Phenotypic Variation for Diastatic Power, b-Amylase Activity, and b-Amylase Thermostability vs. Allelic Variation at the Bmy1 Locus in a Sample of North American Barley Germplasm

Malting quality data were collected on malts from three barley (Hordeum vulgare L.) breeding program trials. We tried to identify causal polymorphisms in the Bmy1 intron III and coding regions for use in marker-assisted selection. Abundant malting quality variation exists in the spring barley germplasm despite the parents having identical Bmy1 intron III and coding regions. After complete Bmy1 sequencing, no polymorphisms associated with malting quality phenotypes, indicating the genetic basis for the observed variation resides outside Bmy1. Complete allele sequencing identified one winter barley parent that had a novel Bmy1 allele (Sd1a) based on amino acid substitutions that are candidates as causative agents for the phenotypic variation. Marker-assisted selection against the Sd1a allele could be effective in improving diastatic power (DP). The Sd1a allele is associated with low DP and is present in only three of the 51 lines, presumably due to preceding generations being selected for high DP. Selection for DP has subsequently eliminated the Sd1a allele from this breeding program. This research shows the importance of having complete allele sequences and knowledge of functional polymorphisms in target genes before using marker-assisted selection.