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
 Grape Genetics Research Unit (GGRU): Geneva, NY
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    CareersSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Geneva, New York Grape Genetics Research Unit (GGRU) 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
                                            SUMMERS, CARLY - Cornell Universityitem
                                            GULLIFORD, COLWYN - Cornell Universityitem
                                            Lillis, Jacquelynitem
                                            CARLSON, MARYN - Cornell Universityitem
                                            Cadle-Davidson, Lanceitem
                                            Gent, David

                                                         - *Dave*item
                                            SMART, CHRISTINE - Cornell University
  Submitted to: PLOS ONE
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 11/3/2015
                                    Publication  Date: 11/23/2015
                                    Citation: Summers, C., Gulliford, C., Lillis, J.A., Carlson, M., Cadle Davidson, L.E., Gent, D.H., Smart, C. 2015. Identification of genetic variation between obligate plant pathogens Psuedoperonospora cubensis and P. humuli using RNA sequencing and genotyping-by-sequencing. PLoS One. doi: 10.1371/journal.pone.0143665.Interpretive Summary: Researchers completed a comparative analysis between genome-wide DNA sequencing versus RNA sequencing for individuals representing two downy mildew species. RNA sequencing produced 1,290 markers, while DNA sequencing produced 11,922 markers. Both techniques allowed us to identify the species. Within the species Pseudoperonospora cubensis, downy mildew individuals collected from squash clustered separately from individuals from cucumber and cantaloupe. Individuals of hops downy mildew clustered by geographic region.  While having thousands of markers is useful, researchers were able to select a handful of markers that can be used to identify the two species, which previously was a challenge. Thus, genome-wide DNA sequencing and RNA sequencing provided useful genetic markers for future research. Due to marker number and retention of more individuals, genome-wide DNA sequencing performed slightly superior in this study.
                                Technical Abstract: RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n=800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.


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