Stability of genome-wide QTL effects on malt α-amylase activity in a barley doubled-haploid population

Abstract

Pre-harvest sprouting (PHS) can be a problem in malting barley (Hordeum vulgare L.) production as it results in lower yield and reduced grade. The presence of PHS is often associated with increased activity of α-amylase, a key enzyme for breakdown of starch into simple sugars. It is difficult to measure α-amylase activity (AA) associated with PHS however, and the same quantitative trait loci (QTL) may be responsible for both PHS AA and malt AA. The objective of this paper was to investigate co-occurrence and stability of QTL controlling malt AA in a barley doubled-haploid (DH) population that was evaluated in eight environments across North America. This population consisted of 150 DH lines developed from a cross between two barley varieties (Steptoe × Morex) for the North American Barley Genome Mapping Project. Malt AA was measured on a composite 400 g sample of each DH line and parent. There were a total of 223 restriction fragment length polymorphism markers covering a total genetic distance of 1221.9 cM across the entire genome. We used an empirical Bayesian method for detecting single QTLs and epistatic QTLs for individual environments. A common QTL was counted if it co-occurred in a pair of environments. Thus, the level of QTL × environment interaction was assessed based on the total frequency of co-occurred QTLs for all possible pairs of eight environments [(8 × 7)/2 = 28]. Heritability estimates (0.62–0.89) for individual environments were moderate to high. Genetic correlations between co-occurred additive and epistatic effects are essentially zero for most environment pairs. These results indicated strong QTL × environment interaction for malt AA. While the efficacy of genome-wide selection for PHS is still unknown especially in the presence of QTL × environment interaction, using the Bayesian approach may help us better understand appropriate methods for measuring and selecting for this trait.