CONSERVATION, CHARACTERIZATION, AND EVALUATION OF CROP GENETIC RESOURCES AND ASSOCIATED INFORMATION
Location: Plant Genetic Resources Conservation Unit
Title: Detection and classification of SPLCV isolates in the U.S. sweetpotato germplasm collection via a real-time PCR assay and phylogenetic analysis
Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 2, 2011
Publication Date: November 1, 2011
Citation: Barkley, N.L., Pinnow, D.L., Wang, M.L., Ling, K., Jarret, R.L. 2011. Detection and classification of SPLCV isolates in the U.S. sweetpotato germplasm collection via a real-time PCR assay and phylogenetic analysis. Plant Disease. 95(11):1385-1391.
Interpretive Summary: Sweet potato leaf curl virus (SPLCV) is a DNA virus that infects sweetpotato. This virus is known to be transmitted by whiteflies. Since its discovery, it has been reported infecting sweetpotato or its near relatives in countries around the world such as Brazil, China, Italy, Japan, Kenya, Peru, Spain, Taiwan, and the US. SPLCV can be difficult to diagnose since it does not always produce clear morphological symptoms upon infection. Even though infection with this virus is not lethal to the plant, it does however lead to yield decline and can affect quality traits. The USDA maintains a germplasm collection of sweetpotato which is distributed to worldwide requestors. This collection has not been previously evaluated for the prevalence of infection with SPLCV. Therefore, the goal of this work was to evaluate the entire germplasm collection for the presence of SPLCV. Overall, a fairly low rate of infection (6.7%) was revealed in this germplasm collection.
The USDA/ARS sweetpotato [Ipomoea batatas (L.) Lam] 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 1980s. The status of viral infection by the emerging Sweet potato leaf curl virus (SPLCV) and other begomoviruses in this germplasm collection has yet to be determined. In order to minimize the potential distribution of virus-infected clones, all accessions in the USDA/ARS sweetpotato germplasm collection were tested for SPLCV utilizing a real-time PCR assay. A total of 47 out of 701 accessions of in vitro plantlets tested positive for SPLCV. The infectivity of SPLCV detected from these materials was confirmed through biological indexing on two indicator plants I. nil (L.) Roth and I. muricata (L.) Jacq. Symptoms appeared more rapidly on I. muricata than on I. nil. Nucleotide polymorphism among the isolates was evaluated by sequencing the AV1 coat protein gene from 24 SPLCV-infected accessions. These results revealed that the SPLCV isolates from these accessions shared high sequence identity with a total of 10 nucleotide substitutions, most of which were synonymous changes. Phylogenetic analysis was conducted on these 24 SPLCV isolates, six described SPLCV species, and various SPLCV strains from GenBank to evaluate the relationships among viral species/strains. Most of the AV1 genes derived from 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 various approaches to be employed to eliminate the virus from the collection.