Real-Time PCR Assays for Detection and Quantification of Sweetpotato Viruses

Kokkinos, C. D.; Clark, Christopher A.

doi:10.1094/pd-90-0783

Cited by 51 publications

(45 citation statements)

References 21 publications

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“…Nevertheless, it cannot be ruled out that the lack of amplification was due to PCR inhibition or low virus titre (Kokkinos & Clark, 2006a). It is possible that the diversity and complexity of the Ipomoea-infecting begomovirus populations could be even higher, since the methodology used in this study may have favoured the amplification of a limited range of sequences, imposed by the specificity of the primer sequences.…”

Section: G Lozano and Others 2556mentioning

confidence: 95%

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Lozano

Trenado

Valverde

et al. 2009

Journal of General Virology

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Viral diseases occur wherever sweet potato (Ipomoea batatas) is cultivated and because this crop is vegetatively propagated, accumulation and perpetuation of viruses can become a major constraint for production. Up to 90 % reductions in yield have been reported in association with viral infections. About 20 officially accepted or tentative virus species have been found in sweet potato and other Ipomoea species. They include three species of begomoviruses (genus Begomovirus, family Geminiviridae) whose genomes have been fully sequenced. In this investigation, we conducted a search for begomoviruses infecting sweet potato and Ipomoea indica in Spain and characterized the complete genome of 15 isolates. In addition to sweet potato leaf curl virus (SPLCV) and Ipomoea yellowing vein virus, we identified three new begomovirus species and a novel strain of SPLCV. Our analysis also demonstrated that extensive recombination events have shaped the populations of Ipomoea-infecting begomoviruses in Spain. The increased complexity of the unique Ipomoea-infecting begomovirus group, highlighted by our results, open new horizons to understand the phylogeny and evolution of the family Geminiviridae. INTRODUCTIONSweet potato (Ipomoea batatas, family Convolvulaceae) is ranked as the seventh most important food crop in global production. This crop originated in South America (O'Brien, 1972) but today it is grown in most tropical, subtropical and temperate regions of the world. Numerous ornamental Ipomoea species are grown worldwide. Ipomoea indica is widely grown ornamentally in the Mediterranean basin, where it is frequently naturalized. The putative role of I. indica and other species in the genus as a reservoir for sweet potato pathogens has not been explored.Because sweet potato is vegetatively propagated, accumulation of viruses can become a major constraint for production. About 20 accepted or tentative virus species have been described in sweet potato . Three begomovirus species have been described as infecting Ipomoea species and their genomes have been fully sequenced. These are: sweet potato leaf curl virus (SPLCV) (Lotrakul et al., 1998;Lotrakul & Valverde., 1999), Ipomoea yellow vein virus (IYVV) (Banks et al., 1999) and sweet potato leaf curl Georgia virus (SPLCGV) (Lotrakul et al., 2003). SPLCV or related begomoviruses have been isolated from sweet potato in the Americas (Lotrakul et al., 2003;Fuentes & Salazar, 2003), Asia (Onuki & Hanada, 1998;Luan et al., 2006) and Africa (Miano et al., 2006) and from I. indica in Europe . Begomoviruses are likely to be present in many regions where sweet potato is grown but their prevalence and distribution is still unknown. Difficulties in detecting and isolating begomoviruses directly from sweet potato plants could have impeded additional reports (Kokkinos & Clark., 2006b).Information about the variability among isolates of the described sweet potato begomoviruses is limited. Comparisons and phylogenetic analyses of partial sequences of the AC1 gene of several isolates collect...

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Section: G Lozano and Others 2556mentioning

confidence: 95%

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Lozano

Trenado

Valverde

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

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“…Although this is an efficient means of propagation, it provides a vehicle for the perpetuation and distribution of systemic (and to some extent localized) viruses or pathogens which can be spread atnong seasons and growing areas from the propagating source rnaterial (4,12). Numerous viruses that infect sweetpotato have been identified and characterized.…”

mentioning

confidence: 99%

“…The first of these was the difficuhy of isolating and purifying the virus. The second was the high incidence of mixed infections and synergistic interactions that induced diseases (12). Until recently, only minimal efforts were made to control specific viral pathogens because the virus either had not been fully characterized or its effect on the crop had not been substantially evaluated (4).…”

mentioning

confidence: 99%

Detection and Classification of SPLCV Isolates in the U.S. Sweetpotato Germplasm Collection via a Real-Time PCR Assay and Phylogenetic Analysis

