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Title: Soybean GeneChip hybridizations to RNA isolated from root pieces colonized by soybean cyst nematode, Heterodera glycines

item Tucker, Mark
item Ehrenfried, Mindy
item Vinyard, Bryan

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2007
Publication Date: 9/20/2007
Citation: Tucker, M.L., Ehrenfried, M.L., Puthoff, D.P., Vinyard, B.T. 2007. Soybean GeneChip hybridizations to RNA isolated from root pieces colonized by soybean cyst nematode, Heterodera glycines. Journal of Experimental Botany. 58:3407-3418.

Interpretive Summary: Soybean cyst nematode (SCN) is the most economically damaging pathogen of soybean. It has been estimated that damage to the United States soybean crop by SCN costs farmers one billion dollars annually. In order for SCN to colonize the plant root it must form a complex feeding structure inside the root. The nematode somehow co-opts the plant into making the enzymes needed to form this feeding structure. We have examined changes in gene expression in SCN infected roots relative to non-infected roots and identified over 500 genes that are up-regulated and another 300 that are down-regulated by SCN. A better understanding of how these genes are regulated by the nematode will greatly improve the ability of scientists and industrial partners to control SCN infection of soybean.

Technical Abstract: The roots of susceptible 14 day-old soybean plants (cv. Williams) were inoculated with J2 soybean cyst nematodes, Heterodera glycines. After 8, 12 and 16 dpi the roots were placed under a stereomicroscope and root pieces (1 to 5 mm) that displayed 1 to many swollen SCN females were dissected out, lateral roots trimmed off, and colleted into liquid nitrogen. Similar root pieces were collected from roots that were not inoculated and kept for 8, 12, and 16 days. RNA was collected from replicate samples and hybridized to Affymetrix soybean GeneChips. Approximately 76% of 37,593 probe sets on the GeneChip indicated above background (p<0.05) expression in SCN inoculated and non-inoculated root pieces. When SCN inoculated is compared to non-inoculated roots, less than 3% and 0.5% of the hybridization signals to probe sets change more than 4-fold and 8-fold, respectively. Clustering of probe sets based on functional grouping indicate notable increases in probe sets associated with histones, disease and defense, and cell wall enzymes. A notable decrease was observed for proteins associated with ion and substrate transporters.