A Cleaved Amplified Polymorphic Sequence Assay to Differentiate Neopestalotiopsis Species With Differing Pathogenicity in Strawberry

ABSTRACT

Strawberries are a widely cultivated high‐value crop in Canada, with an annual farm gate value of approximately $134 million. Recently, a widespread epidemic in eastern North America involving an aggressive Neopestalotiopsis species has had catastrophic impacts on the strawberry industry. From 2020 to 2022, commercial strawberry fields across Ontario were surveyed for Neopestalotiopsis‐like disease symptoms. Of the samples collected, 42% tested positive for Neopestalotiopsis species. Among these, 81% were identified as the aggressive species, while 6% were identified as Neopestalotiopsis rosae and 13% as a previously undescribed strain. The putative undescribed Neopestalotiopsis taxon was less aggressive than the recently described aggressive species, producing milder symptoms with delayed disease development. A cleaved amplified polymorphic sequence (CAPS) assay targeting the translation elongation factor 1α ( tef1 ) gene, using the restriction enzymes BsrBI and/or Cac8I, reliably differentiated the putative new strain from the other two species. A second CAPS assay targeting the partial β‐tubulin ( β‐tub ) gene, using HindIII and BsaWI, distinguished N. rosae from both the aggressive species and the putative new strain. When used in combination, these CAPS assays provide a rapid and effective diagnostic tool for distinguishing the aggressive Neopestalotiopsis species from less aggressive species affecting commercially grown strawberries produced in Ontario.