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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #349059
Title: Molecular characterization and identification of stubby root nematode species from multiple states in the United States

Author
item HUANG, DANQIONG - North Dakota State University
item YAN, GUIPING - North Dakota State University
item GUDMESTAD, NEIL - North Dakota State University
item Whitworth, Jonathan
item FROST, KENNETH - Oregon State University
item BROWN, CHARLES - US Department Of Agriculture (USDA)
item YE, WEIMING - North Carolina Department Of Agriculture & Consumer Services
item AGUDELO, PAULA - Clemson University
item CROW, BILLY - University Of Florida

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2018
Publication Date: 8/31/2018
Citation: Huang, D., Yan, G., Gudmestad, N., Whitworth, J.L., Frost, K., Brown, C., Ye, W., Agudelo, P., Crow, B. 2018. Molecular characterization and identification of stubby root nematode species from multiple states in the United States. Plant Disease. 102(11):2101-2111. https://doi.org/10.1094/PDIS-10-17-1668-RE.
DOI: https://doi.org/10.1094/PDIS-10-17-1668-RE

Interpretive Summary: Molecular Characterization and Identification of Stubby Root Nematode Species from Multiple States in the United States Huang, D., Yan, G. P., Gudmestad, N., Whitworth, J., Frost, K., Brown, C., Weiming, Y., Agudelo, P., and Crow, B. Interpretive summary Stubby root nematode (SRN) is a vector for Tobacco rattle virus which can cause corky ringspot disease in potato. Over a three year period (2015-2017), 184 soil samples and 16 nematode suspensions from North Dakota, Minnesota, Idaho, Oregon, Washington, South Carolina, North Carolina, and Florida were evaluated. SRN was found in 106 soil samples and eight nematode suspensions. Four species were found in the samples; Paratrichodorus allius, P. minor, P. porosus and Trichodorus obtusus. Genomic sequencing of ribosomal DNA and/or species-specific PCR assay allowed detection of these species and characterization of them was done by comparing with reference samples from a gene bank (GenBank). An evolutionary tree was used to demonstrate common ancestry of these SRN species. Results showed that P. allius was more closely related to P. porosus than P. minor and T. obtusus. This study shows the occurrence of SRN across multiple states. Results will be helpful for understanding evolutionary relationships of SRN and can be used for future study for species identification and management.

Technical Abstract: Molecular Characterization and Identification of Stubby Root Nematode Species from Multiple States in the United States Huang, D., Yan, G. P., Gudmestad, N., Whitworth, J., Frost, K., Brown, C., Weiming, Y., Agudelo, P., and Crow, B. Technical abstract Stubby root nematodes (SRN) are important plant-parasitic nematodes infecting many crops and widely distributed in many regions of the United States. Particularly, SRN transmitting Tobacco rattle virus causes potato corky ringspot disease and has a significant economic impact on the potato industry. In 2015, 2016 and 2017, we assayed 184 soil samples and 16 nematode suspensions from North Dakota, Minnesota, Idaho, Oregon, Washington, South Carolina, North Carolina, and Florida. SRN were found in 106 soil samples with densities of 10-320/200 g of soil and in eight of the nematode suspensions. Genomic sequencing of ribosomal DNA and/or species-specific PCR assay revealed the presence of four species including Paratrichodorus allius, P. minor, P. porosus and Trichodorus obtusus. Accordingly, the rDNA sequences were characterized by analyzing D2-D3 of 28S rDNA, 18S rDNA, and ITS rDNA of these four SRN species obtained in this study and retrieved from GenBank. Both intra- and inter-species variation was higher in ITS rDNA than 18S rDNA and D2-D3 of 28S rDNA. A phylogenetic tree demonstrated monophyletic evolution of these four SRN species, with P. allius more closely related to P. porosus than P. minor and T. obtusus. Indel variation of ITS rDNA was present in P. allius populations from the same geographic regions. This study indicated the occurrence of SRN across multiple states. The intra- and inter-species genetic diversity of rDNA in this study will provide more information for understanding the evolutionary relationships of SRN and will be valuable for future studies of SRN species identification and management.