Recombination and darwinian selection as drivers of genetic diversity and evolution of sweet potato leaf curl viruses in Tanzania

Bachwenkizi, Hilda; Temu, Gladness Elibariki; Mbanzibwa, Deusdedith R.; Lupembe, Margareth Daudi; Ngailo, Stephan; Tairo, Fred; Massawe, Deogracious Protas

doi:10.1016/j.pmpp.2022.101853

Cited by 6 publications

(6 citation statements)

References 48 publications

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“…Therefore, the primers developed in this study can readily detect SPLCVs in sweet potato DNA samples not diluted beyond 10 -3 . Sequencing of the PCR products obtained using the primers reported here revealed that it is only DNA of SPLCVs that was amplified (Bachwenkizi et al, 2022), which confirmed specificity of the primers (IPPC, 2006). DNA from all known non-infected samples, as determined using NGS (Bachwenkizi et al, 2022), did not yield any bands on gel electrophoresis; confirming the primers were specific for SPLCVs.…”

Section: Sensitivity and Specificity Of Primerssupporting

confidence: 67%

“…To confirm the specificity of the primer pair d1-SPLCVF/ d1-SPLCVR on amplification of SPLCVs, 32 amplified PCR products were purified, sequenced on both strands, and blast to NCBI database. All sequences were confirmed to be of SPLCVs (Bachwenkizi et al, 2022). Furthermore, this primer pair and another pair of primer (SPLCVcpF1 5'-GAATGCTGT CCCAATTGCTGC-3'/SPLCVcpR1 (5'-CCTGCAACGCAGGGTCTG-3'), were used to detect SPLCVs on the same DNA samples.…”

Section: Splcvs Detection Primersmentioning

confidence: 89%

“…A comprehensive survey of SPLCVs was conducted from 2018 to 2020 in seven agricultural research zones in Tanzania as described in Bachwenkizi et al (2022).…”

Section: Study Areasmentioning

confidence: 99%

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Development of a molecular-based detection tool for sweet potato leaf curl viruses and determination of their incidence levels in Tanzania

Bachwenkizi¹,

Temu²,

Lupembe³

et al. 2022

Afr. Crop Sci. J.

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Sweet potato (Ipomoea batatas L.) is an important food security crop in sub-Saharan Africa, where its production is constrained by devastating diseases; including those caused by sweet potato leaf curl viruses (SPLCVs; Begomovirus; Geminiviridae). The objective of this study was to develop a molecular-based diagnostic detection tool for SPLCVs, as well as to generate information on their geographical distribution and incidence in Tanzania. A comprehensive survey of SPLCVs was done in all major sweet potato growing areas in Tanzania. Incidences of SPLCVs and their causative diseases were determined visually and by polymerase chain reaction (PCR), using primers designed, optimised and validated. DNA was extracted from 4166 sweet potato leaf samples and detection of SPLCVs was done. Visual incidence of disease symptoms ranged from 0 to 100%; while PCR-based incidence of SPLCVs ranged from 0 to 60%. The highest mean PCR-based incidence of SPLCVs was 32%. SPLCVs occurred in all sweet potato growing areas. There was a negative correlation between the visually assessed incidence of disease symptoms and PCR-based incidence of SPCLVs (r = -0.122 and R2 = 0.012). A weak positive correlation between altitude and PCR-based incidence of SPLCVs was also found. In ten-fold serially diluted sweet potato DNA samples, using our new primer pair d1-SPLCVF/d1-SPLCVR, the detection limit of SPLCVs was at the dilution of 10-3. The youngest fully expanded leaf of the sweet potato plant was the best for PCR detection of SPLCVs. These findings will be useful for strategic deployment of planting material and conducting sweet potato breeding experiments for resistance against SPLCVs.

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Section: Sensitivity and Specificity Of Primerssupporting

confidence: 67%

Section: Splcvs Detection Primersmentioning

confidence: 89%

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Development of a molecular-based detection tool for sweet potato leaf curl viruses and determination of their incidence levels in Tanzania

Bachwenkizi¹,

Temu²,

Lupembe³

et al. 2022

Afr. Crop Sci. J.

