Molecular Genetics and Genomics

, Volume 271, Issue 4, pp 426–436 | Cite as

The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L

  • S. Gottwald
  • N. Stein
  • A. Börner
  • T. Sasaki
  • A. GranerEmail author
Original Paper


In this study, comparative high resolution genetic mapping of the GA-insensitive dwarfing gene sdw3 of barley revealed highly conserved macrosynteny of the target region on barley chromosome 2HS with rice chromosome 7L. A rice contig covering the sdw3-orthologous region was identified and subsequently exploited for marker saturation of the target interval in barley. This was achieved by (1) mapping of rice markers from the orthologous region of the rice genetic map, (2) mapping of rice ESTs that had been physically localized on the rice contig, or (3) mapping of barley ESTs that show strong sequence similarity to coding sequences present in the rice contig. Finally, the sdw3 gene was mapped to an interval of 0.55 cM in barley, corresponding to a physical distance of about 252 kb in rice, after employing orthologous EST-derived rice markers. Three putative ORFs were identified in this interval in rice, which exhibited significant sequence similarity to known signal regulator genes from different species. These ORFs can serve as starting points for the map-based isolation of the sdw3 gene from barley.


Comparative mapping Expressed Sequence Tags (ESTs) Gibberellic acid (GA) insensitivity Synteny 



The authors wish to thank Dr. G. Künzel for performing barley translocation breakpoint mapping. We also thank Dr. D. Smilde and Dr. M. Wolf for constructive discussions, and R. Voss, S. Gentz, U. Beier and S. Stegmann for their excellent technical assistance.


