Naked barley (Hordeum vulgare L.) grain threshes freely from its hull during harvesting and cleaning. Much of the available naked barley germplasm is unadapted to U.S. barley growing regions, and few genotypes have been selected to thrive under organic systems. The goal of this research was to characterize a set of spring naked barley genotypes for agronomic traits in the northern United States under organic conditions and estimate the degree of genotype × environment interaction (GEI). To achieve this goal, a multienvironment trial was conducted over 3 yr. Experiments were grown under organic conditions where traits including grain yield, test weight, plant height, heading date, and threshability were evaluated. Contributions of environment, genotype, and GEI to the phenotypic variance were calculated. In the tested germplasm, test weight, plant height, heading date, and threshability were found to have higher variance attributed to genotypic effects compared to GEI. Grain yield variance attributed to GEI was five times greater than that of genotype alone. Genotype + GEI (GGE) and location‐grouping (LG) biplots showed two sets of environments where naked barley genotypes performed similarly. Sensitivity analysis by Finlay–Wilkinson regression found that grain yield was highly sensitive to changes in environment mean yield. These results show that selection for grain yield should be conducted within mega‐environments to leverage GEI patterns. Heading date, plant height, test weight, and threshability can be selected across mega‐environments.

This study aimed to understand how genetics and environment influence organic winter naked barley composition and functionality, and to identify traits that might effectively categorize basic physicochemical functionality of food barley. Across three years, two locations, and 15 genotypes, genotype significantly influenced all 10 food-related traits and was the dominant influence for three. Location significantly influenced eight traits and was dominant for three. Year significantly influenced all traits but was dominant only for one. Of the interactions location * year was the most influential and was the dominant effect for two traits. For all interaction terms where genotype was a component, the effect sizes were either small or non-significant suggesting that even with low leverage traits there is the potential for genetic gain by observing trait rankings across environments. Principal component analysis identified six traits that could serve to categorize basic physicochemical functionality of food barley. These were grain protein content, beta-glucan content, flour-water batter flow, water solvent retention capacity, time to peak viscosity of cooked flour, and hardness of cooked intact grains.

Prediction of trait values in plant breeding populations typically relies on assumptions about marker effect homogeneity across populations. Evidence is presented for winter malting barley (Hordeum vulgare L.) germination traits that a single, causative, largeeffect gene in the Seed dormancy 1 region on Chromosome 5H, HvAlaAT1 (Qsd1), leads to heterogeneous estimated marker effects genome wide between groups of otherwise related individuals carrying different Qsd1 alleles. This led to reduced prediction accuracy across alleles when a model was trained either on individuals carrying both alleles or one allele. Several genomic prediction models were tested to increase prediction accuracy within the Qsd1 allele groups. Small gains (5-12%) in prediction accuracy were realized using structured genomic best linear unbiased predictor models when information about the Qsd1 allele was used to stratify the population. We concluded that a single large-effect locus can lead to heterogeneous marker effects in the same breeding family. Variance partitioning based on largeeffect loci can be used to inform best practices in designing genomic prediction models; however, there are likely few cases for which it may be practical to do this.For malting barley, if germination traits are highly associated with malting quality traits, then similar steps should be considered for malting quality trait prediction.

No abstract

Expansion of malting barley production into non-traditional growing regions and erratic weather has increased the demand for preharvest sprouting (PHS) resistant, high quality malting barley cultivars. This is hindered by the relatively unknown relationships between PHS resistance and malting quality. Here we present a three-year study of malting quality and germination at different after-ripening durations post physiological maturity. Malting quality traits alpha amylase (AA) and free amino nitrogen (FAN) and germination rate at six days post PM shared a common association with a SNP in HvMKK3 on chromosome 5H in the Seed Dormancy 2 (SD2) region responsible for PHS susceptibility. Soluble protein (SP) and soluble over total protein (S/T) both shared a common association with a marker in the SD2 region, but the most significant association was not well correlated with the causative mutation in HvMKK3. Significant genetic correlations between PHS resistance and the malting quality traits AA, FAN, SP, S/T were detected across and within HvMKK3 allele groups. High adjunct malt quality was related to PHS susceptibility. Selection for PHS resistance led to a correlated response in malting quality traits. Results strongly suggest pleiotropy of HvMKK3 on malting quality traits and that the classic “Canadian-style” malt is caused by a PHS susceptible allele of HvMKK3. PHS susceptibility appears to benefit the production of malt intended for adjunct brewing, while PHS resistance is compatible with all-malt brewing specifications. Correlations of germination rate to malting quality traits indicate its potential for use as a secondary trait in selection.