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Threshability, defined here as the propensity of grains to lose their hull after harvest, is a key trait in naked barley (Hordeum vulgare L.). While threshability is a defining characteristic of naked grains and has been found to be associated with grain size and shape, its genetic architecture is poorly described. The goals of this study were to identify quantitative trait loci associated with threshability and evaluate their utility as covariates in genomic prediction models. A genome‐wide association study identified two loci on chromosomes 2H and 3H associated with threshability. The locus on chromosome 2H accounted for 9.9% of the phenotypic variance explained (PVE). The locus on chromosomes 3H accounted for 7.8% of the PVE. With effects on threshability of 0.18 and 0.29 for each marker, respectively, these markers could have a limited impact when implemented in marker‐assisted selection. Predictive ability for threshability was 0.842 using a structured genomic best linear unbiased prediction model. Incorporation of the markers with significant associations as covariates in the model did not improve predictive ability. Predictive ability was improved by the use of a multi‐trait model including grain test weight. The high predictive ability for threshability overall indicate that genomic selection would be useful in selection for threshability in naked barley. Core Ideas: Two markers were identified with significant associations to threshability.Predictive ability for threshability was 0.842 using a structured gBLUP model.Predictive ability was not increased by inclusion of identified QTL as covariates.Predictive ability was increased using a multi‐trait prediction model. [ABSTRACT FROM AUTHOR]

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. Core Ideas: There is five‐times greater genotype × environment interaction (GEI) than genetic variance for grain yield. Biplots define two mega‐environments in the northern United States for naked barley grain yield. Other assessed agronomic traits and threshability are more affected by genotype than GEI. [ABSTRACT FROM AUTHOR]

In plant breeding, the goal of genomewide selection is to predict the merit of unobserved individuals, particularly those in the next breeding generation. Predictions of these individuals in unobserved or future environments would be of additional use to a breeder. For many of the complex traits targeted in breeding, this may require management of genotype × environment interactions by, for example, using data from homogeneous groups of environments. Our objectives were to assess the accuracy of genomewide predictions in unobserved environments both within and between breeding generations; we aimed to compare training sets that included data from all possible environments with those that included data from (a) decreasingly similar environments or (b) discrete clusters of similar environments. A 183‐line spring barley (Hordeum vulgare L.) training population and 50‐line offspring test population were phenotyped in 29 location–year environments for grain yield, heading date, and plant height. Environmental similarities were measured using phenotypic data, geographic distance, or environmental covariables. When using training data from more, but decreasingly similar environments, prediction accuracy increased, but marginal gains declined; in some cases, accuracy declined with additional data. Clusters of environments informed by phenotypes (i.e., phenotypic correlations or multiplicative models) typically improved prediction accuracy within a generation, but not between generations (offspring population). Our study suggests that, as an alternative to using data from all available environments, informative subsets may be advantageous for genomewide predictions within a single breeding generation, but not between generations. [ABSTRACT FROM AUTHOR]