title: RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection.
abstract: BACKGROUND
  Potato virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genotype, the PVY strain, and the environmental conditions. A potato cultivar can induce resistance to a specific PVY strain, yet be susceptible to another. How a single potato cultivar responds to PVY in both compatible and incompatible interactions is not clear.
  
  
  RESULTS
  In this study, we used RNA-sequencing (RNA-Seq) to investigate and compare the transcriptional changes in leaves of potato upon inoculation with PVY. We used two potato varieties: Premier Russet, which is resistant to the PVY strain O (PVY(O)) but susceptible to the strain NTN (PVY(NTN)), and Russet Burbank, which is susceptible to all PVY strains that have been tested. Leaves were inoculated with PVY(O) or PVY(NTN), and samples were collected 4 and 10 h post inoculation (hpi). A larger number of differentially expressed (DE) genes were found in the compatible reactions compared to the incompatible reaction. For all treatments, the majority of DE genes were down-regulated at 4 hpi and up-regulated at 10 hpi. Gene Ontology enrichment analysis showed enrichment of the biological process GO term "Photosynthesis, light harvesting" specifically in PVY(O)-inoculated Premier Russet leaves, while the GO term "nucleosome assembly" was largely overrepresented in PVY(NTN)-inoculated Premier Russet leaves and PVY(O)-inoculated Russet Burbank leaves but not in PVY(O)-inoculated Premier Russet leaves. Fewer genes were DE over 4-fold in the incompatible reaction compared to the compatible reactions. Amongst these, five genes were DE only in PVY(O)-inoculated Premier Russet leaves, and all five were down-regulated. These genes are predicted to encode for a putative ABC transporter, a MYC2 transcription factor, a VQ-motif containing protein, a non-specific lipid-transfer protein, and a xyloglucan endotransglucosylase-hydroxylase.
  
  
  CONCLUSIONS
  Our results show that the incompatible and compatible reactions in Premier Russet shared more similarities, in particular during the initial response, than the compatible reactions in the two different hosts. Our results identify potential key processes and genes that determine the fate of the reaction, compatible or incompatible, between PVY and its host.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. aymeric.goyer@oregonstate.edu.|Hermiston Agricultural Research and Extension Center, Hermiston, OR, USA. aymeric.goyer@oregonstate.edu.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA. aymeric.goyer@oregonstate.edu.
authors.forename: Aymeric
authors.initials: A
authors.lastname: Goyer
authors.affiliation: USDA-ARS, Prosser, WA, USA. Launa.Hamlin@ars.usda.gov.
authors.forename: Launa
authors.initials: L
authors.lastname: Hamlin
authors.affiliation: USDA-ARS, Prosser, WA, USA. Jim.Crosslin@ars.usda.gov.
authors.forename: James M
authors.initials: JM
authors.lastname: Crosslin
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. buchanae@gmail.com.
authors.forename: Alex
authors.initials: A
authors.lastname: Buchanan
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. changj@science.oregonstate.edu.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA. changj@science.oregonstate.edu.
authors.forename: Jeff H
authors.initials: JH
authors.lastname: Chang
mesh_terms: D015536:Down-Regulation / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D005838:Genotype; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology*; D018515:Plant Leaves / Q000235:genetics / Q000821:virology; D010942:Plant Viruses / Q000472:pathogenicity*; D017800:Potyvirus / Q000472:pathogenicity*; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D011198:Solanum tuberosum / Q000235:genetics* / Q000821:virology*; D014158:Transcription, Genetic / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
chemical_list: D012313:RNA