lack of functional annotations of genes greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some aspects of their functions assigned. Therefore, there is an urgent need to develop innovative methods to predict and expand on the currently available functional annotations of plant genes. With open-access catching the ‘pulse’ of modern day molecular research, an integration of the copious amount of transcriptome datasets allows rapid prediction of gene functions in specific biological contexts, which provide added evidence over traditional homology-based functional inference. The main goal of this dissertation was to develop data analysis strategies and tools broadly applicable in systems biology research.

Two user friendly interactive web applications are presented: The Rice Regulatory Network (RRN) captures an abiotic-stress conditioned gene regulatory network designed to facilitate the identification of transcription factor targets during induction of various environmental stresses. The Arabidopsis Seed Active Network (SANe) is a transcriptional regulatory network that encapsulates various aspects of seed formation, including embryogenesis, endosperm development and seed-coat formation. Further, an edge-set enrichment analysis algorithm is proposed that uses network density as a parameter to estimate the gain or loss in correlation of pathways between two conditionally independent coexpression networks.

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Ong, Laura E. "Conservation of pathogen recognition mechanisms in different plant species." [Bloomington, Ind.] : Indiana University, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3215189.

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Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2006.
Source: Dissertation Abstracts International, Volume: 67-04, Section: B, page: 1764. Adviser: Roger W. Innes. "Title from dissertation home page (viewed June 20, 2007)."
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Jensen, Helen Rose. "Insecticidal and synergistic properties of Piper nigrum seed extracts investigated using acute toxicity assays and gene expression profiling of Drosophila melanogaster." Thesis, University of Ottawa (Canada), 2005. http://hdl.handle.net/10393/26933.

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The overall objective of this study was to investigate the insecticidal and synergistic properties of an ethylacetate extract of Piper nigrum L. (Piperaceae) seeds used alone and in conjunction with pyrethrin, a botanical insecticide extracted from the flowers of Chrysanthemum cinerariaefolium Benth. & Hook. (Asteraceae). It was concluded that P. nigrum extract is a highly promising candidate for a novel botanical synergist for pyrethrin and could potentially be used as a replacement for piperonyl butoxide in certain pyrethrum formulations. The upregulation of mRNA transcripts encoding cytochrome P450 detoxification enzymes by a P. nigrum extract may indicate possible target proteins to enhance the toxicity of insecticides and synergists. The seven common genes differentially expressed in two or three of the sublethal treatments with pyrethrin, P. nigrum extract or pyrethrin plus P. nigrum extract merit further study of their functions relating to detoxification processes and defense responses. Future work should include a detailed, tissue-specific characterization of the genes of interest identified in this study and an investigation of the activity of the P. nigrum extract against the CYP enzymes associated with the Cyp genes that were differentially expressed in response to a P. nigrum extract. (Abstract shortened by UMI.)
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Mao, Jingqin. "Improved resistance to insects in maize (Zea mays L) and cowpea (Vigna unguiculata L)." Thesis, University of Ottawa (Canada), 2006. http://hdl.handle.net/10393/27152.

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A novel alteration in secondary metabolism of maize transformed with wheat oxalate oxidase gene (OXO) was determined using HPLC and microscopy. Phenolic concentration was significantly increased, but DIMBOA synthesis was down-regulated. The high levels of soluble phenolic acids, in particular free ferulic acid, most likely contributed to the insect resistance in the OXO maize. To facilitate future cowpea transformation with the OXO, a stable in vitro regeneration system was established in blackeye cowpea via shoot organogenesis. The optimal initiation medium comprised MS salts, B 5 vitamins, 2 mg 1-1 BAP, 3% sucrose and 0.8% agar at pH 5.8. The highest initiation frequency and shoot number were obtained from the shoot apices of 3-5 days old seedlings. For shoot elongation, 0.5-5.0 mg 1-1 GA3 was required. Rooting medium was MS salts supplemented with B5 vitamins, 3% sucrose and 0.8% agar.
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Books on the topic "Agriculture, Plant Pathology. Biology, Bioinformatics"

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(Editor), Y. Elad, B. Williamson (Editor), Paul Tudzynski (Editor), and Nafiz Delen (Editor), eds. Botrytis: Biology, Pathology and Control. Springer, 2004.

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Stirling, Graham, Helen Hayden, Tony Pattison, and Marcelle Stirling. Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture. CSIRO Publishing, 2016. http://dx.doi.org/10.1071/9781486303052.

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Our capacity to maintain world food production depends heavily on the thin layer of soil covering the Earth's surface. The health of this soil determines whether crops can grow successfully, whether a farm business is profitable and whether an enterprise is sustainable in the long term. Farmers are generally aware of the physical and chemical factors that limit the productivity of their soils but often do not recognise that soil microbes and the soil fauna play a major role in achieving healthy soils and healthy crops. Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture provides readily understandable information about the bacteria, fungi, nematodes and other soil organisms that not only harm food crops but also help them take up water and nutrients and protect them from root diseases. Complete with illustrations and practical case studies, it provides growers and their consultants with holistic solutions for building an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and suppressing root pests and pathogens. The book is written by scientists with many years' experience developing sustainable crop production practices in the grains, vegetable, sugarcane, grazing and horticultural industries. This book will be useful for: growers, consultants, agronomists and soil chemists, extension personnel working in the grains, livestock, sugarcane and horticultural industries, professionals running courses in soil health/biological farming, and students taking university courses in soil science, ecology, microbiology, plant pathology and other biological sciences.
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Book chapters on the topic "Agriculture, Plant Pathology. Biology, Bioinformatics"

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Parray, Javid Ahmad, Mohammad Yaseen Mir, and Nowsheen Shameem. "Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools." In Sustainable Agriculture: Biotechniques in Plant Biology, 465–547. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8840-8_10.

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