Skip to main content
SpringerLink
Log in

GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley

  • Short Communication
  • Published:
Functional & Integrative Genomics Aims and scope Submit manuscript

Abstract

The barley sdw1/denso gene not only controls plant height but also yield and quality. The sdw1/denso gene was mapped to the long arm of chromosome 3H. Comparative genomic analysis revealed that the sdw1/denso gene was located in the syntenic region of the rice semidwarf gene sd1 on chromosome 1. The sd1 gene encodes a gibberellic acid (GA)-20 oxidase enzyme. The gene ortholog of rice sd1 was isolated from barley using polymerase chain reaction. The barley and rice genes showed a similar gene structure consisting of three exons and two introns. Both genes share 88.3% genomic sequence similarity and 89% amino acid sequence identity. A single nucleotide polymorphism was identified in intron 2 between barley varieties Baudin and AC Metcalfe with Baudin known to contain the denso semidwarf gene. The single nucleotide polymorphism (SNP) marker was mapped to chromosome 3H in a doubled haploid population of Baudin × AC Metcalfe with 178 DH lines. Quantitative trait locus analysis revealed that plant height cosegregated with the SNP. The sdw1/denso gene in barley is the most likely ortholog of the sd1 in rice. The result will facilitate understanding of the molecular mechanism controlling semidwarf phenotype and provide a diagnostic marker for selection of semidwarf gene in barley.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  • Ahn S, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241:483–490

    Article  PubMed  CAS  Google Scholar 

  • Barua UM, Chalmers KJ, Thomas WTB, Hackett CA, Lea V, Jack P, Forester BP, Waugh R, Powell W (1993) Molecular mapping of genes determining height, time to heading, and growth habit in barley (Hordeum vulgare). Genome 36:1080–1087

    Article  PubMed  CAS  Google Scholar 

  • Bellgard M, Gojobori J, Appels R (2004) The bioinformatics challenges in comparative analysis of cereal genomics—an overview. Func Integr Genom 4:1–11

    Article  CAS  Google Scholar 

  • Bezant J, Laurie D, Pratchett N, Chojecki J, Kearsey M (1997) Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression. Molecular Breeding 3:29–38

    Article  CAS  Google Scholar 

  • Cakir M, Gupta S, Li C, Eckermann P, Hayden M, Ablett G, Platz G, Broughton S, Mather CD, Chalmers K, Loughman R, Appels R, Jones MGK, Galwey N, Lance R (2009) Genetic map construction and QTL analysis of the disease traits in the barley population Baudin × AC Metcalfe. Mol Breed (in press)

  • Coventry SJ, Barr AR, Eglinton JK, McDonald GK (2003) The determinants and genome locations influencing grain weight and size in barley ( Hordeum vulgare L.). Aust J Agric Res 54:1103–1115

    Article  CAS  Google Scholar 

  • Chono M, Honda I, Zeniya H, Yoneyama K, Saisho D, Takeda K, Takatsuto S, Hoshino T, Watanabe Y (2003) A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor. Plant Physiol 133:1209–1219

    Article  PubMed  CAS  Google Scholar 

  • Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142:285–294

    PubMed  CAS  Google Scholar 

  • 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 264:283–290

    Article  PubMed  CAS  Google Scholar 

  • Dunford RP, Kurata N, Laurie DA, Money TA, Minobe Y, Moore G (1995) Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Necleic Acids Res 23:2724–2728

    Article  CAS  Google Scholar 

  • Dunford RP, Yano M, Kurata N, Sasaki T, Huestis G, Rocheford T, Laurie DA (2002) Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161:825–834

    PubMed  CAS  Google Scholar 

  • Fettell NA, Moody DB, Long N, Flood RG (2001) Determinants of grain size in malting barley. In: Proceedings of the 10th Australian Barley Technical Symposium, September 16–20, 2001. Canberra, ACT, Australia

  • Foster AE, Thompson AP (1987) Effects of a semidwarf gene from Jotun on agronomic and quality traits of barley. In: Yasuda S, Kanishi T (eds) Proceedings of the 5th international barley genetics symposium, 1986. Sanyo, Okayama, pp 979–982

    Google Scholar 

  • Franckowiak JD, Pecio A (1992) Coordinator’s report: a listing of genetic stocks. Barley Genet Newsl 21:116–126

    Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci U S A 95:1971–1974

    Article  PubMed  CAS  Google Scholar 

  • Gale MD, Flintham JE, Devos KM (2002) Cereal comparative genetics and pre-harvest sprouting. Euphytica 126:21–25

    Article  CAS  Google Scholar 

  • Gallagher LW, Jackson LF, Schaller CW, Puri YP, Vogt HE (1996) Registration of ‘UC 828’ barley. Crop Sci 36:466

    Google Scholar 

  • Gottwald S, Stein N, Borner A, Sasaki T, Graner A (2004) The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7 L. Mol Gen Genet 271:426–436

