U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Horticultural Crops Research Unit: Corvallis, OR
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Other
                        History
                                    Useful Links
                    HortHappenings News PageSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Pacific West Area Corvallis, Oregon Horticultural Crops Research Unit Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications

Title:   Author  item
                                            HANSEN, ZACHARIAH - Cornell Universityitem
                                            Knaus, Brianitem
                                            TABIMA, JAVIER - Oregon State Universityitem
                                            Press, Carolineitem
                                            JUDELSON, HOWARD - University Of Californiaitem
                                            Grunwald, Niklaus

                                                         - *Nik*item
                                            SMART, CHRISTINE - Cornell University
  Submitted to: Plant Disease
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 12/3/2015
                                    Publication  Date: 3/10/2016
                                    Citation: Hansen, Z.R., Knaus, B.J., Tabima, J.F., Press, C.M., Judelson, H.S., Grunwald, 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.Interpretive Summary: Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, reproduces as distinct genetic clones in the US. Each clone can differ in resistance to fungicide or other phenotypic characteristics. Distinguishing clones using PCR assays could be a novel tool allowing more rapid identification of clones compared to traditional genotyping techniques. We used available whole genome sequences to find candidate regions that distinguish clones and developed and validated PCR assays.
                                Technical 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 US for the past several years, from three other US 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 base pairs. 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 PCR 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.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov