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Background  Flavonoids are an important class of secondary compounds in angiosperms. Next to certain biological functions in plants, they play a role in the brewing process and have an effect on taste, color and aroma of beer. The aim of this study was to reveal the haplotype diversity of candidate genes involved in the phenylpropanoid biosynthesis pathway in cultivated barley varieties ( Hordeum vulgare  L.) and to determine associations to kernel and malting quality parameters.    Results  Five genes encoding phenylalanine ammonia-lyase ( PAL ), cinnamate 4-hydroxylase ( C4H ), chalcone synthase ( CHS ), flavanone 3-hydroxylase ( F3H ) and dihydroflavonol reductase ( DFR ) of the phenylpropanoid biosynthesis pathway were partially resequenced in 16 diverse barley reference genotypes. Their localization in the barley genome, their genetic structure, and their genetic variation e.g. single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel) patterns were revealed. In total, 130 SNPs and seven InDels were detected. Of these, 21 polymorphisms were converted into high-throughput pyrosequencing markers. The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters.    Conclusions  SNP patterns were found to be highly variable for the investigated genes. The developed high-throughput markers are applicable for assessing the genetic variability and for the determination of haplotype patterns in a set of barley accessions. The candidate genes  PAL ,  C4H  and  F3H  were shown to be associated to several malting properties like glassiness ( PAL ), viscosity ( C4H ) or to final attenuation ( F3H ).

Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley