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Euphytica

, 181:341 | Cite as

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

  • András CseriEmail author
  • Mátyás Cserháti
  • Maria von Korff
  • Bettina Nagy
  • Gábor V. Horváth
  • András Palágyi
  • János Pauk
  • Dénes Dudits
  • Ottó Törjék
Article

Abstract

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.

Keywords

Allele mining EcoTILLING Drought tolerance Candidate genes Barley 

Notes

Acknowledgments

This work was funded by the OMFB (Országos Műszaki Fejlesztési Bizottság) 445733—00514/2007 NAP BIO and OTKA (Országos Tudományos Kutatási Alapprogramok) 72366. We are grateful to Krisztina G. Talpas for excellent technical assistance. We also thank Ernő Homolya and Gábor Németh for help in the initialization of the website. We thank Georg Strompen (University of Potsdam, Germany) for Cel1 aliquots.

Conflict of interest

None.

Supplementary material

10681_2011_445_MOESM1_ESM.pdf (86 kb)
Supplementary material 1 (PDF 85 kb)
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Supplementary material 2 (PDF 309 kb)
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Supplementary material 3 (PDF 30 kb)
10681_2011_445_MOESM4_ESM.pdf (53 kb)
Supplementary material 4 (PDF 53 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • András Cseri
    • 1
    Email author
  • Mátyás Cserháti
    • 1
  • Maria von Korff
    • 2
  • Bettina Nagy
    • 1
  • Gábor V. Horváth
    • 1
  • András Palágyi
    • 3
  • János Pauk
    • 3
  • Dénes Dudits
    • 1
  • Ottó Törjék
    • 1
    • 4
  1. 1.Institute of Plant Biology, Biological Research CenterHungarian Academy of SciencesSzegedHungary
  2. 2.Max Planck Institute for Plant Breeding ResearchKölnGermany
  3. 3.Cereal Research Non-Profit CompanySzegedHungary
  4. 4.KWS SAAT AGEinbeckGermany

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