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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #314313
Title: Identification of genetic variation between obligate plant pathogens Psuedoperonospora cubensis and P. humuli using RNA sequencing and genotyping-by-sequencing

Author
item SUMMERS, CARLY - Cornell University
item GULLIFORD, COLWYN - Cornell University
item Lillis, Jacquelyn
item CARLSON, MARYN - Cornell University
item Cadle-Davidson, Lance
item 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.