title: Development of qPCR systems to quantify shoot infections by canker-causing pathogens in stone fruits and nut crops.
abstract: OBJECTIVE
  To develop real-time PCR assays for quantification of shoot infection levels of canker disease of stone fruits and nut crops caused by six fungal pathogen groups.
  
  
  RESULTS
  This study focused on six major canker-causing fungal pathogen groups: Phomopsis sp., Botryosphaeria dothidea, Lasiodiplodia sp., Cytospora sp., Neofusicoccum sp. and Diplodia sp., occurring in stone fruits and nut crops in California. DNA primers were designed to specifically target each of the six pathogen groups after the specificity tests using canker-causing and non-canker-causing pathogens and by using DNA sequences of other species from GenBank using blast. The quantitative real-time PCR (qPCR) systems were developed and used to quantify the infection levels of inoculated dried plum shoots.
  
  
  CONCLUSIONS
  For Neofusicoccum sp. and Phomopsis sp., which were used in inoculation of walnut shoots, the values of the molecular severity ranged from 5·60 to 6·94 during the 16 days of latent infection period. The qPCR assays were more efficient, accurate and precise to quantify latent infections caused by canker-causing pathogens as compared to the traditional plating methods.
  
  
  CONCLUSIONS
  This study demonstrated the potential of using the developed qPCR systems for epidemiological studies on canker diseases of woody plants.
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: S
authors.initials: S
authors.lastname: Gu
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: D
authors.initials: D
authors.lastname: Felts
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: R D
authors.initials: RD
authors.lastname: Puckett
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: D P
authors.initials: DP
authors.lastname: Morgan
authors.affiliation: Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, USA.
authors.forename: T J
authors.initials: TJ
authors.lastname: Michailides
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D018556:Crops, Agricultural; D017931:DNA Primers; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D005638:Fruit / Q000382:microbiology; D009754:Nuts / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology*; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal
keywords: fungal pathogen; nut crops; quantification; real-time PCR; shoot infection; stone fruits