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 results from gene expression in both species. Dwarfed sweet o...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/6/1144 |
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| author | Irene Lavagi-Craddock Tyler Dang Stacey Comstock Fatima Osman Sohrab Bodaghi Georgios Vidalakis |
| author_facet | Irene Lavagi-Craddock Tyler Dang Stacey Comstock Fatima Osman Sohrab Bodaghi Georgios Vidalakis |
| author_sort | Irene Lavagi-Craddock |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T23:00:31Z |
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| id | doaj.art-e755ef4a0190499896befb8f8df9ae03 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T23:00:31Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-e755ef4a0190499896befb8f8df9ae032023-11-23T18:03:43ZengMDPI AGMicroorganisms2076-26072022-06-01106114410.3390/microorganisms10061144Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange RootstockIrene Lavagi-Craddock0Tyler Dang1Stacey Comstock2Fatima Osman3Sohrab Bodaghi4Georgios Vidalakis5Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USADepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USADepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USADepartment of Plant Pathology, University of California, Davis, CA 95616, USADepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USADepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USADwarfed 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.https://www.mdpi.com/2076-2607/10/6/1144RNA-seqCDVdtransmissible small nuclear ribonucleic acid (TsnRNA)mRNAfunctional analysisdifferentially expressed genes (DEGs) |
| spellingShingle | Irene Lavagi-Craddock Tyler Dang Stacey Comstock Fatima Osman Sohrab Bodaghi Georgios Vidalakis Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock Microorganisms RNA-seq CDVd transmissible small nuclear ribonucleic acid (TsnRNA) mRNA functional analysis differentially expressed genes (DEGs) |
| title | Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock |
| title_full | Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock |
| title_fullStr | Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock |
| title_full_unstemmed | Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock |
| title_short | Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock |
| title_sort | transcriptome analysis of citrus dwarfing viroid induced dwarfing phenotype of sweet orange on trifoliate orange rootstock |
| topic | RNA-seq CDVd transmissible small nuclear ribonucleic acid (TsnRNA) mRNA functional analysis differentially expressed genes (DEGs) |
| url | https://www.mdpi.com/2076-2607/10/6/1144 |
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