An investigation of resistance-breaking isolates of Citrus tristeza virus

Abstract

The ability of certain isolates of Citrus tristeza virus to overcome resistance expressed by the economically important rootstock species, Poncirus trifoliata was investigated. The identity, distribution and evolutionary history of resistance breaking (RB) isolates was determined by comparing the complete genome sequence of five RB isolates, with known non-RB isolates. The RB isolates were found to be members of a novel genotype distinct from known extant isolates. They probably originated from a common ancestor shared with the T36 genotype, and subsequently recombined with T30 and VT-Iike genotypes. A survey found the RB genotype present in 52.6% of all New Zealand citrus, and across the South Pacific from the Marianas to Polynesia. RB isolates from both regions form a single phylogenetic clade that shows little diversification, suggesting it spread throughout the Pacific, and did not evolve in New Zealand. The interaction of RB isolates in mixtures with non-RB isolates was investigated through challenge inoculation to determine whether the RB isolates are potentially useful for mild-strain cross protection. The resistance-breaking genotype was competitive and resistant to displacement in mixtures with known stem pitting isolates. Inoculation with the RB genotype retarded accumulation of the VT-like stem pitting isolate NZ-B18 and symptom expression in the short term, although observations from field trees suggest that no long-term protection is obtained. A threshold level for genomic RNA and specific sgRNAs such as p23 and p20 is proposed to be the cause of symptom expression. Finally, the accumulation and translocation of resistance breaking isolates within P. trifoliata was monitored over time to determine how resistance might be expressed. The spread of the RB isolates through the plant followed the same pattern in both P. trifoliata and susceptible species, but with reduced virus titre in P. trifoliata indicating that resistance affects virus replication and accumulation. It is proposed that the resistance breaking phenotype results from the ability of RB isolates to (partially) silence the host defence mechanisms. These data cumulatively suggest that Poncirus trifoliata and hybrid species may not be relied upon to provide durable resistance to Citrus tristeza virus isolates.