Phytophthora cinnamomi populations affecting avocado in California show low differentiation, phenotypic variability, and introductions from Mexico

Authors: SHANDS, A - University Of California, Riverside; MONDRAGION-FLORES, A - Universidad Michoacana De San Nicolas De Hidalgo; VALENCIA, V - University Of California, Riverside; HUA, V - University Of California, Riverside; CAULDRON, N - Oregon State University; Grunwald, Niklaus; FERNANDEZ-PAVIA, S - Universidad Michoacana De San Nicolas De Hidalgo; MANOSALVA, P - University Of California, Riverside

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2025
Publication Date: 10/24/2025
Citation: Shands, A.C., Mondragón-Flores, A., Valencia, V., Hua, V., Cauldron, N.C., Grünwald, N.J., Fernández-Pavía, S.P., Manosalva, P.M. 2025. Phytophthora cinnamomi populations affecting avocado in California show low differentiation, phenotypic variability, and introductions from Mexico. Molecular Plant-Microbe Interactions. 38(5):708-721. https://doi.org/10.1094/MPMI-08-24-0101-R.
DOI: https://doi.org/10.1094/MPMI-08-24-0101-R

Interpretive Summary: Phytophthora root rot (PRR), caused by the pathogen Phytophthora cinnamomi, is one of the most devastating avocado diseases worldwide. We previously reported a group of a genetic group II that is genetically distinct, more pathogenic, and less fungicide sensitive isolates from Southern California (CA) that could have been introduced from Mexico (MX). Here, we tested the hypothesis of migration of P. cinnamomi from Mexico using whole-genome sequencing and genetic analysis. Our study that strains from Mexico are placed into the same genetic group as those from California supporting a scenario of migration. Monitoring and characterizing the genetic and phenotypic variability of P. cinnamomi populations is critical to develop effective and durable control methods for PRR management.

Technical Abstract: Phytophthora root rot (PRR), caused by Phytophthora cinnamomi, is one of the most devastating avocado diseases worldwide. We previously reported a group of A2 Clade II genetically distinct, more virulent, and less fungicide sensitive isolates from Southern California (CA) that could have been introduced from Mexico (MX). Here, we tested this hypothesis by characterizing the genetic and phenotypic diversity of P. cinnamomi populations from CA and MX using whole-genome sequencing. We found that the P. cinnamomi populations at these places belong to two previously described CA A2 clades. Higher genetic differentiation was detected among Mexican isolates when compared with the CA populations, however, majority of Mexican isolates clustered with the CA A2 clade II populations providing evidence for the introduction of Mexican isolates into Southern CA. Despite clonality, large phenotypic variability was detected within and among populations regarding growth rate, optimal growth temperature, and fungicide sensitivity. Moreover, our virulence results yielded contrasting patterns depending on the host and infected tissue utilized. With the exception of one Mexican isolate, diploid, all the isolates were inferred to be triploid suggesting that polyploidization could explain this phenotypic variability. Our study reveals the adaptation capacity of P. cinnamomi clonal populations to local environments and disease control methods and more importantly reported a movement of pathogen isolates between Mexico and California which could be detrimental for these two major avocados industries. Monitoring and characterizing the genetic and phenotypic variability of P. cinnamomi populations is critical to develop effective and durable control methods for PRR management.