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

András Cseri, Mátyás Cserháti, Maria von Korff, Bettina Nagy, Gábor V. Horváth, András Palágyi, János Pauk, Dénes Dudits, Ottó Törjék

Research output: Contribution to journalArticle

14 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)341-356
Number of pages16
Issue number3
Publication statusPublished - Oct 1 2011


  • Allele mining
  • Barley
  • Candidate genes
  • Drought tolerance

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science
  • Horticulture

Fingerprint Dive into the research topics of 'Allele mining and haplotype discovery in barley candidate genes for drought tolerance'. Together they form a unique fingerprint.

  • Cite this