Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics

Monika Kałużna; Andjelka Prokić; Aleksa Obradović; William A Weldon; Virginia O Stockwell; Joël F Pothier

doi:10.3389/fpls.2023.1254107

Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics

Front Plant Sci. 2023 Sep 13:14:1254107. doi: 10.3389/fpls.2023.1254107. eCollection 2023.

Authors

Monika Kałużna¹, Andjelka Prokić², Aleksa Obradović², William A Weldon³, Virginia O Stockwell⁴, Joël F Pothier⁵

Affiliations

¹ The National Institute of Horticultural Research, Skierniewice, Poland.
² University of Belgrade, Faculty of Agriculture, Belgrade, Serbia.
³ Valent BioSciences, Libertyville, IL, United States.
⁴ United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, United States.
⁵ Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.

Abstract

Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR^® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.

Keywords: Corylus avellana; Corylus spp.; LAMP; PCR; diagnosis; qPCR.

Grants and funding

This study was partly financed by the National Science Centre, Poland (Narodowe Centrum Nauki), grant UMO- 2017/26/M/NZ9/01024 granted to MK. AP was granted a Short-Term Scientific Mission by the European Cooperation in Science and Technology COST Action CA16107 EuroXanth to conduct some analysis in Wädenswil (Switzerland). AO and AP were supported by the Ministry of Science, Technological Development and Innovation, Republic of Serbia and the Faculty of Agriculture contract number 451-03-47/2023-01/200116. VS and WW were supported by base funds of USDA ARS Project 2072-22000-045-000D and a 2020 USDA ARS HQ Administrator-funded Postdoctoral Award. Support was also provided to JP by the Department of Life Sciences and Facility Management of the Zurich University of Applied Sciences (ZHAW) in Wädenswil. The open access article processing charges of this publication were funded by the National Science Centre, Poland (grant UMO- 2017/26/M/NZ9/01024).