Skip to main content
SpringerLink
Log in

Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor

  • Original Paper
  • Published:
Functional & Integrative Genomics Aims and scope Submit manuscript

Abstract

Wheat prolamin-box binding factor (WPBF) was shown to be an activator of Triticum aestivum L. storage protein genes. Three homoeologous genes encoding this transcription factor were isolated from a bacterial artificial chromosome genomic library and sequenced. The genes all have two exons separated by an intron of approximately 1,000 bp where the second exon contains the entire coding sequence. Many differences were found between homoeologous sequences, but none of them is predicted to significantly alter the sequence of the putative encoded protein. The three homoeologous genes are specifically expressed in grain from 3 to 39 days after anthesis. The allelic variation of a genetically diverse collection of 27 bread wheat lines was assessed. One, five, and one single-nucleotide polymorphisms (SNPs) were detected in the wPbf genes for the A, B, and D genomes, respectively. Physical and genetic mapping utilizing some of the SNPs identified confirmed that wPbf genes are located close to the centromeres on the homoeologous group 5 chromosomes. The low level of allelic diversity found in wPbf genes may suggest that these genes play a key role and are thus constrained by selection.

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
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Albani D, Hammond-Kosack MCU, Smith C, Conlan S, Colot V, Holdsworth M, Bevan MW (1997) The wheat transcriptional activator SPA: a seed-specific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes. Plant Cell 9:171–184

    Article  PubMed  CAS  Google Scholar 

  • Boisson M, Mondon K, Torney V, Nicot N, Laine AL, Bahrman N, Gouy A, Daniel-Vedele F, Hirel B, Sourdille P, Dardevet M, Ravel C, Le Gouis J (2005) Partial sequences of nitrogen metabolism genes in hexaploid wheat. Theor Appl Genet 110:932–940

    Article  PubMed  CAS  Google Scholar 

  • Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936

    Article  PubMed  Google Scholar 

  • Branlard G, Dardevet M. (1985) Diversity of grain protein and bread wheat quality. II. Correlation between high molecular weigh subunits of glutenin and flour quality characteristics. J Cereal Sci 3:345–354

    Article  CAS  Google Scholar 

  • Branlard G, Dardevet M, Saccomano R, Lagoutte F, Gourdon J (2001) Genetic diversity of wheat storage proteins and bread wheat quality. Euphytica 119:59–67

    Article  CAS  Google Scholar 

  • Cadalen T, Boeuf C, Bernard S, Bernard M (1997) An intervarietal molecular marker map in Triticum aestivum L. em. Thell. and comparison with a map from a wide cross. Theor Appl Genet 94:367–377

    Article  CAS  Google Scholar 

  • Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie, K Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22:231–238

    Article  PubMed  CAS  Google Scholar 

  • Chalhoub B, Allouis S, Safar J, Janda J, Bellec A, Sarda X, Arar C, Lefèvre A, Rouault P, Pateyron S, Dupin A, Burgio G, Georget C, Sourdille P, Faivre-Rampant P, Caboche M, Moore G, Bernard M, Dolezel J (2003) Towards precise analysis of the wheat genome: preparation of genomic resources for structural and functional characterisation. In: Pogna NE, Romanò M, Pogna EA, Galterio G (eds) The proceedings of the Xth international wheat genetics symposium. Istituto Sperimentale per la Cerealicoltura, Paestum, pp 229–233

    Google Scholar 

  • Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD (1989) RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor Appl Genet 78:495–504

    Article  CAS  Google Scholar 

  • Colot V, Bartels D, Thompson R, Flavell R (1989) Molecular characterization of an active wheat LMW glutenin gene and its relation to other wheat and barley prolamin genes. Mol Gen Genet 216:81–90

    Article  PubMed  CAS  Google Scholar 

  • Conlan RS, Hammond-Kosack M, Bevan M (1999) Transcription activation mediated by the bZIP factor SPA on the endosperm box is modulated by ESBF-1 in vitro. Plant J 19:173–181

    Article  PubMed  CAS  Google Scholar 

  • DePaolis A, Sabatini S, DePascalis L, Costantino P, Capone I (1996) A rolB regulatory factor belongs to a new class of single zinc finger plant proteins. Plant J 10:215–223