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“…As observed in nature, multiple phytopathogen infections can occur in a single plant, and their competitiveness, suppression, or synergism may impact on the visible symptoms. The capacity for multiplexing under natural field conditions is therefore highly necessary [95].…”

Section: Barcodingmentioning

confidence: 99%

Applicability of Smart Tools in Vegetable Disease Diagnostics

Ovesná

Tsiropoulos²,

Collier

et al. 2023

Agronomy

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Various diseases and pests cause serious damage to vegetable crops during the growing season and after harvesting. Growers attempt to minimize losses by protecting their crops, starting with seed and seedling treatments and followed by monitoring their stands. In many cases, synthetic pesticide treatments are applied. Integrated pest management is currently being employed to minimize the impact of pesticides upon human health and the environment. Over the last few years, “smart” approaches have been developed and adopted in practice to predict, detect, and quantify phytopathogen occurrence and contamination. Our review assesses the currently available ready-to-use tools and methodologies that operate via visual estimation, the detection of proteins and DNA/RNA sequences, and the utilization of brand-new innovative approaches, highlighting the availability of solutions that can be used by growers during the process of diagnosing pathogens.

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“…Several begomoviruses have been found to infect sweet potato worldwide, namely, Sweet potato leaf curl Uganda virus (SPLCUV), Sweet potato leaf curl South Carolina virus (SPLCSCV), Sweet potato leaf curl Sao Paulo virus (SPLCSPV), and Sweet potato leaf curl isolate China (SPLCV‐CN) (Albuquerque et al., 2011; Luan et al., 2007; Wasswa et al., 2011; Zhang & Ling, 2011). SPLCV closely related to SPLCSPV and SPLCUV were also detected in Tanzania, and these were found to be genetically diverse (Bachwenkizi et al., 2022). SPLCSPV, SPLCV, and Sweet potato mosaic virus (SPMV) were reported in South Africa (Esterhuizen et al., 2012a; Mulabisana et al., 2018a; Nhlapo et al., 2018a), and are transmitted by the B‐biotype whiteflies ( Bemisia tabaci ) (Esterhuizen et al., 2012b).…”

Section: Introductionmentioning

confidence: 99%

Detection of SPV2 and SPCSV and their possible influence on the yield in multiple virus infections

Mmboyi,

Mulabisana,

Laurie

et al. 2023

Crop Science

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The prevalence of Sweet potato virus 2 (SPV2) and Sweet potato chlorotic stunt virus (SPCSV) in the Limpopo, Mpumalanga and Gauteng provinces of South Africa was determined using serological and nucleic acid based methods. Cloning and sequencing part of the coat protein (CP) gene and the complete genome using Next Generation Sequencing (NGS) were also conducted to characterize and determine the sequence variability in SPV2 isolates. Primers designed in the current study successfully detected and confirmed the prevalence of SPV2 in the three provinces surveyed. The pairwise comparison of the amino acid (aa) sequences encoding the CP gene region confirmed that isolates in this study are related to SPV2, sharing a 94% to 99% CP aa identity with those originally reported in South Africa. The East African (EA) strain of SPCSV was also detected in the three provinces surveyed. Phylogenetic analysis using part of the CP encoding nucleotide (nt) sequences showed that the South African isolates correspond to but are distinct from the other EA strains of SPCSV used as reference sequences. Assessment of varieties and breeding lines’ response to multiple infection of potyviruses identified variety NC1560, breeding lines 2002‐21‐1 and 2006‐5‐4 as promising for inclusion in future breeding programs as sources of parent material for virus tolerance.This article is protected by copyright. All rights reserved

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Recombination and darwinian selection as drivers of genetic diversity and evolution of sweet potato leaf curl viruses in Tanzania

Cited by 6 publications

References 48 publications

Development of a molecular-based detection tool for sweet potato leaf curl viruses and determination of their incidence levels in Tanzania

Development of a molecular-based detection tool for sweet potato leaf curl viruses and determination of their incidence levels in Tanzania

Applicability of Smart Tools in Vegetable Disease Diagnostics

Detection of SPV2 and SPCSV and their possible influence on the yield in multiple virus infections

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