Skip to main content
SpringerLink
Log in

Novel haplotype description and structural background of the eventual functional significance of the barley β-amylase gene intron III rearrangements

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

To extend the knowledge on the haplotype variability of the Bmy1 gene, region of the intron III was sequenced in a set of 20 Latvian accessions and Danish variety Maja, the data were compared to the previously reported allelic variants of the structural gene. Taking into account the polymorphisms of 59 loci and the microsatellite (MS) motif, 11 Latvian varieties turned out to have haplotype similar to cultivar Adorra, 1 – to Haruna Nijo, and 8 – to the newly described Abava Bmy1 intron III haplotype. High level of polymorphisms of (TG) m as well as (G) n component of MS was revealed for all the haplotypes studied. We conclude that the MS motif rather than the MS size length polymorphism correlates with mutations in the coding region of the β-amylase gene. Five graphical haplotype-specific intron III structures were constructed on the basis of the co-localization of the transcription factor binding sites (TFBSs), remnants of the transposable elements, and intron III polymorphic loci. Inter- and intrahaplotype variability was analyzed on the eventual functional significance of the Bmy1 intron III rearrangements. Novel data on the intron III nucleotide sequences of the Bmy1 gene were deposited in the GenBank (http://www.ncbi.nlm.nih.gov/) under accession numbers DQ316895–DQ316905.

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

  • Eglinton JK, Langridge P, Evans DE (1998) Thermostability variation in alleles of barley β-amylase. J Cereal Sci 28:301–309

    Article  CAS  Google Scholar 

  • Erkkilä MJ, Ahokas H (2001) Special barley β-amylase allele in a Finnish landrace line HA52 with high grain enzyme activity. Hereditas 134:91–95

    Article  PubMed  Google Scholar 

  • Erkkilä MJ, Leah R, Ahokas H, Cameron-Mills V (1998) Allele-dependent barley grain β-amylase activity. Plant Physiol 117:679–685

    Article  PubMed  Google Scholar 

  • Fiume E, Christou P, Giani S, Beviarion D (2004) Introns are key regulatory elements of rice tubulin expression. Planta 218:693–703

    Article  PubMed  CAS  Google Scholar 

  • Fu D, Szücs P, Yan L, Helguera M, Skinner JS, von Zitzewitz J, Hayes PM, Dubkovskii J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics 273:54–65

    Article  PubMed  CAS  Google Scholar 

  • Gazzani S, Gendali AR, Lister C, Dean C (2003) Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol 132:1107–1114

    Article  PubMed  CAS  Google Scholar 

  • Gomez-Cadenas A, Zentella R, Walker-Simmons MK, Ho T-HD (2001) Gibberellin/abscisic acid antagonism in barley aleurone cells: site of action of the protein kinase PKABA1 in relation to gibberellin signaling molecules. Plant Cell 13:667–679

    Article  PubMed  CAS  Google Scholar 

  • Gubler F, Kalla R, Roberts JK, Jacobsen JV (1995) Giberellin-regulated expression of myb gene in barley aleurone cells: evidence for Myb transactivation of a high-pI alpha-amylase gene promoter. Plant Cell 7:1879–1891

    Article  PubMed  CAS  Google Scholar 

  • Kaneko T, Kihara M, Ito K (2000) Genetic analysis of β-amylase thermostability to develop a DNA marker for malt fermentability improvement in barley, Hordeum vulgare. Plant Breed 119:197–201

    Article  CAS  Google Scholar 

  • Kapranov P, Routt SM, Bankaitis VA, de Bruiji FJ, Szczyglowski K (2001) Nodule-specific regulation of phosphatidylinositol transfer protein expression in Lotus japonicus. Plant Cell 13:1369–1382

    Article  PubMed  CAS  Google Scholar 

  • Kreis M, Williamson M, Buxton B, Pywell J, Heigaard J, Svendsen I (1987) Primary structure and differential expression of β-amylase in normal and mutant barleys. Eur J Biochem 169:517–525

    Article  PubMed  CAS  Google Scholar 

  • Lewin B (2004) Genes VIII. Pearson, Prentice Hall

  • Lu CA, Ho T-HD, Ho S-L, Yu S-M (2002) Three novel MYB proteins with one DNA binding repeat mediate sugar and hormone regulation of α-amylase gene expression. Plant Cell 14:1963–1980

