Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock

Abstract

Dwarfed citrus trees for high-density plantings or mechanized production systems will be key for future sustainable citrus production. Citrus trees consist of two different species of scion and rootstock. Therefore, any observed phenotype results from gene expression in both species. Dwarfed sweet orange trees on trifoliate rootstock have been produced using citrus dwarfing viroid (CDVd). We performed RNA-seq transcriptome analysis of CDVd-infected stems and roots and compared them to non-infected controls. The identified differentially expressed genes validated with RT-qPCR corresponded to various physiological and developmental processes that could be associated with the dwarfing phenotype. For example, the transcription factors MYB13 and MADS-box, which regulate meristem functions and activate stress responses, were upregulated in the stems. Conversely, a calcium-dependent lipid-binding protein that regulates membrane transporters was downregulated in the roots. Most transcriptome reprogramming occurred in the scion rather than in the rootstock; this agrees with previous observations of CDVd affecting the growth of sweet orange stems while not affecting the trifoliate rootstock. Furthermore, the lack of alterations in the pathogen defense transcriptome supports the term “Transmissible small nuclear ribonucleic acid,” which describes CDVd as a modifying agent of tree performance with desirable agronomic traits rather than a disease-causing pathogen.

Understanding Citrus Viroid Interactions: Experience and Prospects

“…Vd-siRNA may act as an inducer of symptom expression by mediating host mRNA cleavage or the methylation of promoter regions. Several research teams have reported the changes in host miRNA after viroid infection [ 58 , 59 , 60 , 61 ]. Numerous potential target genes for transcription factors and other regulatory proteins may occupy important positions in viroid–host interactions.…”

A Mini Review of Citrus Rootstocks and Their Role in High-Density Orchards

“…Citrus growers worldwide are attracted to dwarfing citrus rootstocks because they are ideal for high-density plantations and are suitable for mechanized farming [ 25 ]. Dwarfing citrus rootstocks are well represented in research reports ( Table 1 ).…”

“…Plant dwarfism has been linked with several viruses and viroids [ 25 , 48 , 49 ]. The citrus exocortis viroid seems to cause dwarfism in citrus plants by increasing the aboveground hydraulic resistance [ 50 ].…”

“…Further information was revealed regarding the putative biological mechanism through which CDVd affects specific scion/rootstock combinations to reduce plant height [ 55 ]. According to Lavagi [ 25 ], CDVd has been used to produce dwarf citrus trees when grafted on trifoliate rootstock. Further findings demonstrate that CDVd modulates the expression profile of citrus growth and developmental processes, which may be responsible for reduced vegetative growth.…”

Global transcriptomic analysis in avocado nursery trees reveals differential gene expression during asymptomatic infection by avocado sunblotch viroid (ASBVd)

“…(2022) ). In recent years, next-generation sequencing (NGS) technology has enabled the global transcriptomic analyses of several different hosts infected with PSTVd ( Chi et al., 2022 ; Góra-Sochacka et al., 2019 ; Hadjieva et al., 2021 ; Więsyk et al., 2020 ), HSVd ( Xia et al., 2017 ; Xu et al., 2020 ), citrus exocortis viroid (CEVd) ( Wang et al., 2019 ), CDVd ( Lavagi-Craddock et al., 2022 ) and dendrobium viroid (DVd) ( Li et al., 2022 ). These studies have shown that several host pathways were commonly altered by pospiviroid infection, including host defence signalling, phytohormone networks, secondary metabolism, transport, transcription, as well as protein synthesis and modification ( Joubert et al., 2022 ).…”