title: Disease Management in the Genomics Era-Summaries of Focus Issue Papers.
abstract: 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 .
authors.affiliation: 2016 Focus Issue Senior Editors First author: U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS), 1636 E. Alisal Street, Salinas, CA 93905; second author: Department of Plant Pathology, University of Florida, Gainesville 32611; third author: USDA-ARS, One Shields Avenue, Davis, CA 95616; and fourth author: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg 24061.
authors.forename: S J
authors.initials: SJ
authors.lastname: Klosterman
authors.affiliation: 2016 Focus Issue Senior Editors First author: U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS), 1636 E. Alisal Street, Salinas, CA 93905; second author: Department of Plant Pathology, University of Florida, Gainesville 32611; third author: USDA-ARS, One Shields Avenue, Davis, CA 95616; and fourth author: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg 24061.
authors.forename: J R
authors.initials: JR
authors.lastname: Rollins
authors.affiliation: 2016 Focus Issue Senior Editors First author: U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS), 1636 E. Alisal Street, Salinas, CA 93905; second author: Department of Plant Pathology, University of Florida, Gainesville 32611; third author: USDA-ARS, One Shields Avenue, Davis, CA 95616; and fourth author: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg 24061.
authors.forename: M R
authors.initials: MR
authors.lastname: Sudarshana
authors.affiliation: 2016 Focus Issue Senior Editors First author: U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS), 1636 E. Alisal Street, Salinas, CA 93905; second author: Department of Plant Pathology, University of Florida, Gainesville 32611; third author: USDA-ARS, One Shields Avenue, Davis, CA 95616; and fourth author: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg 24061.
authors.forename: B A
authors.initials: BA
authors.lastname: Vinatzer
mesh_terms: D018556:Crops, Agricultural / Q000276:immunology / Q000382:microbiology / Q000469:parasitology; D060467:Disease Resistance / Q000235:genetics*; D049751:Genome, Helminth / Q000235:genetics; D064349:Genome, Microbial / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D010935:Plant Diseases / Q000276:immunology / Q000382:microbiology / Q000469:parasitology / Q000517:prevention & control*; D017422:Sequence Analysis, DNA; D014774:Virulence