    CAS  Google Scholar 

  • Han F, Kleinhofs A, Ullrich SE, Kilian A, Yano M, Sasaki T (1998) Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions. Genome 41:373–380

    Article  CAS  Google Scholar 

  • Hellewell KB, Rasmusson DC, Gallo-Meagher M (2000) Enhancing yield of semidwarf barley. Crop Sci 40:352–358

    Google Scholar 

  • Helliwell CA, Chandler PM, Poole A, Dennis ES, Peacock WJ (2001) The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway. Proc Natl Acad Sci U S A 98:2065–2070

    Article  PubMed  CAS  Google Scholar 

  • Ivandic V, Malyshev S, Korzum V, Gramer A, Börner A (1999) Comparative mapping of a gibberellic acid-insensitive dwarfing gene (Dwf2) on chromosome 4HS in barley. Theor Appl Genet 98:728–731

    Article  CAS  Google Scholar 

  • Kush GS (1993) Breeding rice for sustainable agricultural systems. In: Buxton DR, Shibles R, Forsberg RA, Blad BL, Asay KH et al (eds) International crop science I. Proceedings from International Crop Science Congress, Ames, IA, July 14–22, 1992. Crop Science Society of America, Madison, WI, pp 189–199

    Google Scholar 

  • Kurata N, Moore G, Nagamura Y, Foote T, Nano M, Minobe Y, Gale MD (1994) Conservation of genome structure between rice and wheat. Bio-Technology 12:276–278

    CAS  Google Scholar 

  • Laurie DA, Pratchett N, Romero C, Simpson E, Snape JW (1993) Assignment of the denso dwarfing gene to the long arm of chromosome 3(3H) of barley by use of RFLP markers. Plant Breed 111:198–203

    Article  Google Scholar 

  • Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R (2004) Genes controlling seed dormancy and preharvest sprouting in a rice–wheat–barley comparison. Func Integr Genom 4:84–93

    Article  CAS  Google Scholar 

  • Manly KF (1993) A Macintosh program for storage and analysis of experimental genetic mapping data. Mamm Genome 4:303–313

    Article  PubMed  CAS  Google Scholar 

  • Martins-lopes P, Zhang H, Koebner R (2001) Detection of single nucleotide mutations in wheat using single strand conformation polymorphism gels. Plant Mol Biol Rep 19:159–162

    Article  CAS  Google Scholar 

  • Mickelson HR, Rasmusson DC (1994) Genes for short stature in barley. Crop Sci 34:1180–1183

    Article  Google Scholar 

  • Milach SCK, Federizzi LC (2001) Dwarfing genes in plant improvement. Adv Agron 73:35–65

    Article  CAS  Google Scholar 

  • Nedel JL, Ullrich SE, Clancy JA, Pan WL (1993) Barley semidwarf and standard isotype yield and malting quality response to nitrogen. Crop Sci 33:258–263

    CAS  Google Scholar 

  • Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) “Green Revolution” genes encode mutant gibberellin response modulators. Nature 400:256–261

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Thomas WB, Baird E, Lawrence P, Booth A, Harrower B, Mcnicol JW, Waugh R (1997) Analysis of quantitative traits in barley by the use of amplified fragment length polymorphisms. Heredity 79:48–59

    Article  CAS  Google Scholar 

  • Rasmusson DC (1991) A plant breeder’s experience with ideotype breeding. Field Crops Res 26:191–200

    Article  Google Scholar 

  • Saisho D, Tanno K, Chono M, Honda I, Kitano H, Takeda K (2004) Spontaneous brassinolide-insensitive barley mutants ‘uzu’ adapted to east Asia. Breeding Sci 54:409–416

    Article  CAS  Google Scholar 

  • Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, Miyao A, Hirochika H, Kitano H, Ashikari M, Matsuoka M (2004) An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol 134:1–12

    Article  CAS  Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) A mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  PubMed  CAS  Google Scholar 

  • Savov A, Angelicheva D, Jordanova A, Eigel A, Kalaydjieva L (1992) High percentage acrylamide gels improve resolution in SSCP analysis. Nucleic Acids Res 20:6741–6742

    Article  PubMed  CAS  Google Scholar 

  • Sears RG, Kronstad WE, Metzger RJ (1981) Inheritance of dwarf and semidwarf plant height in barley. Crop Sci 21:828–833

    Google Scholar 

  • Sherman JD, Fenwick AL, Namuth DM, Lapitan NLV (1995) A barley RFLP map: alignment of the three barley maps and comparisons to Gramineae species. Theor Appl Genet 91:681–690

    Article  CAS  Google Scholar 

  • 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 44:361–367

    Article  PubMed  CAS  Google Scholar 

  • Sorrells ME (2000) The evolution of comparative plant genetics. In: Gustafson JP (ed) Genomes: proceedings of the 22nd Stadler symposium, June 6–8, 1998, Columbia, MO. Kluwer Academic, Norwell, MA

    Google Scholar 

  • Sorrells ME, La Rota CM, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin Mahmoud A, Gustafson JP, Qi LL, Echalier B, Gill BS, Matthews D, Lazo G, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain KG, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827

