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 α-amylase gene amy1 mapping to chromosome 6H was investigated.
In the investigated part of the amy1 gene, four SNPs were detected in the last exon comprising two silent mutations and two amino acid exchanges, followed by the 3UTR with two additional SNPs 1 bp apart from each other. The second SNP led to an asparagine-serine exchange after translation at amino-acid position 372. The non-synonymous mutation of the fourth SNP causes an alanine-glycine exchange at amino-acid position 410. All six SNPs could be converted into high-throughput-markers. By genotyping 326 barley varieties consisting of 153 spring and 173 winter forms with all six developed pyrosequencing markers four different haplotypes were detected and termed amy1_H1 to amy1_H4.
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 for all varieties and 35% in a subset of 72 winter barleys. The diagnostic SNP3 was associated with a 45% difference in the malting quality index. 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. Here we present the haplotype-analysis of 326 barley varieties.