Theoretical and Applied Genetics

, Volume 106, Issue 7, pp 1171–1177 | Cite as

Identification of genetically linked RGAs by BAC screening in maize and implications for gene cloning, mapping and MAS

  • M. Quint
  • C. M. Dußle
  • A. E. Melchinger
  • T. LübberstedtEmail author


The resistance gene analogue (RGA) pic19 in maize, a candidate for sugarcane mosaic virus (SCMV) resistance gene (R gene) Scmv1, was used to screen a maize BAC library to identify homologous sequences in the maize genome and to investigate their genomic organisation. Fifteen positive BAC clones were identified and could be classified into five physically independent contigs consisting of overlapping clones. Genetic mapping clustered three contigs into the same genomic region as Scmv1 on chromosome 6S. The two remaining contigs mapped to the same region as a QTL for SCMV resistance on chromosome 1. Thus, RGAs mapping to a target region can be successfully used to identify further-linked candidate sequences. The pic19 homologous sequences of these clones revealed a sequence similarity of 94–98% on the nucleotide level. The high sequence similarity reveals potential problems for the use of RGAs as molecular markers. Their application in marker-assisted selection (MAS) and the construction of high-density genetic maps is complicated by the existence of closely linked homologues resulting in 'ghost' marker loci analogous to 'ghost' QTLs. Therefore, implementation of genomic library screening, including genetic mapping of potential homologues, seems necessary for the safe application of RGA markers in MAS and gene isolation.


RGA SCMV Maize pic19 Ghost marker BAC 



The present study was supported by a grant from the Deutsche Forschungsgemeinschaft, Grant No. LU601/3. The authors gratefully acknowledge the skilled technical assistance of Elisabeth Kokai-Kota. We would also like to thank Michael D. McMullen for linkage analysis and Matthias Frisch for his helpful suggestions on the issue of "ghost" markers.


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Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • M. Quint
    • 1
  • C. M. Dußle
    • 1
  • A. E. Melchinger
    • 1
  • T. Lübberstedt
    • 1
    • 2
    Email author
  1. 1.Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany
  2. 2.Danish Institute of Agricultural Sciences, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark

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