et al. 2011

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Barkley, N. A., Pinnow, D. L., Wang, M. L.. Ling. K. S.. and Jarret. R. L. 2011. Detection and classification of SPLCV isolates in the U.S. sweetpotato germplastn collection via a real-time PCR assay and phylogenetic analysis. Plant Dis. 95:1385-1391.The United States Department of Agriculture-Agricultural Research Service sweetpotato (Ipomoea batatas) germplasm collection contains accessions that were initially collected from various countries worldwide. These materials have been maintained and distributed as in vitro plantlets since the mid-1980s. The status of viral infection by the emerging Sweet potato leaf curl virus (SPLCV) and other Begomovirus spp. in this germplasm has yet to be determined. In order to minimize the potential distribution of virus-infected clones, all accessions in the collection were tested for SPLCV using a real-time polymerase chain reaction assay. In total. 47 of 701 accessions of in vitro plantlets tested positive for SPLCV. The presence of SPLCV detected in these materials was confirmed via biological indexing using the indicator plants /. nil and /. murkata. Symptoms appeared more rapidly on /. muricata than on /. nil. Nucleotide polymorphisms among the isolates were evaluated by sequencing the AVI coat protein gene from 24 SPLCVinfected accessions. The results revealed that the SPLCV isolates shared high sequence identity. Ten nucleotide substitutions were identified, most of which were synonymous changes. Phylogenetic analysis was conducted on those 2^ SPLCV isolates in combination with six described SPLCV species and various SPLCV strains from GenBank to evaluate the relationships among viral species or strains. The results from this analysis indicated that most of the AVI genes derived from previously classified SPLCV species clustered together, some of which formed well-supported monophyletic clades. further supporting the current taxonomy. Overall, identification of SPLCV-infected germplasm will allow approaches to be employed to eliminate the virus from the collection and limit the distribution of infected materials.

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“…Even though, at 3 weeks after inoculation, the titres of SPFMV were not different among the three hosts, the titre levels of potyviruses in I. setosa and I. nil were clearly and consistently above the threshold of detection; whereas, in sweetpotato plants, they often were near or below the threshold (Kokkinos & Clark 2006).…”

Section: Kokkinos and Clark (2006) Have Developed A Real-time Polymerasmentioning

confidence: 77%

“…There are several major viral diseases in sweetpotato but only a few have been studied and identified (Kokkinos & Clark 2006;Salazar et al 2001). At least twenty two viruses are known to be pathogens of sweetpotato of which more than ten types are recognized to cause damage to the sweetpotato industry worldwide (Ling et al 2010;Wang et al 2010).…”

Section: Major Virus Diseases In Sweetpotatomentioning

confidence: 99%

Studies on propagation materials and growing conditions for sweetpotato [Ipomoea Batatas (L.) Lam] production

Atu¹

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A thesis submitted for the degree of Master of Philosophy atThe University of Queensland in 2013 School of Agriculture and Food Sciences i ABSTRACTSweetpotato propagation is cultivated through use of sprout (slip) or vine cutting. Production of sprout is increased by best selection of storage root sizes to optimize growth and yield.Cultivars of different storage root sizes produced variable numbers of sprouts, varying in length and thickness and to explore this four storage root sizes in an open field bed were trialed. Beauregard and Northern Star storage roots selected from the large, medium, smallmedium and small storage root category sown in bed and sprouts at three length classes were first measured 47 days after sowing. The next three harvests were measured at 21 days interval while the fifth harvest was at 44 days after the fourth, calculated from the Growing Degree Days (GDD) units. Beauregard produced significantly higher number of sprout at >20 cm but fewer > 35 cm length than Northern Star. The sprout length 20 -35 cm class increased for both varieties after Harvest 1 but Beauregard tended to increase less for this class than Northern Star with progressive harvests. In the fifth harvest 20 -35 cm length class for both varieties had reduced although Northern Star produced more for this class than Beauregard. A significantly higher number of sprouts were produced by large root but not significantly different from the medium root. Sprout categories for < 20 and 20 -35 cm were greater for large and medium roots than smaller roots. The thickness of sprout progressively decreased in numbers as storage roots size decreased. Sprouts longer than 20 cm are considered best propagation material for farmers and to achieve this within the best possible short period is an advantage to farmers.The experiment study on seven sweetpotato varieties for pathogen tested (PT) and nonpathogen tested (NPT) was investigated at 60 days after planting (DAP), 120 DAP and 220 DAP for yield differences. There was no significant difference (P < 0.05) for all varieties for early root growth at 60 (DAP). No significant difference was observed for PT and Non-PT for the marketable yield but a significant increase in non-marketable yield at 120 DAP and 220 DAP for PT and non-PT was presumably due to virus infection.The number of marketable storage root production declined as the crop grew older but the opposite trend occurred for the non-marketable yield which increased three fold in the final harvest compared to the previous harvest. Northern Star produced the highest number and weight of marketable and non-marketable roots compared to the other six varieties.ii LD02 and Beauregard were the second best varieties in terms of marketable roots while L49, Vekeoli and Lola Tonga had the least potential. Northern Star followed by Beauregard and LD02 proved their supremacy by their ability to partition dry matter to bulk storage root.Beauregard was the only variety observed with SPFMV infection in the foliage.High soil temperatures affected the...

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Real-Time PCR Assays for Detection and Quantification of Sweetpotato Viruses

Cited by 51 publications

References 21 publications

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Detection and Classification of SPLCV Isolates in the U.S. Sweetpotato Germplasm Collection via a Real-Time PCR Assay and Phylogenetic Analysis

Studies on propagation materials and growing conditions for sweetpotato [Ipomoea Batatas (L.) Lam] production

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