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United States Department of Agriculture

Agricultural Research Service

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Location: Nematology Laboratory

2009 Annual Report

1a. Objectives (from AD-416)
Objective 1: Discover, refine, and implement improved molecular approaches to modernize classification and aid the identification and control of nematodes in alfalfa cropping systems. Objective 2: Identify and develop novel sources of resistance to nematodes.

1b. Approach (from AD-416)
1. Molecular markers, including ribosomal, mitochondrial, Hsp90, and other nuclear genes will be used to develop new diagnostic assays, including RFLPs, and conventional or real-time PCR assays for Meloidogyne spp., Pratylenchus spp., and Ditylenchus spp. 2. Molecular information from the diagnostic work will be integrated with morphological data and information regarding biogeography, pathogenicity, and host range to generate new and improved phylogenetic schemes. 3. Bioinformatic analysis of EST sequences of selected species will be used to uncover genes that meet selective criteria for use as diagnostic markers and for phylogenetic comparisons. Selected gene sequences will be used to design oligonucleotide primers for amplification,in polymerase chain reactions, of specific gene sequences from populations of phytopathogenic nematodes to evaluate them for genus level, species-wide, and species-specific identification. 4. Novel gene targets from Meloidogyne spp. and Pratylenchus spp. will be advanced through a pipeline of cloning, mRNA expression profiling, and functional characterization, leading to identification of specific genes with the best potential for further development into novel control methods. 5. Based on the information obtained above, selected genes will be targeted for silencing by gene-specific dsRNA; nematodes treated with dsRNA will be monitored for the ability to move, infect host plants, feed and reproduce. Effects on gene expression will be monitored by mRNA extraction and PCR using gene-specific primers directed at the gene to be silenced. Genes that show the most promising phenotypes in the soaking experiments will be transformed into M. truncatula hairy roots using Agrobacterium-mediated transformation methods. Transgenic plants containing target gene RNAi will be infected with root-knot or lesion nematodes and assessed for decreases in nematode infection and reproduction; knock out of target genes will be verified through RT-PCR and in situ detection methods.

3. Progress Report
Molecular Diagnostics of Nematodes. Root-knot nematode (RKN) species are parasitic on a wide range of host plants, including alfalfa, turfgrasses, and numerous other crops. The anatomical features of many RKNs are similar, confounding accurate species identification. DNA markers, including ribosomal, mitochondrial, and nuclear Hsp90, were analyzed from several RKN populations that had been isolated from turfgrass throughout the western United States. A database of sequence information was created for the development of new molecular diagnostic assays for accurate identification of these RKNs. In addition, several populations of potato cyst and tobacco cyst nematodes (Globodera spp.) were molecularly characterized for ribosomal, mitochondrial, and nuclear markers, expanding the sequence databases that will enhance the accuracy of cyst nematode species identifications.

4. Accomplishments

Review Publications
Yan, G., Smiley, R., Okubara, P.A., Skantar, A.M., Easley, S.A., Sheedy, J.G., Thompson, A.L. 2008. Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil. Plant Disease. 92(11):1480-1487.

Skantar, A.M., Carta, L.K., Handoo, Z.A. 2008. Molecular and morphological characterization of an unusual Meloidogyne arenaria population from traveler’s tree Ravenala madagascariensis. Journal of Nematology. 40(3):179-189.

Last Modified: 10/18/2017
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