    Article  PubMed  CAS  Google Scholar 

  • Deyholos MK, Sieburth LE (2000) Separable whorl-specific expression and negative regulation by enhancer elements within the AGAMOUS second intron. Plant Cell 12:1799–1810

    Article  PubMed  CAS  Google Scholar 

  • Diaz I, Vicente-Carbajosa J, Abraham Z, Martinez M, Isabel-La Moneda I, Carbonero P (2002) The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. Plant J 29:453–464

    Article  PubMed  CAS  Google Scholar 

  • Dupont FM, Hurkman WJ, Vensel WH, Tanaka C, Kothari KM, Chung OK, Altenbach SB (2005) Protein accumulation and composition in wheat grains: effects of mineral nutrients and high temperature. Eur J Agron (in press)

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307

    CAS  Google Scholar 

  • Groos C, Gay G, Perretant MR, Gervais L, Bernard M, Dedryver F, Charmet G (2002) Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white X red grain bread wheat cross. Theor Appl Genet 104:39–47

    Article  PubMed  CAS  Google Scholar 

  • Guyomarc’h H, Sourdille P, Charmet G, Edwards K, Bernard M (2002a) Characterisation of polymorphic microsatellite markers from Aegilops tauschii and transferability to the D-genome of bread wheat. Theor Appl Genet 104:1164–1172

    Article  PubMed  CAS  Google Scholar 

  • Guyomarc’h H, Sourdille P, Edwards K, Bernard M (2002b) Studies of the transferability of microsatellites derived from Triticum tauschii to hexaploid wheat and to diploid related species using amplification, hybridization and sequence comparisons. Theor Appl Genet 105:736–744

    Article  PubMed  CAS  Google Scholar 

  • Hammond-Kosack MCU, Holdsworth MJ, Bevan MW (1993) In vivo footprinting of a low molecular weight glutenin gene (LMWG-1D1) in wheat endosperm. EMBO J 12:545–554

    PubMed  CAS  Google Scholar 

  • Isidore E, Scherrer B, Chalhoub B, Feuillet C, Keller B (2005) Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res 15:526–536

    Article  PubMed  CAS  Google Scholar 

  • Izawa T, Foster R, Nakajima M, Shimamoto K, Chua NH (1994) The rice bZIP transcriptional activator RITA-1 is highly expressed during seed development. Plant Cell 6:1277–1287

    Article  PubMed  CAS  Google Scholar 

  • Kisu Y, Ono T, Shimofurutani N, Suzuki M, Esaka M. (1998) Characterization and expression of a new class of zinc finger protein that binds to silencer region of ascorbate oxidase gene. Plant Cell Physiol 39:1054–1064

    PubMed  CAS  Google Scholar 

  • Kosambi DD (1944) The estimations of map distance from recombination value. Ann Eugeni 12:172–175

    Google Scholar 

  • Lander ES, Gene P, Abrahanson J, Barlow A, Daly MJ, Lincoln SE, Newbur L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Landry J (2002) A linear model for quantitating the accumulation of zeins and their fractions (α+δ, β&γ) in developing endosperm of wild-type and mutant maizes. Plant Sci 163:111–115

    Article  CAS  Google Scholar 

  • Mena M, Vicente-Carbajosa J, Schmidt RJ, Carbonero P (1998) An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native b-hordein promoter in barley endosperm. Plant J 16:53–62

    Article  PubMed  CAS  Google Scholar 

  • Mena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P (2002) A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol 130:111–119

    Article  PubMed  CAS  Google Scholar 

  • Metakovsky EV, Félix I, Branlard G (1997) Association between dough quality (W value) and certain gliadin alleles in French common wheat cultivars. J Cereal Sci 26:371–373

    Article  CAS  Google Scholar 

  • Morimoto R, Kosugi T, Nakamura C, Takumi S (2005) Intragenic diversity and functional conservation of the three homoeologous loci of the KN1-type homeobox gene Wknox1 in common wheat. Plant Mol Biol 57:907–924

    Article  PubMed  CAS  Google Scholar 

  • Murai J, Taira T, Ohta D (1999) Isolation and characterization of the three Waxy genes encoding the granule-bound starch synthase in hexaploid wheat. Gene 24:71–79