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: Genome composition, collinearity and compatibility. Trends Genet 9:259–261PubMedGoogle Scholar
  3. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128–133CrossRefPubMedGoogle Scholar
  4. Börner A, Lehmann CO, Mettin D (1987) Preliminary results of a screening for GA3 response in wheats of the Gatersleben gene bank. Kulturpflanze 35:179–186Google Scholar
  5. Börner A, Korzun V, Malyshev S, Ivandic V, Graner A (1999) Molecular mapping of two dwarfing genes differing in their GA response on chromosome 2H of barley. Theor Appl Genet 99:670–675CrossRefGoogle Scholar
  6. Brueggeman R, Rostoks N, Kundra D, Killian 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 99:1–6CrossRefPubMedGoogle Scholar
  7. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus. Genetics 164:673–683PubMedGoogle Scholar
  8. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao Z, Yu Z, Roland PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274PubMedGoogle Scholar
  9. Chandler PM, Marion-Poll A, Gubler F (2002) Mutants at the Slender 1 locus of barley cv Himalaya. Molecular and physiological characterization. Plant Physiol 129:181–190CrossRefPubMedGoogle Scholar
  10. Chen M, et al (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545PubMedGoogle Scholar
  11. Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu J-L, Huckelhoven R, Stein M, Freialdenhoven A, Somerville SC, Schulze-Lefert P (2003) SNARE protein mediated disease resistance at the plant cell wall. Nature 425:973–977CrossRefPubMedGoogle Scholar
  12. 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
  13. Di Laurenzio L, Wysocka-Diller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, Hahn MG, Feldmann KA, Benfey PN (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86:423–33PubMedGoogle Scholar
  14. 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
  15. Favret EA, Favret GC, Malvarez EM (1975) Genetic regulatory mechanisms for seedling growth in barley. In: Barley Genetics III (Proceedings of the Third International Barley Genetics Symposium, Garching, Germany), pp 37–42Google Scholar
  16. Finkelstein RR, Gampala SSL, Rock C (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 14:15–45Google Scholar
  17. Freeling M (2001) Grasses as a single genetic system. Reassessment 2001. Plant Physiol 125:1191–1197CrossRefPubMedGoogle Scholar
  18. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci 95:1971–1974PubMedGoogle Scholar
  19. Gallego F, Feuillet C, Messmer M, Penger A, Graner A, Yano M, Sasaki T, Keller B (1998) Comparative mapping of two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome 41:328–336CrossRefPubMedGoogle Scholar
  20. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15–28CrossRefGoogle Scholar
  21. Gocal GFW, Sheldon CC, Gubler F, Moritz T, Bagnall DJ, MacMillan CP, Li SF, Parish RW, Dennis ES, Weigel D, King RW (2001) GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis. Plant Physiol 127:1682–1693PubMedGoogle Scholar
  22. Goff S, et al (2002) A draft sequence of the rice genome (Oryza sative L. ssp. japonica). Science 296:92–100PubMedGoogle Scholar
  23. Graner A, Siedler H, Jahoor A, Herrmann RG, Wenzel G (1990) Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theor Appl Genet 80:826–832Google Scholar
  24. 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
  25. Gubler F, Watts RJ, Kalla R, Mattews P, Keys M, Jacobsen JV (1997) Cloning of a rice cDNA encoding a transcriptional factor homologous to barley GAMYB. Plant Cell Physiol 38:362–365Google Scholar
  26. Harushima Y, et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  27. Havukkala IJ (1996) Cereal genome analysis using rice as a model. Curr Opin Genet Dev 6:711–714CrossRefPubMedGoogle Scholar
  28. Hedden P (2003) The genes of the Green Revolution. Trends Genet 19:5–9CrossRefPubMedGoogle Scholar
  29. Hooley R (1994) Gibberellins: perception, transduction and response. Plant Mol Biol 26:1529–1555PubMedGoogle Scholar
  30. Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J (2001) Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13:999–1010PubMedGoogle Scholar
  31. Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174Google Scholar
  32. Kilian A, Chen J, Han F, Steffenson B, Kleinhofs A (1997) Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol 35:187–195PubMedGoogle Scholar
  33. Kleinhofs A, et al (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712Google Scholar
  34. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Google Scholar
  35. Kovtun Y, Chiu W-L, Zeng W, Sheen J (1998) Suppression of auxin signal transduction by a MAPK cascade in higher plants. Nature 395:716–720CrossRefPubMedGoogle Scholar
  36. 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
  37. Langridge P, Karakousis A, Collins N, Kretschmer J, Manning S (1995) A consensus linkage map of barley. Mol Breed 1:389–395Google Scholar
  38. Laurie DA, Devos KM (2002) Trends in comparative genetics and their potential impacts on wheat and barley research. Plant Mol Biol 48:729–740CrossRefPubMedGoogle Scholar
  39. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370–375PubMedGoogle Scholar
  40. Li H, Shen J-J, Zheng Z-L, Lin Y, Yang Z (2001) The Rop GTPase switch controls multiple developmental processes in Arabidopsis. Plant Physiol 126:670–684CrossRefPubMedGoogle Scholar
  41. Li J, Chory J (1997) A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. Cell 90:929–938PubMedGoogle Scholar
  42. Martin DN, Proebsting WM, Parks TD, Dougherty WG, Lange T, Lewis MJ, Gaskin P, Hedden P (1996) Feed-back regulation of gibberellin metabolism and gene expression in Pisum sativum L. Planta 200:159–166PubMedGoogle Scholar
  43. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis. A rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832PubMedGoogle Scholar
  44. 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
  45. Ogawa M, Kusano T, Katsumi M, Sano H (2000) Rice gibberellin-insensitive gene homologue, OsGAI , encodes a nuclear localized protein capable of gene activation at transcriptional level. Gene 245:21–29CrossRefPubMedGoogle Scholar
  46. Peng J, Carol P, Richards DE, King KE, Cowling RJ, Murphy GP, Harberd NP (1997) The Arabidopsis GAI gene defines a signalling pathway that negatively regulates gibberellin response. Genes Dev 11:3194–3205PubMedGoogle Scholar
  47. Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F (1999) “Green Revolution” genes encode mutant gibberellin response modulators. Nature 400:256–261PubMedGoogle Scholar
  48. Perovic D, Stein N, Zhang, H, Drescher A, Prasad M, Kota R, Kopahnke D, Graner A (2004) An integrated approach for comparative mapping in rice and barley with special reference to the Rph16 resistance locus. Funct Integr Genomics, in pressGoogle Scholar
  49. Pysh LD, Wysocka-Diller, Camilleri C, Bouchez D, Benefy PN (1999) The GRAS gene family in Arabidopsis: sequence characterisation and basic expression analysis of the SCARECROW-LIKE genes. Plant J 18:111–119CrossRefPubMedGoogle Scholar
  50. Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379–394Google Scholar
  51. Richards DE, King KE, Ait-ali T, Harberd P (2001) How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellin signaling. Annu Rev Plant Physiol Plant Mol Biol 52:67–88CrossRefPubMedGoogle Scholar
  52. Robertson M, Swain SM, Chandler PM, Olszewski NE (1998) Identification of a negative regulator of gibberellin action, HvSPY, in barley. Plant Cell 10:995–1008Google Scholar
  53. Saghai Maroof MA, Yang GP, Biyashev RM, Maughan PJ, Zhang Q (1996) Analysis of the barley and rice genomes by comparative RFLP linkage mapping. Theor Appl Genet 92:541–551Google Scholar
  54. 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 Acids Res 30:98–102CrossRefPubMedGoogle Scholar
  55. Sheen J (2001) Update on signal transduction: signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol 127:1466–1475CrossRefPubMedGoogle Scholar
  56. Silverstone AL, Ciampaglio CN, Sun T-p (1998) The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell 10:155–69PubMedGoogle Scholar
  57. 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
  58. Swain SM, Olszewski NE (1996) Genetic analysis of gibberellin signal transduction. Plant Physiol 112:11–17PubMedGoogle Scholar
  59. 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
  60. Van Deynze AE, Sorrells ME, Park WD, Ayres NM, Fu H, Cartinhour SW, Paul E, McCouch SR (1998) Anchor probes for comparative mapping of grass genera. Theor Appl Genet 97:356–369CrossRefGoogle Scholar
  61. Van Ooijen JW, Voorrips RE (2001) Join Map 3.0 Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  62. Wu J, (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535PubMedGoogle Scholar
  63. Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144PubMedGoogle Scholar
  64. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci 100:6263–6268CrossRefPubMedGoogle Scholar
  65. Yoshimura A, Ideta O, Iwata N (1997) Linkage map of phenotype and RFLP markers in rice. Plant Mol Biol 35:49–60PubMedGoogle Scholar
  66. Yu J, 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

  • S. Gottwald
    • 1
  • N. Stein
    • 1
  • A. Börner
    • 1
  • T. Sasaki
    • 2
  • A. Graner
    • 1
    Email author
  1. 1.Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Genome Research DepartmentNational Institute of Agrobiological SciencesTsukubaJapan

Personalised recommendations