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Title: Identification and characterization of Citrus tristeza virus isolates breaking resistance in trifoliate orange in California

item Yokomi, Raymond - Ray
item SELVARAJ, VIJAY ANAND RAJ - Foreign Agricultural Service (FAS, USDA)
item MAHESHWARI, YOGITA - Foreign Agricultural Service (FAS, USDA)
item SAPONARI, MARIA - National Research Council - Italy
item GIAMPETRUZZI, ANNALISA - National Research Council - Italy
item CHIUMENTI, MICHELA - National Research Council - Italy
item HAJERI, SUBHAS - Central California Tristeza Eradication Agency

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2017
Publication Date: 2/27/2017
Citation: Yokomi, R.K., Selvaraj, V., Maheshwari, Y., Saponari, M., Giampetruzzi, A., Chiumenti, M., Hajeri, S. 2017. Identification and characterization of Citrus tristeza virus isolates breaking resistance in trifoliate orange in California. Phytopathology. 107(7):901-908.

Interpretive Summary: Citrus tristeza virus (CTV) is the most important citrus virus worldwide. Control is complicated due to different CTV strains that range in severity from asymptomatic to causing rapid tree death. Host-range biocharacterization identified eight diverse California CTV isolates. Next Generation Sequencing (NGS) methods were used to determine the entire genome sequence of each isolate. Data indicated the Dekopon isolate contained a mixture of isolates including a virulent (VT) strain indicative of an introduction from abroad. The Murcott isolate was a mixture of a mild (T30) and a unique resistance breaking (RB) strain that replicates in trifoliate orange, a popular rootstock resistant to most CTV isolates. Several isolates grouped with the T68/B165 and the T36 genotypes whose members are associated with severe disease. However, all CTV isolates in this study were classified as mild except Dekopon VT. This information is needed to support selective eradication of only virulent CTV strains. Selective eradication makes possible use of alternative citrus disease management practices in California, including CTV cross-protection and recombinant CTV as a friendly viral vector expressing therapeutic genes against new diseases/pests such as huanglongbing and the Asian citrus psyllid.

Technical Abstract: Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB 115; CA-RB-AT25 and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99% and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared to severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from ~1960’s and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB115-like; ten isolates collected from 1968 to 2010 from Riverside, Fresno and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.