    Article  PubMed  CAS  Google Scholar 

  • Ma YF, Evans DE, Logue SJ, Langridge P (2001) Mutations of barley β-amylase that improve substrate-binding affinity and thermostability. Mol Genet Genomics 266:345–352

    Article  PubMed  CAS  Google Scholar 

  • Malisheva L, Ganal MW, Röder MS (2004) Evaluation of cultivated barley (Hordeum vulgare L.) germplasm for the presence of thermostable alleles of β-amylase. Plant Breed 123:128–131

    Article  Google Scholar 

  • Michaels SD, He Y, Scortecci KC, Amasino RM (2003) Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behaviour in Arabidopsis. Proc Natl Acad Sci USA 100:10102–10107

    Article  PubMed  CAS  Google Scholar 

  • Paris M, Jones MGK, Eglinton JK (2002) Genotyping single nucleotide polymorphisms for selection of barley β-amylase alleles. Plant Mol Biol Rep 20:149–159

    CAS  Google Scholar 

  • Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using MS markers. Theor Appl Genet 91:1001–1007

    Article  CAS  Google Scholar 

  • Polakova K, Laurie D, Vaculova K, Ovesna J (2003) Characterization of β-amylase alleles in 79 barley varieties with pyrosequencing. Plant Mol Biol Rep 21:439–447

    CAS  Google Scholar 

  • Sheldon CC, Conn AB, Dennis ES, Peacock WJ (2002) Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression. Plant Cell 14:2527–2537

    Article  PubMed  CAS  Google Scholar 

  • Sjakste T, Röder M (2004) Distribution and inheritance of beta-amylase alleles in North European barley varieties. Hereditas 141:39–45

    Article  PubMed  Google Scholar 

  • Sjakste TG, Rashal I, Röder MS (2003) Inheritance of microsatellite alleles in pedigrees of Latvian barley varieties and related European ancestors. Theor Appl Genet 106:539–549

    PubMed  CAS  Google Scholar 

  • Van Wormhoudt A, Sellos D (2003) Highly variable polymorphism of the alpha-amylase gene family in Litopenaeus vannamei (Crustacea Decapoda). J Mol Evol 57:659–761

    Article  PubMed  CAS  Google Scholar 

  • Wang HY, Lee MM, Schiefelbein JW (2002) Regulation of the cell expansion gene RHD3 during Arabidopsis development. Plant Physiol 129:638–649

    Article  PubMed  CAS  Google Scholar 

  • Wullmout RL, Rushton PJ, Hooley R, Lazarus CM (1998) DNAase I footprints suggest the involvement of at least three types of transcription factors in the regulation of α-Amy2/A by gibberellin. Plant Mol Biol 38:817–825

    Article  Google Scholar 

  • Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Jia Q (2006) The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107–124

    Article  PubMed  CAS  Google Scholar 

  • Yoshigi N, Okada Y, Sahara H, Tamaki T (1995) A structural gene encoding β-amylase of barley. Biosci Biotechnol Biochem 10:1991–1993

    Article  Google Scholar 

  • Yutzey KE, Kline RL, Konieczny SF (1989) An internal regulatory element controls troponin I gene expression. Mol Cell Biol 9:1397–1405

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The study was supported by a grant from the Latvian Council of Sciences. Sequencing was performed by the Sequencing Service of the Biomedical Research Centre (Riga). We thank M. Bleidere for explanations on the malting quality of Latvian barley varieties and N. Sjakste for helpful discussion of the manuscript.

Author information

Authors and Affiliations

  1. Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera Str. 3, Salaspils, 2169, Latvia

    T. G. Sjakste & A. F. Zhuk

Authors
  1. T. G. Sjakste
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. F. Zhuk
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T. G. Sjakste.

Additional information

Communicated by F. Ordon

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sjakste, T.G., Zhuk, A.F. Novel haplotype description and structural background of the eventual functional significance of the barley β-amylase gene intron III rearrangements. Theor Appl Genet 113, 1063–1079 (2006). https://doi.org/10.1007/s00122-006-0366-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-006-0366-3

Keywords

Search

Navigation