Disease Management in the Genomics Era-Summaries of Focus Issue Papers.

The genomics revolution has contributed enormously to research and disease management applications in plant pathology. This development has rapidly increased our understanding of the molecular mechanisms underpinning pathogenesis and resistance, contributed novel markers for rapid pathogen detection and diagnosis, and offered further insights into the genetics of pathogen populations on a larger scale. The availability of whole genome resources coupled with next-generation sequencing (NGS) technologies has helped fuel genomics-based approaches to improve disease resistance in crops. NGS technologies have accelerated the pace at which whole plant and pathogen genomes have become available, and made possible the metagenomic analysis of plant-associated microbial communities. Furthermore, NGS technologies can now be applied routinely and cost effectively to rapidly generate plant and/or pathogen genome or transcriptome marker sequences associated with virulence phenotypes in the pathogen or resistance phenotypes in the plant, potentially leading to improvements in plant disease management. In some systems, investments in plant and pathogen genomics have led to immediate, tangible benefits. This focus issue covers some of the systems. The articles in this focus issue range from overall perspective articles to research articles describing specific genomics applications for detection and control of diseases caused by nematode, viral, bacterial, fungal, and oomycete pathogens. The following are representative short summaries of the articles that appear in this Focus Issue .

[1]  Shawn W. Polson,et al.  Genotyping-by-Sequencing to Predict Resistance to Lima Bean Downy Mildew in a Diversity Panel. , 2016, Phytopathology.

[2]  J. Burdon,et al.  Addressing the Challenges of Pathogen Evolution on the World's Arable Crops. , 2016, Phytopathology.

[3]  T. Paulitz,et al.  Characterizing and Mapping Resistance in Synthetic-Derived Wheat to Rhizoctonia Root Rot in a Green Bridge Environment. , 2016, Phytopathology.

[4]  J. Léon,et al.  Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi. , 2016, Phytopathology.

[5]  Qi Sun,et al.  Lessons from a Phenotyping Center Revealed by the Genome-Guided Mapping of Powdery Mildew Resistance Loci. , 2016, Phytopathology.

[6]  D. Gent,et al.  Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew Pathogen. , 2016, Phytopathology.

[7]  F. White,et al.  Analysis of Sequenced Genomes of Xanthomonas perforans Identifies Candidate Targets for Resistance Breeding in Tomato. , 2016, Phytopathology.

[8]  F. Zalom,et al.  Phylogeny of Geminivirus Coat Protein Sequences and Digital PCR Aid in Identifying Spissistilus festinus as a Vector of Grapevine red blotch-associated virus. , 2016, Phytopathology.

[9]  B. McDonald,et al.  Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors in Parastagonospora nodorum. , 2016, Phytopathology.

[10]  K. Garrett,et al.  Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management. , 2016, Phytopathology.

[11]  G. Hartman,et al.  Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies. , 2016, Phytopathology.

[12]  U. Nagalakshmi,et al.  Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses. , 2016, Phytopathology.

[13]  N. Kaur,et al.  Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control. , 2016, Phytopathology.

[14]  Youfu Zhao,et al.  Perspectives on the Transition From Bacterial Phytopathogen Genomics Studies to Applications Enhancing Disease Management: From Promise to Practice. , 2016, Phytopathology.

[15]  D. See,et al.  Molecular Mapping of Stripe Rust Resistance Gene Yr76 in Winter Club Wheat Cultivar Tyee. , 2016, Phytopathology.

[16]  Michael F. Seidl,et al.  The Age of Effectors: Genome-Based Discovery and Applications. , 2016, Phytopathology.

[17]  B. Bluhm,et al.  Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation. , 2016, Phytopathology.