Search PMN  

 

PDF version
for printing

Peer Reviewed
Impact
Statement




© 2011 Plant Management Network.
Accepted for publication 17 January 2011. Published 9 February 2011.


Molecular Characterization of Potato leafroll virus, Potato virus A, and Potato virus X Isolates from Potatoes in Alaskan Cities and Villages


Nancy L. Robertson, USDA-ARS, Arctic and Subarctic Plant Gene Bank, Palmer, AK 99645; Jeffrey Smeenk and Jodie M. Anderson, School of Natural Resources and Agricultural Sciences, University of Alaska-Fairbanks, Palmer, AK 99645


Corresponding author: Nancy L. Robertson.  nancy.robertson@ars.usda.gov


Robertson, N. L., Smeenk, J., and Anderson, J. M. 2011. Molecular characterization of Potato leafroll virus, Potato virus A, and Potato virus X isolates from potatoes in Alaskan cities and villages. Online. Plant Health Progress doi:10.1094/PHP-2011-0209-01-BR.


Commercialized potatoes (Solanum tuberosum L.) in Alaska are mainly grown in the Matanuska Valley, Tanana Valley, and Delta Junction, and are routinely monitored for viruses and pests. In contrast, non-commercial potato production sites occurring throughout Alaska are rarely scrutinized for diseases. In addition, virtually no information has been reported on the molecular aspects of Alaskan potato viruses and their relatedness to potato viruses outside of Alaska. In 2008, 88 non-commercial potato producers participated in a survey that involved mailing potato tubers from their gardens to the University of Alaska, Fairbanks. A total of 157 tubers were planted in gallon plastic pots in the greenhouse. Leaves from each plant were sampled and commercially tested by Agdia Inc. (Elkhart, IN) for Potato latent virus (PotLV), Potato leafroll virus (PLRV), Potato virus X (PVX), and potyviruses. Typically, these viruses are found wherever potatoes are grown in the world (5). Positive results from 12 sites included plants infected with PLRV, PVX, and Potato virus A (PVA); PotLV was not detected. Molecular confirmation of the viruses was completed by reverse transcription-polymerase chain reaction (RT-PCR) with appropriate primers for PLRV (4), PVA (1), and PVX (3). The PCR products were directly sequenced commercially by Davis Sequencing, Davis, CA. Resulting partial genomic sequences were viewed with Sequencher 4.10.1 (Gene Codes Corp., Ann Arbor, MI) and analyzed with Clustal X (2).

Potato virus A is a member of the genus Potyvirus and is transmitted by aphids in a non-persistent manner. Potato plants are the only natural host for PVA and infected plants usually have leaves with light and dark green mosaic symptoms and tubers that are slightly reduced in size. The only PVA isolate detected in the survey was from Auke Bay in southeastern Alaska. Comparison of PVA-Auke Bay’s partial genomic nucleotides (GenBank accession number in parenthesis) for helper component protease (HC-Pro, HQ622712), cylindrical inclusion (CI, HQ622711) and first protein, proteinase (P1, HQ622713) genes to PVA isolates from Finland (AJ131400), Germany (AJ131401), Hungary (Z21670), Sweden (AJ29311), Shetland Island (GU144321), and United States (AJ131402) ranged from 96% to 98% identity. Phylogenetic comparisons of the CI nucleotides among the PVA isolates depicted the Auke Bay-Alaska isolate to cluster with the Shetland Island and Finland isolates (Fig. 1).


 

Fig. 1. Phylogenetic tree depicting relationships of Potato virus A (PVA) isolates from Auke Bay, AK (blue letters and underlined) and other regions of the world by comparing their cylindrical inclusion gene nucleotides. PVA isolates are denoted by country and corresponding GenBank accession number. Bootstrap analysis was completed with 1000 replicates with values depicted > 60%. The PVA isolates were rooted with an outgroup, Turnip mosaic virus (TuMV).