    PubMed  CAS  Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), green revolution rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99:9043–9048

    Article  PubMed  CAS  Google Scholar 

  • Spielmeyer W, Ellis M, Robertson M, Ali S, Lenton JR, Chandler PM (2004) Isolation of gibberellin metabolic pathway genes from barley and comparative mapping in barley, wheat and rice. Theor Appl Genet 109:847–855

    Article  PubMed  CAS  Google Scholar 

  • Takahashi R, Yamashi J (1951) Studies on the classification and the geographical distribution of the Japanese barley varieties. III. On the linkage relations and the origin of the “uzu” or semibrachytic characters in barley. Ber Ohara Inst Landwirtch Biol Okayama Univ 9:399–410

    Google Scholar 

  • Thomas WTB, Powell W, Swanston JS (1991) The effects of major genes on quantitatively varying characters in barley. 4. The GPert and denso loci and quality characters. Heredity 66:381–389

    Article  Google Scholar 

  • Thomas WTB, Powell W, Waugh R, Forster BP, Chalmers KJ, Barua UM, Swanston JS, Ellis RP (1994) Quantitative trait loci in a North West European spring barley cross-Blenheim × E224/3. Barley Genet Newsl 24:41–45

    Google Scholar 

  • Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells M (1995) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744–754

    Article  PubMed  Google Scholar 

  • 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 97:356–369

    Article  Google Scholar 

  • Yamamuro C, Ihara Y, Wu X, Noguchi T, Fujioka S, Takatsuto S, Ashikari M, Kitano H, Matsuoka M (2000) Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant cell 12:1591–1605

    Article  PubMed  CAS  Google Scholar 

  • Yang J, Hu CC, Ye XZ, Zhu J (2005) Qtlnetwork 2.0. Hangzhou, China: Institute of Bioinformatics. Zhejiang University [http://ibi.zju.edu.cn/software/qtlnetwork]

  • Yin X, Stam P, Johan Dourleijn C, Krop MJ (1999) AFLP mapping of quantitative trait loci for yield-determining physiological characters in spring barley. Theor Appl Genet 99:244–253

    Article  CAS  Google Scholar 

  • Zhang J (1994) Changes in plant height of varieties and analysis of dwarf sources with progress in barley breeding in China. Barley Sci 4:11–13 (In Chinese)

    CAS  Google Scholar 

  • Zhang J (2000) Inheritance of agronomic traits from the Chinese barley dwarfing gene donors ‘Xiaoshan Lixiahuang’ and ‘Cangzhou Luodamai’. Plant Breed 119:523–524

    Article  Google Scholar 

  • Zhang J, Zhen L, Zhang CH (2006) Analysis on the dwarfing genes in Zhepi 1 and Aizao 3: two dwarfing gene donors in barley breeding in China. Agri Sci China 5:643–647

    CAS  Google Scholar 

  • Zietkiewicz E, Yotova V, Jarnik M, Korab-Laskowska M, Kidd KK, Modiano D, Scozzari R, Stoneking M, Tishkoff S, Batzer M, Labuda D (1997) Nuclear DNA diversity in worldwide distributed human populations. Gene 205:161–171

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgment

This project is supported by the Grain Research & Development Corporation of Australia, Major International Scientific and Technological Joint Research Program of Zhejiang (2008C14072) and National Natural Science Foundation of China (30800686)

Author information

Authors and Affiliations

  1. Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China

    Qiaojun Jia

  2. Department of Agriculture & Food, Government of Western Australia, 3 Baron-Hay Court, South Perth, Western Australia, 6151, Australia

    Qiaojun Jia, Sharon Westcott, Reg Lance & Chengdao Li

  3. Western Australian Agricultural Biotechnology Centre, Murdoch University, Perth, Australia

    Jingjuan Zhang, Sharon Westcott, Xiao-Qi Zhang & Chengdao Li

  4. Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, Australia

    Mathew Bellgard

Authors
  1. Qiaojun Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jingjuan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sharon Westcott
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiao-Qi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mathew Bellgard
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Reg Lance
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chengdao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chengdao Li.

Electronic supplementary materials

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

The relationship between barley semidwarf gene-sdw1 and rice semidwarf gene-sd1 (The map of barley chromosome 3H was from http://barleygenomics.wsu.edu/arnis/linkage_maps/maps-svg1.html and the map of rice 1 was from Smilde et al. 2001) (PPT 242 KB)

Supplementary Fig. 2

Distribution of plant height in 178 DH lines in the Baudin × AC Metcalfe DH population from two year experiments (PPT 80 KB)

Supplementary Fig. 3

Association of the SNP with plant height in the Baudin × AC Metcalfe DH population (PPT 120 KB)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jia, Q., Zhang, J., Westcott, S. et al. GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley. Funct Integr Genomics 9, 255–262 (2009). https://doi.org/10.1007/s10142-009-0120-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10142-009-0120-4

Keywords

Search

Navigation