Gene Expression Profi ling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers

White mold, caused by Sclerotinia sclerotiorum (Lib.) de Bary, can be a serious disease of crops grown under cool, moist environments. In many plants, such as soybean [Glycine max (L.) Merr.], complete genetic resistance does not exist. To identify possible genes involved in defense against this pathogen, and to determine possible physiological changes that occur during infection, a microarray screen was conducted using stem tissue to evaluate changes in gene expression between partially resistant and susceptible soybean genotypes at 8 and 14 hours post inoculation. RNA from 15 day-old inoculated plants was labeled and hybridized to soybean cDNA microarrays. ANOVA identifi ed 1270 signifi cant genes from the comparison between time points and 105 genes from the comparison between genotypes. Selected genes were classifi ed into functional categories. The analyses identifi ed changes in cell-wall composition and signaling pathways, as well as suggesting a role for anthocyanin and anthocyanidin synthesis in the defense against S. sclerotiorum. In-silico mapping of both the differentially expressed transcripts and of public markers associated with partial resistance to white mold, provided evidence of several differentially expressed genes being closely positioned to white mold resistance markers, with the two most promising genes encoding a PR-5 and anthocyanidin synthase. T HE FUNGAL PATHOGEN Sclerotinia sclerotiorum (Lib.) de Bary is an important pathogen that infects a wide variety of vegetables, ornamentals, and fi eld crops causing a disease known as either white mold or Sclerotinia stem rot. Plants susceptible to this pathogen encompass 75 families, 278 genera, and 408 species (Boland and Hall, 1994). One of the main pathogenic factors of S. sclerotiorum is oxalic acid (OA) (Godoy et al., 1990). Recently, Kim et al. (2008) provided evidence to the hypothesis that OA induces cell death to help the pathogen on initial infection of the tissue. Additional mechanisms of action for the secreted OA have been proposed, and other pathogensecreted factors such as cell-wall degrading enzymes and polygalacturnases have also been implicated as pathogenicity factors (Cessna et al., 2000; Favaron et al., 2004; Published in The Plant Genome 2:149–166. Published 10 July 2009. doi: 10.3835/plantgenome2008.02.0008 © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. B. Calla, T. Vuong, O. Radwan, G.L. Hartman, and S.J. Clough, Dep. of Crop Sciences, Univ. of Illinois, Urbana, IL 61801; G.L. Hartman and S.J. Clough, USDA-ARS, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, Urbana, IL 61801. Work supported by the USDA-CREES National Sclerotinia Initiative and USDA-ARS CRIS project 3611-21000-018-00D. Mention of trade names or commercial products in this publication is solely for the purpose of providing specifi c information and does not imply recommendation or endorsement by the United States Department of Agriculture. Normalized microarray data has been deposited in NCBI GEO as accession #GSE15369. Received 2 Feb. 2009. *Corresponding author ([email protected]). Abbreviations: ACC, 1-aminocyclopropane-1-carboxylic acid; CCR, cynnamoyl CoA reductase; CT, cycle threshold; Cy3, cyanine 3 fl uorescent dye; Cy5, cyanine 5 fl uorescent dye; ERF1, ethylene responsive factor1; EST, expressed sequence tag; ET, ethylene; FDR, false discovery rate; glowess, global lowess; hpi, hours post inoculation; IFRs, isofl avone reductase homologs; JA, jasmonic acid; LDOX, leucoanthocyanidin dioxygenase; lowess, locally weighted linear regression; OA, oxalic acid; PR, pathogenesis-related; qRTPCR, quantitative reverse transcription-polymerase chain reaction; QTL, quantitative trait loci; rlowess, Regional lowess; ROS, reactive oxygen species; R, partially resistant soybean PI 194639; S, susceptible soybean ‘Williams 82’; Satt, satellite repeat sequence; SSR, simple sequence repeat.