Fine Mapping and Candidate Gene Discovery at the Rsv 3 Locus

The Soybean mosaic virus (SMV) resistance locus, Rsv3, previously mapped between markers A519F/R and M3Satt in the soybean molecular linkage group B2 (chromosome 14), has been characterized by examination of the soybean genome sequence. The 154 kbp interval encompassing Rsv3 contains a family of closely related coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) genes. Tightly linked to this region are additional CC-NB-LRR genes and several leucine-rich repeat receptor-like kinase (LRR-RLK) genes, thereby indicating that members of both multigene families constitute a heterogeneous cluster at the Rsv3 chromosomal region. To further confi rm the sequence and genetic map concordance, we developed 16 markers from the genomic sequence including predicted CC-NB-LRR genes and their fl anking sequences. Mapping of the resultant markers in three populations showed parallel alignment between the genetic and sequence maps in the Rsv3-containing region. Phylogenetic analysis of fi ve CC-NB-LRR genes including a pseudogene showed they were highly similar to each other and formed a subclade within a CCNB-LRR gene clade with representatives from several plant families including legume species. These results demonstrate that the Rsv3 locus is associated with this cluster of CC-NB-LRR genes, thereby suggesting that the Rsv3 gene most likely encodes a member of this gene family. In addition, information from this study should facilitate marker-assisted selection and pyramiding of resistance genes. IN PLANTS, most characterized disease resistance genes (R genes) encode nucleotide-binding leucine-rich repeat (NB-LRR) proteins characterized by nucleotide-binding (NB) and leucine-rich repeat (LRR) structures as well as variable aminoand carboxy-terminal domains (Collier and Moff ett, 2009). Th ese genes tend to cluster in short chromosomal regions (Michelmore and Meyers, 1998). On the basis of their N-termini, two subfamilies of NB-LRR resistance proteins are known: the fi rst is characterized by the Toll/interleukin-1 receptor (TIR)-domain homologous to the Drosophila Toll and mammalian interleukin-1 receptors and the second is characterized by a coiled-coil (CC) structure. Truncated versions of NB-LRR genes exist that encode proteins lacking either a domain near the N-terminus of NB or the LRR region or that consist only of a TIR domain. Th e two subfamilies cluster separately in phylogenetic analysis using their NB domains (McHale et al., 2006). Resistance genes mediate dominant resistance to pathogens possessing corresponding avirulence (Avr) genes (Collier and Moff ett, 2009; Jones and Dangl, 2006). Single dominant R genes typically respond diff erentially to pathogen strains or races. Th e typical dominant resistance response is associated with several defense-related events, including rapid induction of reactive oxygen species, phytoalexin accumulation, Published in The Plant Genome 4:55–64. Published 16 Mar. 2011. doi: 10.3835/plantgenome2010.11.0024 © Crop Science Society of America 5585 Guilford 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. S.J. Suh, N. Jeong, K. Yang, and S.C. Jeong, Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea; B.C. Bowman, C. Kastl, and M.A. Saghai Maroof, Dep. of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 20461; S.A. Tolin, Dep. of Plant Pathology, Physiology & Weed Science, Virginia Tech, Blacksburg, VA 24061; Su Jeong Suh and Brian C. Bowman contributed equally to this work. Received 11 Nov. 2010. *Corresponding author ([email protected]). Abbreviations: Avr, avirulence; CC, coiled-coil; GI, gene identifi cation; LRR, leucine-rich repeat; LL, ‘L29’ × ‘Lee68’; LS, ‘L29’ × ‘Sowon’; MLG, molecular linkage group; NB, nucleotidebinding; PCR, polymerase chain reaction; R genes, resistance genes; RLK, receptor-like kinase; SMV, Soybean mosaic virus; TIR, Toll/ interleukin-1 receptor; TL, ‘Tousan 140’ × ‘Lee68’.