Development of an RT-PCR assay to detect genetically divergent wheat streak mosaic virus isolates for plant quarantine inspections in South Korea.

Wheat streak mosaic virus (WSMV), a member of the genus Tritimovirus in the family Potyviridae, has been designated as a plant quarantine pathogen in South Korea. Several diagnostic methods can be applied to diagnose viral infections in plants, but polymerase chain reaction and enzyme-linked immunosorbent assay, which can identify viral species with speed and accuracy, are mainly used in Korean plant quarantine. Many variants of different viral species with highly divergent genomic sequences are constantly being discovered by high-throughput sequencing technology. This means that previously established primers may no longer be suitable for diagnostic use. In this study, we developed a reverse transcription polymerase chain reaction assay for detecting WSMV isolates/strains using all of the WSMV sequences available in NCBI GenBank. All 13 primer sets were able to produce amplicons of the expected sizes from WSMV-infected samples. To check whether nonspecific reactions occur, some closely related viruses (one tritimovirus and five potyviruses) and target imported plants (wheat, maize, oat, and proso millet) were tested. Consequently, four primer sets, which did not produce nonspecific bands, were finally selected among the 13 primer sets. Concentration-dependent amplification tests showed that the four primer sets are adequate for use in the diagnosis of WSMV in Korean plant quarantine.

Phylogeography of the highly invasive sugar beet nematode, Heterodera schachtii (Schmidt, 1871), based on microsatellites.

Plant-parasitic nematodes (PPNs) threaten crop production worldwide. Yet few studies have examined their intraspecific genetic diversity or patterns of invasion, critical data for managing the spread of these cryptic pests. The sugar beet nematode Heterodera schachtii, a global invader that parasitizes over 200 plant species, represents a model for addressing important questions about the invasion genetics of PPNs. Here, a phylogeographic study using 15 microsatellite markers was conducted on 231 H. schachtii individuals sampled from four continents, and invasion history was reconstructed through an approximate Bayesian computation approach, with emphasis on the origin of newly discovered populations in Korea. Multiple analyses confirmed the existence of cryptic lineages within this species, with the Korean populations comprising one group (group 1) and the populations from Europe, Australia, North America, and western Asia comprising another (group 2). No multilocus genotypes were shared between the two groups, and large genetic distance was inferred between them. Population subdivision was also revealed among the populations of group 2 in both population comparison and STRUCTURE analyses, mostly due to different divergent times between invasive and source populations. The Korean populations showed substantial genetic homogeneity and likely originated from a single invasion event. However, none of the other studied populations were implicated as the source. Further studies with additional populations are needed to better describe the distribution of the potential source population for the East Asian lineage.

Morphometric and molecular characterization of populations of Pratylenchus kumamotoensis and P. pseudocoffeae (Nematoda, Pratylenchidae) newly recorded in Korea.

At least 70 species of root-lesion nematodes, Pratylenchus spp., have been identified worldwide, many of which are serious pests of various agricultural crop plants. In Korea, only 14 species have been recorded in vegetable and fruit fields. Here, we report two new records of root-lesion nematode species in Korea based on morphometric and molecular methods. Soil samples were collected from chrysanthemum cultivars in various regions. Morphometric diagnosis showed that two new records for Korea: Pratylenchus kumamotoensis in Chilgok County and Pratylenchus pseudocoffeae in Geumsan County. In addition, molecular diagnosis using the two sequences of the internal transcribed spacer (ITS) and the D2-D3 region of ribosomal DNA showed that these two species were most similar with those from Japan, Costa Rica and USA. The similarities of the ITS and D2-D3 sequences were 99.85 and 99.74%, respectively, for Pratylenchus kumamotoensis and 99.99 with Costa Rica populations and 99.86% with USA populations, respectively, for Pratylenchus pseudocoffeae. To our knowledge, this is the first report of two species in Korea.