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

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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.

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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.

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Author notes

  1. Ottó Törjék

    Present address: KWS SAAT AG, Grimsehlstrasse 31, 37555, Einbeck, Germany

Authors and Affiliations

  1. Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary

    András Cseri, Mátyás Cserháti, Bettina Nagy, Gábor V. Horváth, Dénes Dudits & Ottó Törjék

  2. Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany

    Maria von Korff

  3. Cereal Research Non-Profit Company, Alsó kikötő sor 9, Szeged, 6726, Hungary

    András Palágyi & János Pauk

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  1. András Cseri
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  2. Mátyás Cserháti
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  3. Maria von Korff
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  4. Bettina Nagy
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Correspondence to András Cseri.

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András Cseri and Mátyás Cserháti are contributed equally to this work.

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Cseri, A., Cserháti, M., von Korff, M. et al. Allele mining and haplotype discovery in barley candidate genes for drought tolerance. Euphytica 181, 341–356 (2011). https://doi.org/10.1007/s10681-011-0445-7

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