Advertisement

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. Lübberstedt
Article

Abstract.

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.

Keywords.

RGA SCMV Maize pic19 Ghost marker BAC 

Notes

Acknowledgements.

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.

References

  1. Bennetzen JL, Qin MM, Ingels S, Ellingboe AH (1988) Allele-specific and mutator-associated instability at the Rp1 disease-resistance locus of maize. Nature 332:369–370Google Scholar
  2. Collins NC, Webb CA, Seah S, Ellis JG, Hulbert SH, Pryor A (1998) The isolation and mapping of disease resistance gene analogues in maize. Mol Plant Microbe Interact 11:968–78PubMedGoogle Scholar
  3. Collins NC, Drake J, Aycliffe M, Sun Q, Ellis J (1999) Molecular characterisation of the maize Rp1-D rust resistance haplotype and its mutants. Plant Cell 11:1365–1376PubMedGoogle Scholar
  4. Davis G, Musket T, Melia-Hancock S, Duru N, Qu J, Sharopova N, Schultz L, McMullen MD, Woodman WL, Long MJ, Lee M, Vogel JM (2000) A high-resolution genetic map of the B73 × Mo17 population. Maize Genetics Conference Abstracts 42:P79Google Scholar
  5. Ellis J, Lawrence GJ, Finnegan EJ, Anderson PA (1995) Contrasting complexity of two rust resistance loci in flax. Proc Natl Acad Sci USA 92:4185–4188Google Scholar
  6. Frisch M, Quint M, Lübberstedt T, Melchinger AE (2003) Duplicate marker loci can result in incorrect locus order on linkage maps. (submitted)Google Scholar
  7. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809–6814PubMedGoogle Scholar
  8. Hammond-Kosack KE, Jones JDG (1997) Plant disease resistance genes. Annu Rev Plant Physiol Plant Mol Biol 48:575–607Google Scholar
  9. Helentjaris T (1995) Atlas of duplicated sequences. Maize Genet Coop Newslett 69:67Google Scholar
  10. Hu G, Hulbert S (1994) Evidence for the involvement of gene conversion in meiotic instability of the Rp1 rust resistance genes in maize. Genome 37:742–746Google Scholar
  11. Kesseli R, Witsenboer H, Stanghellini M, Vandermark G, Michelmore RW (1993) Recessive resistance to Plasmopara lactucae-radicis maps by bulked segregant analysis to a cluster of dominant resistance genes in lettuce. Mol Plant-Microbe Interact 6:722–728Google Scholar
  12. Liu SS, Kowalsky SP, Lan TH, Feldmann KA, Peterson AH (1996) Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics 142:247–258PubMedGoogle Scholar
  13. Lander ES, Green P, Abraramson J, Baslow A, Daly MJ, Lincoln SE, Newburg L (1987) MapMaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–184PubMedGoogle Scholar
  14. Landry BS, Kesseli R, Farrara B, Michelmore RW (1987) A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance and morphological markers. Genetics 116:331–337Google Scholar
  15. Leipoldt M, Schmidtke J (1982) In: Dover G, Flavell R (eds) Genome evolution. Academic Press, New York, pp 219–236Google Scholar
  16. Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–6PubMedGoogle Scholar
  17. Martinez O, Curnow RN (1992) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480–488Google Scholar
  18. Meyers BC, Chin, DB, Shen KA, Sivaramakrishnan S, Lavelle DO, Zhang Z, Michelmore RW (1998a) The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell 10:1817–1832PubMedGoogle Scholar
  19. Meyers BC, Shen KA, Rohani P, Gaut BS, Michelmore RW (1998b) Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell 11:1833–1846CrossRefGoogle Scholar
  20. Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317–332CrossRefPubMedGoogle Scholar
  21. Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130PubMedGoogle Scholar
  22. Parniske M, Hammond-Kosack KE, Golstein C, Thomas CM, Jones DA, Harrison K, Wulff BB, Jones JD (1997) Novel disease resistance specifities results from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91:821–832PubMedGoogle Scholar
  23. Pryor T (1987) Stability of alleles of Rp (resistance to Puccinia sorghi). Maize Genet Newslett 61:37–38Google Scholar
  24. Quint M, Melchinger AE, Dußle CM, Lübberstedt T (2000) Breeding for virus resistance in maize. Genetika 32:529–545Google Scholar
  25. Quint M, Mihaljevic R, Dußle CM, Xu ML, Melchinger AE, Lübberstedt T (2002) Development of RGA-CAPS markers and genetic mapping of candidate genes for SCMV resistance in maize. Theor Appl Genet 105:355–363Google Scholar
  26. Saxena KMS, Hooker AL (1968) On the structure of a gene for disease resistance in maize. Proc Natl Acad Sci USA 61:1300–1305Google Scholar
  27. Shen KA, Meyers BC, Islani-Faridi MN, Chin DB, Stelly DM, Michelmore RW (1998) Resistance gene candidates indetified by PCR with degenerate oligonnucleotide primos map to clusters of resistance genes in lettuce. Mol Plant-Microbe Interact 8:815–823Google Scholar
  28. Sudupak MA, Bennetzen JL, Hulbert SH (1993) Unequal exchange and meiotic instability of disease-resistance genes in the Rp1 region on maize. Genetics 133:119–125PubMedGoogle Scholar
  29. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815PubMedGoogle Scholar
  30. Thomas CM, Jones DA, Parniske M, Harrison K, Balint-Kurti PJ, Hatzixanthis K, Jones JDG (1997) Characterisation of the tomato Cf-4 gene for resistance to Cladiosporum fulvum identifies sequences that determine recognitial specifity in Cf-4 and Cf-9. Plant Cell 9:2209–2224Google Scholar
  31. Witsenboer H, Kesseli R, Fortin MG, Stanghellini M, Michelmore RW (1995) Sources and genetic fine structure of a cluster of genes for resistance to three pathogens of lettuce Theor Appl Genet 91:178–188Google Scholar
  32. Xia XC, Melchinger AE, Kuntze L, Lübberstedt T (1999) Quantitative trait loci mapping of resistance to sugarcane mosaic virus in maize. Phytopathology 89:660–667Google Scholar
  33. Zhao B, Lin X, Leach JE, Hulbert S (2001) Molecular analysis of the maize gene conferring a non-host hypersensitive reaction to rice bacterial streak. Plant and Animal Genome IX Conference, p 90Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • M. Quint
    • 1
  • C. M. Dußle
    • 1
  • A. E. Melchinger
    • 1
  • T. Lübberstedt
    • 1
    • 2
  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

Personalised recommendations