Transcriptome analysis of citrus dwarfing viroid induced dwarfing phenotype of sweet orange on trifoliate orange rootstock

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 is the result of 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 in comparison to non-infected controls. Differentially expressed genes validated with RT-qPCR corresponded to various physiological and developmental processes that could be associated with the dwarfing phenotype. For example, in stems, the transcription factors MYB13 and MADS-box, which regulate meristem functions and activate stress-responses, respectively, were up-regulated. Conversely, in roots, a calcium-dependent lipid-binding protein, that regulates membrane transporters, was down-regulated. Most of the transcriptome reprogramming occurred in the scion rather than in the rootstock. This is in agreement with previous observations of CDVd affecting the growth of sweet orange stems while not affecting the trifoliate rootstock. Lack of alterations in the pathogen defense transcriptome supported the term Transmissible small nuclear ribonucleic acid to describe the CDVd as a modifying agent of tree performance with desirable agronomic traits rather than a pathogen causing a disease.