Allele mining and haplotype discovery in barley candidate genes for drought tolerance Andra ´s Cseri • Ma ´tya ´s Cserha ´ti • Maria von Korff • Bettina Nagy • Ga ´bor V. Horva ´th • Andra ´s Pala ´gyi • Ja ´nos Pauk • De ´nes Dudits • Otto ´ To ¨rje ´k Received: 17 January 2011 / Accepted: 26 April 2011 / Published online: 7 May 2011 Ó Springer Science+Business Media B.V. 2011 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 EcoTILL- ING, 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 inte- grated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound infor- mation 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 Á EcoTILLING Á Drought tolerance Á Candidate genes Á Barley Introduction Drought is one of the main factors limiting yield in cereals. Plants respond to drought by altering the Andra ´s Cseri and Ma ´tya ´s Cserha ´ti are contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s10681-011-0445-7) contains supplementary material, which is available to authorized users. A. Cseri (&) Á M. Cserha ´ti Á B. Nagy Á G. V. Horva ´th Á D. Dudits Á O. To ¨rje ´k Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Temesva ´ri krt. 62, Szeged 6726, Hungary e-mail: cseria@brc.hu M. von Korff Max Planck Institute for Plant Breeding Research, Carl-von-Linne ´-Weg 10, 50829 Ko ¨ln, Germany A. Pala ´gyi Á J. Pauk Cereal Research Non-Profit Company, Also ´ kiko ¨t} o sor 9, Szeged 6726, Hungary Present Address: O. To ¨rje ´k KWS SAAT AG, Grimsehlstrasse 31, 37555 Einbeck, Germany 123 Euphytica (2011) 181:341–356 DOI 10.1007/s10681-011-0445-7