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Transcriptional plasticity enables oomycetes to rapidly adapt to environmental challenges including emerging host resistance. For example, the soybean pathogen  Phytophthora sojae  can overcome resistance conferred by the host resistance gene  Rps1b  through natural silencing of its corresponding effector gene,  Avr1b-1 . With the  Phytophthora  CRISPR/Cas9 genome editing system, it is possible to generate site-specific knock-out (KO) and knock-in (KI) mutants and to investigate the biological functions of target genes. In this study, the  Avr1b-1  gene was deleted from the  P. sojae  genome using a homology-directed recombination strategy that replaced  Avr1b-1  with a gene encoding the fluorescent protein mCherry. As expected, all selected KO transformants gained virulence on  Rps1b  plants, while infection of plants lacking  Rps1b  was not compromised. When a sgRNA-resistant version of  Avr1b-1  was reintroduced into the  Avr1b -1 locus of an Avr1b KO transformant, KI transformants with a well-transcribed  Avr1b-1  gene were unable to infect  Rps1b -containing soybeans. However, loss of expression of the incoming  Avr1b-1  gene was frequently observed in KI transformants, which resulted in these transformants readily infecting  Rps1b  soybeans. A similar variability in the expression levels of the incoming gene was observed with AVI- or mCherry-tagged Avr1b-1 constructs. Our results suggest that  Avr1b-1  may be unusually susceptible to transcriptional variation.

Transcriptional Variability Associated With CRISPR-Mediated Gene Replacements at the Phytophthora sojae Avr1b-1 Locus