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Functional & Integrative Genomics

, Volume 4, Issue 2, pp 74–83 | Cite as

An integrated approach for comparative mapping in rice and barley with special reference to the Rph16 resistance locus

  • Dragan Perovic
  • Nils Stein
  • Hangning Zhang
  • Anke Drescher
  • Manoj Prasad
  • Raja Kota
  • Doris Kopahnke
  • Andreas GranerEmail author
Original Paper

Abstract

The accumulated sequence information of the almost completed rice genome and the transcriptome of other cereals provide an excellent starting point for comparative genome analysis. We performed targeted synteny-based marker saturation for the Rph16 leaf rust resistance locus in barley by extensively exploiting these newly available resources. Out of a collection of over 320,000 public barley ESTs 309 non-redundant candidate syntenic clones have been identified for this region in a two-step in silico selection procedure. For mapping, 54 barley cDNA-clones were selected due to the even distribution of their homologs on a putatively collinear 3-Mb rice BAC contig. Out of these, 97% (30) of the polymorphic markers could be genetically assigned in collinearity to the target region in barley and a set of 11 markers was integrated into an rph16 high-resolution map. Although, the collinear target region of rice does not contain an obvious candidate gene for rph16 the results demonstrate the potential of the presented procedure to efficiently utilize EST resources for synteny-based marker saturation. The systematic genome-wide exploitation of the increasing sequence data resources will strongly improve our current view of genome conservation and likely facilitate a synteny-based isolation of genes conserved across cereal species.

Keywords

Synteny EST High resolution map Leaf rust 

Notes

Acknowledgements

The presented work was supported by grant no. Gr.1317/4-3 of the Deutsche Forschungsgemeinschaft (DFG), Germany. The authors would like to thank A. Kleinhofs, Washington State University, United States and P. Hayes, Oregon State University, United States for kindly providing seeds of the S × M and OWB D × R mapping populations. We would also like to thank D. Smilde, JIC, Norwich, United Kingdom for helpful comments on the manuscript and S. Stegmann, B. Hoppe and J. Perovic for technical assistance.