    Article  Google Scholar 

  • Nelson JC, Van Deynze AE, Sorrells ME, Lu YH, Atkinson M, Bernard M, Leroy P, Faris J, Anderson JA (1995) Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5 and 7. Genetics 141:721–731

    PubMed  CAS  Google Scholar 

  • Norre F, Peyrot C, Garcia C, Rancé I, Drevet J, Theisen M, Gruber V (2002) Powerful effect of an atypical bifactorial endosperm box from wheat HMWG-Dx5 promoter in maize endosperm. Plant Mol Biol 50:699–712

    Article  PubMed  CAS  Google Scholar 

  • Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F (2001) A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif. J Biol Chem 27:14139–14152

    Google Scholar 

  • Payne PI (1987) Genetics of wheat storage proteins and the effect of allelic variation on bread making quality. Annu Rev Plant Physiol 38:141–153

    Article  CAS  Google Scholar 

  • Pirovano L, Lanzini S, Hartings H, Lazzaroni N, Rossi V, Joshi R, Thompson RD, Salamini F, Motto M (1994) Structural and functional-analysis of an Opaque2-related gene from sorghum. Plant Mol Biol 24:515–523

    Article  PubMed  CAS  Google Scholar 

  • Plesch G, Ehrhardt T, Mueller-Roeber B (2001) Involvement of TAAAG elements suggests a role for DOF transcription factors in guard cell-specific gene expression. Plant J 28:455–464

    Article  PubMed  CAS  Google Scholar 

  • Purugganan MD (2000) The molecular population genetics of regulatory genes. Mol Ecol 9:1451–1461

    Article  PubMed  CAS  Google Scholar 

  • Quarrie SA, Steed AA, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusié D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa P, Sanguineti MC, Hollington PA, Aragués R, Royo A, Dodig D (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet 110:865–880

    Article  PubMed  CAS  Google Scholar 

  • Ravel C, Praud S, Canaguier A, Dufour P, Giancola S, Balfourier F, Chalhoub B, Brunel D, Linossier L, Dardevet M, Beckert M, Rousset M, Murigneux A, Charmet G (2004) DNA sequence polymorphism and their application in bread wheat. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation for plant breeding. EUCARPIA, Tulln, pp 177–181

    Google Scholar 

  • Ravel C, Praud S, Murigneux A, Linossier L, Dardevet M, Balfourier F, Dufour P, Brunel D, Charmet G (2005) An association study to discriminate candidate genes in bread wheat (Triticum aestivum). Theor Appl Genet http://dx.doi.org/10.1007/s00122-005-0178-x

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Rychlik W and Rhoads RE (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 17:8543–8551

    Article  PubMed  CAS  Google Scholar 

  • Santi L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C, Muller K, Muller J, Rohde W, Salamini F (2003) The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J 34:813–826

    Article  PubMed  CAS  Google Scholar 

  • Sauer S, Lechner D, Berlin K, Plancon C, Heuermann A, Lehrach H, Gut IG (2000) Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 28:E100

    Article  PubMed  CAS  Google Scholar 

  • Schmidt RJ, Ketudat M, Aukerman M, Hoschek G (1992) OPAQUE-2 is a transcriptional activator that recognizes a specific target site in 22 kD-zein genes. Plant Cell 4:689–700

    Article  PubMed  CAS  Google Scholar 

  • Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R and. Lewis KR (eds) Chromosome manipulations and plant genetics. Olivier and Boyd, Edinburgh, pp 29–45

    Google Scholar 

  • Sourdille P, Cadalen T, Guyomarc’h H, Snape JW, Perretant MR, Charmet G, Boeuf C, Bernard S, Bernard M (2003) An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat. Theor Appl Genet 108:530–538

    Google Scholar 

  • Staden R, Beal KF, Bonfield JK (2000) The Saden package, 1998. Methods Mol Biol 132:115–130

    PubMed  CAS  Google Scholar 

  • Suzuki A, Wu CY, Washida H, Takaiwa F (1998) Rice MYB protein OSMYB5 specifically binds to the AACA motif conserved among promoters of genes for storage protein glutelin. Plant Cell Physiol 39:555–559

