Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley

Amylases play an essential role in the germination and malting process. Therefore, these genes are interesting candidates for marker development in order to improve malting quality as an important breeding aim. The intervarietal diversity of the alpha-amylase gene amy1 mapping to chromosome 6H was investigated. A total of six single nucleotide polymorphisms ( SNPs) were detected which defined four haplotypes. Associations between SNP-markers and important malting parameters were discovered in a collection of 117 European spring and winter barley cultivars, representing the current commercial germplasm. Haplotype amy1_H2 was significantly associated with a number of malting related traits and explained 19% of the phenotypic variation of the malting quality index (MQI) for all varieties and 35% in a subset of 72 winter barleys. The diagnostic SNP3 was associated with a 45% difference in the MQI. Within the spring barleys, the average value of haplotype amy1_H1 for friability was significantly higher than that of amy1_H4. All discovered SNPs were converted into high-throughput markers for pyrosequencing and can be used for marker assisted selection.