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218Google Scholar
  3. Avramova Z, Tikhonov A, SanMiguel P, Jin Y-K, Liu C, Woo S-S, Wing RA, Bennetzen JL (1996) Gene identification in a complex chromosomal continuum by local genomic cross-referencing. Plant J 10:1163–1168CrossRefPubMedGoogle Scholar
  4. Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet 9:259–261PubMedGoogle Scholar
  5. Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci USA 99(14):9328–9333CrossRefPubMedGoogle Scholar
  6. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low copy DNA interrupts the microcolinearity between rice and barley at the Rph7 locus. Genetics 164:673–683PubMedGoogle Scholar
  7. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78–94CrossRefPubMedGoogle Scholar
  8. Büschges R, Hollrichter K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Töpsch S, Vos P, Salamini F, Schulze Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695–705PubMedGoogle Scholar
  9. Chen M, Presting G, Barabazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S et al (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545PubMedGoogle Scholar
  10. Collins NC, Lahaye T, Peterhänsel C, Freialdenhoven A, Corbit M, Schulze-Lefert P (2001) Sequence haplotypes revealed by sequence-tagged site fine mapping of the Ror1 gene in the centromeric region of barley chromosome 1H. Plant Physiol 125:1236–1247PubMedGoogle Scholar
  11. Costa JM, Corey A, Hayes PM, Jobet C, Kleinhofs A, Kopisch-Obusch A, Kramer SF, Kudrna D, Li M, Riera-Lizarazu O, Sato K, Szucs P, Toojinda T, Vales MI, Wolfe RI (2001) Molecular mapping of the Oregon Wolfe barleys: a phenotypically polymorphic doubled-haploid population. Theor Appl Genet 103:415–424Google Scholar
  12. Drescher A, Graner A (2002) PCR-genotyping of barley seedlings using DNA samples from tissue prints. Plant Breed 121:228–231CrossRefGoogle Scholar
  13. Druka A, Kudrna D, Han F, Kilian A, Steffenson B, Frisch D, Tomkins J, Wing R, Kleinhofs A (2000) Physical mapping of the barley stem rust resistance gene rpg4. Mol Gen Genet 264:283–290PubMedGoogle Scholar
  14. Dubcovsky J, Ramakrishna W, San Miguel PJ, Busso CS, Yan L, Shiloff BA, Benetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342–1353PubMedGoogle Scholar
  15. Dunford RP, Yano M, Kurata N, Sasaki T, Huestis G, Rocheford T, Laurie DA (2002) Comparative mapping of the barley Ppd-H11 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161:825–834Google Scholar
  16. Feng Q, Zhang Y, Hao P, Wang S et al (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320CrossRefPubMedGoogle Scholar
  17. Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implication in maize. Proc Natl Acad Sci USA 99(14):9573–9578PubMedGoogle Scholar
  18. Fulton MT, Van der Hoeven R, Eannetta TN, Tanksley DS (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467Google Scholar
  19. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedGoogle Scholar
  20. Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map in barley. Theor Appl Genet 83:250–256Google Scholar
  21. Graner A, Bauer E, Kellermann A, Kirschner S, Muraya JK, Jahoor A, Wenzel G (1994) Progress of RFLP-map construction in winter barley. Barley Genet Newsl 23:53–59Google Scholar
  22. Han F, Kilian A, Chen JP, Kundrna D, Steffenson B, Yamamoto K, Matsumoto T, Sasaki T, Kleinhofs A (1999) Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42:1071–1076CrossRefPubMedGoogle Scholar
  23. Hulbert SH, Webb CA, Smith SM, Sun Q (2001) Resistance gene complexes: evolution and utilization. Ann Rev Phytopathol 39:285–312CrossRefGoogle Scholar
  24. Ivandic V, Walther U, Graner A (1998) Molecular mapping of new gene in wild barley conferring complete resistance to leaf rust (Puccinia hordei Otth). Theor Appl Genet 97:1235–1239Google Scholar
  25. Kleinhofs A, Kilian A, Saghai Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwich A, Blake TK, Kanazin V et al (1993) A molecular, isozyme and morphological map of barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712Google Scholar
  26. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Google Scholar
  27. Kota R, Wolf M, Michalek W, Graner A (2001) Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.). Genome 44:523–528CrossRefPubMedGoogle Scholar
  28. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412PubMedGoogle Scholar
  29. Lahaye T, Shirasu K, Schulze-Lefert P (1998) Chromosome landing at the barley Rar1 locus. Mol Gen Genet 260:92–101CrossRefPubMedGoogle Scholar
  30. Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedGoogle Scholar
  31. Laurie DA (1997) Comparative genetics of flowering time. Plant Mol Biol 35:167–177PubMedGoogle Scholar
  32. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner, Schulce-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereals genomes. Proc Natl Acad Sci USA 95:370–375PubMedGoogle Scholar
  33. Levine MN, Cherewick WJ (1952) Studies on dwarf leaf rust of barley. US Dept Agric Technol Bull 1056:1–17Google Scholar
  34. Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J, Waterman EH, Jahoor A, Ayliffe M, Pryor AJ, Langridge P, Schulze-Lefert P, Stougaard J (2003) Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping. Mol Gen Genomics 269:150–161Google Scholar
  35. Michalek W, Weschke W, Pleissner KP, Graner A (2002) EST analysis in barley defines a unigene set comprising 4000 genes. Theor Appl Genet 104:97–103Google Scholar
  36. Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution: grasses, line up and form a circle. Curr Biol 5:737–739PubMedGoogle Scholar
  37. Moseman JG, Nevo E, El-Morshidy MA (1990) Reactions of Hordeum spontaneum to infection with two cultures of Puccinia hordei from Israel and USA. Euphytica 49:169–175Google Scholar
  38. Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K (2002) RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acid Res 30:98–102CrossRefPubMedGoogle Scholar
  39. Sasaki T, Matsumoto T, Yamamoto K et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316CrossRefPubMedGoogle Scholar
  40. Smilde WD, Haluskova J, Sasaki T, Graner A (2001) New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags. Genome 44:361–367PubMedGoogle Scholar
  41. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549–1555CrossRefPubMedGoogle Scholar
  42. Stam P (1993) Construction of integrated genetic linkage maps by means of a computer package: JOINMAP. Plant J 3:739–744Google Scholar
  43. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of the 340 kb of DNA around Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:381–391PubMedGoogle Scholar
  44. Thiel T, Michalek W, Varshney RK, Graner A (2003a) Exploiting EST databases for development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  45. Thiel T, Kota R, Grosse I, Stein N, Graner A (2003b) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32(1):e5CrossRefGoogle Scholar
  46. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409–7414PubMedGoogle Scholar
  47. Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744–754PubMedGoogle Scholar
  48. Van Ooijen JW, Voorrips RE (2001) Join Map 3.0 software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  49. Weerasena JS, Steffenson B, Falk AB (2003) Conversion of an amplified fragment length polymorphism marker into a co-dominant marker in the mapping of the Rph15 gene conferring resistance to barley leaf rust, Puccinia hordei Otth. Theor Appl Genet. DOI 10.1007/s00122-003-1470-2Google Scholar
  50. Wei F, Gobelman-Werner K, Morrol SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise PR (1999) The Mla powdery mildew resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S(1HS) of barley. Genetics 154:1929–1948Google Scholar
  51. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada Ch, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J et al (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535PubMedGoogle Scholar
  52. Yu J, Hu S, Wang J, Wong GK-S et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–91PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Dragan Perovic
    • 1
  • Nils Stein
    • 1
  • Hangning Zhang
    • 1
  • Anke Drescher
    • 1
    • 3
  • Manoj Prasad
    • 1
  • Raja Kota
    • 1
  • Doris Kopahnke
    • 2
  • Andreas Graner
    • 1
    Email author
  1. 1.Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Federal Centre for Breeding Research on Cultivated PlantsInstitute for Epidemiology and ResistanceAscherslebenGermany
  3. 3.Allgemeine Genetik/ZMBPUniversität TübingenTübingenGermany

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