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Title: Disease management in the genomics era - Summaries of focus issue papers

Author
item Klosterman, Steven
item ROLLINS, JEFFREY - University Of Florida
item Sudarshana, Mysore
item VINATZER, BORIS - Virginia Tech

Submitted to: Phytopathology
Publication Type: Review Article
Publication Acceptance Date: 7/25/2016
Publication Date: 9/21/2016
Citation: Klosterman, S.J., Rollins, J.R., Sudarshana, M.R., Vinatzer, B.A. 2016. Disease management in the genomics era - Summaries of focus issue papers. Phytopathology. 106:1068-1070.

Interpretive Summary: The complete individual genetic codes or sequences that underpin the observed traits in plants and plant pathogens have become available only in the past 15 years. By using this sequence information, researchers have been able to deliver astonishingly rapid advancements in tools and strategies to more quickly breed crop disease resistance and diagnostic tools to quickly and more accurately identify the pathogens causing the diseases. This review examines a series of focus issue articles that explore genomic perspectives and applications to promote more rapid development of plant disease resistance or diagnostic tools. These applications have also led to a greater understanding of pathogen populations as a whole. It is clear that the combinations of recent genomic advances have led to increased abilities to detect and control diseases caused by nematode, viral, bacterial, fungal, and oomycete pathogens.

Technical 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. Perspective articles in this issue provide broad overviews over individual topics, and other, research focused articles deal with the 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.