 

A persistent, aphid vectored virus, PLRV is a member of the genus Polerovirus and infects potato and occasionally other solanaceous plant species such as tomato. Potato leafroll virus infected plants may develop rolled, leathery leaves and net necrosis in tubers resulting in significant yield and quality losses. Four PLRV isolates were found in geographically distinct regions that included Anchorage, King Salmon, and Fairbanks; two of the isolates from Anchorage were from tubers that were co-infected with PVX. Partial genomic sequences for the coat protein (CP) gene of PLRV-1 Anchorage (HQ622707), PLRV-2 Anchorage (HQ622708), PLRV-Fairbanks (HQ622709), and King Salmon (HQ622710) were submitted to GenBank (accession numbers in parenthesis). Alaska PLRV isolates ranged from 99% to 100% in nucleotide identity. Blast searches in GenBank detected 65 PLRV isolates that were 97% to 99% identical. Interestingly, all four Alaskan PLRV isolates formed a cluster with a Canada isolate when the coat protein was analyzed for relatedness (Fig. 2).


 

Fig. 2. Cladogram depicting Potato leafroll virus (PLRV) relationships among four isolates from Alaska (blue letters and underlined) and other countries using the nucleotide sequences of the coat protein gene for analysis. The PLRV isolates were rooted with an outgroup, Barley yellow dwarf virus (BYDV)-PAS. GenBank accession number is denoted with each virus isolate.

 

The most prevalent potato virus detected in this survey and in the world is PVX. It has no known vector, and is mechanically transmitted from plant to plant by leaves touching, potato machinery, and planting infected tubers. Plant symptoms may vary from mild leaf mottle to extreme stunting with reduction in tuber yield. Sixteen PVX isolates were found in Anchorage (HQ541810, HQ541807), Auke Bay (HQ541811), Chalkyitsik (HQ541812), Dillingham (HQ541819), Douglas Island (HQ541817), Eagle (HQ541808), Fairbanks (HQ541815, HQ541816, HQ541820), Healy (HQ541809, HQ541822), Nanwalek (HQ541814), Sleetmute (HQ541813), and Wiseman (HQ541821). Partial coat protein nucleotide sequences among the Alaskan isolates ranged between 95% to 99% identity. A phylogenetic tree for CP nucleotide comparison depicted 16 PVX Alaskan isolates to cluster in two distinct groups with PVX isolates from other countries (Fig. 3). To our knowledge, this is the first report of molecular data and phylogenetic analyses for potato viruses occurring in Alaska. The resulting molecular data obtained from PVA, PLRV, and PVX Alaskan isolates provide a time reference and genetic baseline for future phylogenetic studies.


 

Fig. 3. Cladogram depicting relationships among Potato virus X (PVX) isolates by comparison of their coat protein nucleotides. Sixteen Alaskan PVX isolates (blue letters and underlined) and 13 PVX isolates from selected countries are identified with their GenBank accession number. The PVX isolates were rooted with an outgroup, Potato leafroll virus (PLRV).

 

Literature Cited

1. Ha, C., Coombs, S., Revill, P. A., Harding, R. M., Vu, M., and Dale, J. L. 2008. Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Arch. Virol. 153:25-36.

2. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2974-2948.

3. Nie, X., and Singh, R. P. 2000. Detection of multiple potato viruses using an oligo (dT) as a common cDNA primer in multiplex RT-PCR. J. Virol. Methods 86:179-185.

4. Singh, R. P., Kurz, J., Boiteau, G., and Bernard, G. 1995. Detection of Potato leafroll virus in single aphids by the reverse transcription polymerase chain reaction and its potential epidemiological application. J. Virol. Methods 55:133-143.

5. Stevenson, W. R., Loria, R., Franc, G. D., and Weingartner, D. P., eds. 2001. Compendium of Potato Diseases, 2nd Edn. American Phytopathological Society, St. Paul, MN.