Genomic Analysis of the Snn 1 Locus on Wheat Chromosome Arm 1 BS and the Identifi cation of Candidate Genes

The pathogen Stagonospora nodorum produces multiple hostselective toxins (HSTs) that induce cell death and necrosis in sensitive wheat (Triticum sp.) genotypes. One such HST is SnTox1, which interacts with the host gene Snn1 on wheat chromosome arm 1BS to cause necrosis leading to disease susceptibility. Toward the positional cloning of Snn1, we developed saturated and high-resolution maps of the Snn1 locus and evaluated colinearity of the region with rice (Oryza sativa L.). An F2 population of 120 individuals derived from ‘Chinese Spring’ (CS) and the CS–T. dicoccoides chromosome 1B disomic substitution line was used to map 54 markers consisting of restriction fragment length polymorphisms (RFLPs), simple sequence repeats, and bin mapped expressed sequence tags (ESTs). Colinearity between wheat 1BS and rice was determined by aligning EST and RFLP probe sequences to the rice genome. Overall, colinearity was poorly conserved due to numerous complex chromosomal rearrangements, and of 48 wheat EST-RFLP sequences mapped, 30 had signifi cant similarity to sequences on nine different rice chromosomes. However, 12 of the wheat sequences had similarity to sequences on rice chromosome 5 and were in a colinear arrangement with only a few exceptions, including an inversion of the markers fl anking Snn1. High-resolution mapping of the Snn1 locus in 8510 gametes delineated the gene to a 0.46-cM interval. Two EST-derived markers that cosegregated with Snn1 were found to share homology to nucleotide binding site–leucine rich repeat–like genes and are considered potential candidates for Snn1. W (Triticum sp.) is attacked by a large variety of pathogens, the majority being of fungal origin. Th e fungus Stagonospora nodorum (Berk.) Castellani & E.G. Germano (telomorph Phaeosphaeria nodorum) causes Stagonospora nodorum blotch (SNB) on both common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD genomes) and durum wheat (T. turgidum L., 2n = 4x = 28, AABB genomes). Because it has the ability to cause yield losses up to 50% and negatively impact grain quality, SNB is considered a disease of major importance in wheat-growing areas (King et al., 1983; Scharen et al., 1985; Weber, 1922). Th e pathogen produces typical lens-shaped necrotic and chlorotic lesions on susceptible genotypes but small-restricted lesions on resistant genotypes. To date, four host selective toxins (HSTs) produced by S. nodorum have been identifi ed (Liu et al., 2004a, 2006; Friesen et al., 2006, 2007, 2008). Th e toxins, designated SnToxA, SnTox1, SnTox2, and SnTox3, were all shown to be proteinaceous in nature and interact with specifi c host sensitivity genes to cause necrosis. It has been hypothesized that the SnToxA gene was horizontally transferred from S. nodorum to the tan spot fungus (Pyrenophora triticiPublished in The Plant Genome 1:55–66. Published 16 July 2008. doi: 10.3835/plantgenome2008.03.0181 © 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. L. Reddy, Dep. of Plant Sci., North Dakota State Univ., Fargo, ND 58105; T.L. Friesen, S. Chao, and J.D. Faris, USDA-ARS Cereal Crops Research Unit, Northern Crop Sci. Laboratory, 1307 18th St. N., Fargo, ND 58105; S.W. Meinhardt, Dep. Plant Pathology, North Dakota State Univ., Fargo, ND 58105. Received 29 Apr. 2008. *Corresponding author (justin.faris@ars.usda.gov). Abbreviations: BAC, bacterial artifi cial chromosome; CS, Chinese Spring; CS-DIC 1B, Chinese Spring-Triticum dicoccoides 1B disomic substitution line; EST, expressed sequence tag; HST, host selective toxin; ITMI, International Triticeae Mapping Initiative; LOD, logarithm of odds; N1B T1D, nullisomic 1B tetrasomic 1D; NBS-LRR, nucleotide binding site–leucine rich repeat; NCBI, National Center for Biotechnology Information; NSF, National Science Foundation; PAC, P1-derived artifi cial chromosome; PCR, polymerase chain reaction; RFLP, restriction fragment length polymorphism; SNB, Stagonospora nodorum blotch; SSCP, single-stranded conformational polymorphism; SSR, simple sequence repeat; TC, tentative consensus.