    PubMed  CAS  Google Scholar 

  • Takaiwa F, Yamanouchi U, Yoshihara T, Washida H, Tanabe F, Kato A, Yamada K (1996) Characterization of common cis-regulatory elements responsible for the endosperm-specific expression of members of the rice glutelin multigene family. Plant Mol Biol 30:1207–1221

    Article  PubMed  CAS  Google Scholar 

  • Vettore AL, Yunes J A, Cord Neto G, da Silva MJ, Arruda, P, Leite A (1998) The molecular and functional characterization of an Opaque2 homoeologue gene from Coix and a new classification of plant bZIP proteins. Plant Mol Biol 36:249–263

    Article  PubMed  CAS  Google Scholar 

  • Vicente-Carbajosa J, Moose SP, Parsons RL, Schmidt RJ (1997) A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2. Proc Natl Acad Sci U S A 94:7685–7690

    Article  PubMed  CAS  Google Scholar 

  • Vicente-Carbajosa J, Onate L, Lara P, Diaz I, Carbonero P (1998) Barley BLZ1: a bZIP transcriptional activator that interacts with endosperm-specific gene promoters. Plant J 13:629–640

    Article  PubMed  CAS  Google Scholar 

  • Washio K (2001) Identification of DOF proteins with implication in the gibberellin-regulated expression of a peptidase gene following the germination of rice grains. Biochim Biophys Acta 1520:54–62

    PubMed  CAS  Google Scholar 

  • Yanagisawa S (1995) A novel DNA binding domain that may form a single zinc finger motif. Nucleic Acids Res 23:3403–3410

    Article  PubMed  CAS  Google Scholar 

  • Yanagisawa S (2000) DOF1 and DOF2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant J 21:281–288

    Article  PubMed  CAS  Google Scholar 

  • Yanagisawa S (2001) The transcriptional activation domain of the plant-specific Dof1 factor functions in plant, animal, and yeast cells. Plant Cell Physiol 42:813–822

    Article  PubMed  CAS  Google Scholar 

  • Yanagisawa S (2002) The DOF family of plant transcription factors. Trends Plant Sci 7:555–560

    Article  PubMed  CAS  Google Scholar 

  • Zhang B, Chen W, Foley RC, Buttner M, Singh KB (1995) Interactions between distinct types of DNA binding proteins enhance binding to ocs element promoter sequences Plant Cell

Download references

Acknowledgement

The authors wish to thank M. R. Perretant for genetic mapping. This research was funded by the French-German federative genomic program GabiGénoplante.

Author information

Authors and Affiliations

  1. Institu National de la Recherche Agronomique (INRA), UMR1095, Amélioration et Santé des Plantes, 234 avenue du Brezet, Clermont-Ferrand, 63039, France

    Catherine Ravel, Ila J. Nagy, Pierre Sourdille, Mireille Dardevet, François Balfourier, Caroline Pont & Gilles Charmet

  2. Campus des Cézeaux, Université Blaise Pascal, UMR1095, Aubière, 63170, France

    Catherine Ravel, Ila J. Nagy, Pierre Sourdille, François Balfourier, Caroline Pont & Gilles Charmet

  3. Institu National de la Recherche Agronomique (INRA), Unité de Recherche Agronomie, 234 avenue du Brézet, Clermont-Ferrand, 63100, France

    Pierre Martre

  4. Institu National de la Recherche Agronomique (INRA), Centre National de Génotypage, CP5708, Evry, 91057, France

    Sandra Giancola

  5. Biogemma, Les Cézeaux, Aubière, 63170, France

    Sébastien Praud

  6. Agricultural Research Institute, Brunszvik u. 2, Martonvasar, 2462, Hungary

    Ila J. Nagy

Authors
  1. Catherine Ravel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ila J. Nagy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pierre Martre
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pierre Sourdille
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mireille Dardevet
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. François Balfourier
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Caroline Pont
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sandra Giancola
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sébastien Praud
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Gilles Charmet
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Catherine Ravel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ravel, C., Nagy, I.J., Martre, P. et al. Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor. Funct Integr Genomics 6, 310–321 (2006). https://doi.org/10.1007/s10142-006-0022-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10142-006-0022-7

Keywords

Search

Navigation