Article
 

SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis

Public Deposited

Downloadable Content

Download PDF
https://ir.library.oregonstate.edu/concern/articles/3x816p09k

Descriptions

Attribute NameValues
Creator
Abstract
  • Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were aligned and single nucleotide polymorphisms (SNPs) identified as targets for the development of clonal-lineage-specific molecular diagnostic tools. Informative SNPs were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US-23, the predominant lineage in the Eastern United States for the past several years, from three other U.S. lineages. Three different primer pairs targeting one to three SNPs were capable of separating lineage US-23 from lineages US-8, US-11, and US-24 using HRM analysis. A fourth HRM primer pair targeted a highly variable genomic region containing nine polymorphisms within 63 bp. These primers separated US-23, US-11, and US-8 plus US-24 into three separate groups following HRM analysis but did not separate US-8 from US-24. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US-23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US-8, US-11, and US-24.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Hansen, Z. R., Knaus, B. J., Tabima, J. F., Press, C. M., Judelson, H. S., Grünwald, N. J., & Smart, C. D. (2016). SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis. Plant Disease, 100(7), 1297-1306. doi:10.1094/PDIS-11-15-1247-RE
Journal Title
Journal Volume
  • 100
Journal Issue/Number
  • 7
Academic Affiliation
Rights Statement
Funding Statement (additional comments about funding)
  • This work was supported, in part, by the United States Department of Agriculture (USDA) Agricultural Research Service Grant 5358-22000-039-00D (N. J. Grunwald) and USDA National Institute of Food and Agriculture Grant 2011-68004-30154 (H. S. Judelson, C. D. Smart, and N. J. Grunwald).
Publisher
Peer Reviewed
Language
Replaces

Relationships

Parents:

This work has no parents.

Items

Thumbnail Title Date Uploaded Visibility Actions
file details HansenSNPBasedDifferentiation.pdf 2017-07-26 Public Download