1
|
Ali A, Umar UUD, Naqvi SAH, Shakeel MT, Tahir MN, Khan MF, Altaf MT, Ölmez F, Dababat AA, Haq ZU, Nadeem MA, Hatipoğlu R, Baloch FS, Chung YS. Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan. Front Genet 2023; 13:1104635. [PMID: 36712883 PMCID: PMC9878587 DOI: 10.3389/fgene.2022.1104635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Citrus viroid infection is emerging as a serious threat because of its efficient systemic movement within the host plant and its quick spread due to contaminated pruning tools. A survey was conducted to investigate the primary distribution and molecular characterization of Citrus bent leaf viroid (CBLVd) and its variants in different citrus cultivars. A total of 154 symptomatic citrus samples were collected and detected by RT‒PCR with newly designed specific primers with the incidence of 36.33%. During biological indexing study on Etrog citron, expressions of reduced leaf size, yellowing with a light green pattern, and bending were observed. Amplified products were sequenced and analyzed using a nucleotide BLAST search, which showed 98% homology with other CBLVd isolates. The results of the phylogenetic tree analysis showed the presence of two main groups (A and B), with the predominant variants of CBLVd, i.e., CVd-I-LSS (Citrus viroid Low Sequence Similarity) sequences, clustering in subgroup A1 along with newly detected CVd-I-LSS from Palestinian sweet lime (Citrus limettioides), which has been identified as a new host of CVd-I-LSS in Pakistan. Further analysis of the sequences in subgroup A1 showed that the variant of CVd-I-LSS infecting citrus cultivars had a close relationship with isolates reported from China, Japan, and Iran, which may have resulted from the exchange of planting material. This study also unveiled the variability in nucleotide sequences of CBLVd, which made it unable to be detected by old primers. The results of this study indicate that the widespread presence of divergent variants of CBLVd is a major concern for the citrus industry in Pakistan and other countries where virulent isolates of CBLVd are prevalent. These findings suggest the need for future research on effective management and quarantine measures to stop the spread of CBLVd.
Collapse
Affiliation(s)
- Amjad Ali
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Ummad ud Din Umar
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | | | - Muhammad Nouman Tahir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Fahad Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | | | - Zia ul Haq
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| |
Collapse
|
2
|
Identification and primary distribution of Citrus viroid V in citrus in Punjab, Pakistan. Mol Biol Rep 2022; 49:11433-11441. [PMID: 36002656 DOI: 10.1007/s11033-022-07677-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Citrus plants are prone to infection by different viroids which deteriorate their vigor and production. Citrus viroid V (CVd-V) is among the six citrus viroids, belongs to genus Apscaviroid (family Pospiviroidae) which induces symptoms of mild necrotic lesions on branches and cracks on trunk portion. METHODS AND RESULTS A survey was conducted to evaluate the prevalence of CVd-V in core and non-core citrus cultivated areas of Punjab, Pakistan. A total of 154 samples from different citrus cultivars were tested for CVd-V infection by RT-PCR. The results revealed 66.66% disease incidence of CVd-V. Citrus cultivars Palestinia Sweet lime, Roy Ruby, Olinda Valencia, Kaghzi lime, and Dancy were identified as new citrus hosts of CVd-V for the first time from Pakistan. The viroid infection was confirmed by biological indexing on indicator host Etrog citron. The reported primers used for the detection of CVd-V did not amplify, rather showed non-specific amplification, which led to the designing of new primers. Whereas, new back-to-back designed primers (CVd-V AF1/CVd-V AR1) detected CVd-V successfully and obtained an expected amplified product of CVd-V with 294 bp. Sequencing analysis confirmed the new host of CVd-V showing 98-100% nucleotide sequence homology with those reported previously from other countries while 100% sequence homology to the isolates reported from Pakistan. Based on phylogenetic analysis using all CVd-V sequences in GenBank, two main CVd-V groups (I and II) were identified, and newly identified isolates during this study fall in the group I. CONCLUSION The study revealed that there are some changes in the nucleotide sequences of CVd-V which made difficult for their detection using reported primers. All isolates of Pakistan showed high sequence homology with other isolates of CVd-V from Iran and USA whereas; the isolates from China, Japan, Tunisia, and Africa are distantly related. It is evident that CVd-V is spreading in all citrus cultivars in Pakistan.
Collapse
|