The use of genome‐wide association studies (GWAS) to detect quantitative trait loci (QTL) controlling complex traits has become a popular approach for studying key traits in crop plants. The goal of this study was to identify the genomic regions of barley ( Hordeum vulgare L.) that impact five agronomic and one quality trait in U.S. elite barley breeding lines, as well as to identify markers tightly linked with these loci for further use in barley improvement. Advanced recombinant inbred lines submitted to the U.S. Barley Coordinated Agricultural Project (CAP) were genotyped using a platform of 3072 single nucleotide polymorphism (SNP) markers from the barley oligonucleotide pool assays (BOPAs) 1 and 2. In each of 4 yr, approximately 770 lines were evaluated in a replicated, randomized complete block design under both irrigated and dryland conditions. This gave an overall population size of >3000 lines, which we analyzed in a hierarchical fashion, including analyzing the lines in aggregate using a mixed model to account for population structure and relatedness among the lines. We identified 41 significant marker–trait associations, of which 31 had been previously reported as QTL using biparental mapping techniques; 10 novel marker‐trait associations were identified. The results of this work show that genes with major effects are still segregating in U.S. barley germplasm and demonstrate the utility of GWAS in barley breeding populations.

Fourteen genotypes of barley were compared for response to salinity by monitoring the parameters gas exchange and chlorophyll fluorescence. We present relationships between stomatal conductance (g_s) gas exchange chlorophyll fluorescence parameters and aboveground dry matter (AGDM). We found that genetic variability provided a continuum of data for g_s across control and saline conditions. We used this continuum of g_s values to test the overall relationships between g_s and net photosynthesis (A), leaf internal CO₂ concentration (C_i), actual quantum yield of PSII electron transport (ΦPSII), relative electron yield over net CO₂ assimilation rate (ETR/A), and AGDM. The relationship between g_s and A was highly significant (p < 0.0001) for both control and saline treatments, while correlations between g_s and C_i, and C_i and A were significant only under control conditions. Unexpectedly, we found positive correlations between g_s and ΦPSII (p < 0.0001) for both conditions. A comparison between relationships of g_s and A, and g_s and ΦPSII seemed to indicate a possible acclimation to salinity at the chloroplastic level. Finally, the relationships between g_s and ETR/A were exceptionally strong for both growing conditions (p < 0.0001) indicating that, as g_s values were negatively affected in barley by genetics and salinity as main or interactive effects, there was a progressive increase in photorespiration in barley. Overall, we found that stomatal conductance was a key parameter in the study of barley responses to limiting situations for photosynthesis. We also found a strong relationship between AGDM and g_s regardless of growing conditions and genotypes. For breeding evaluations to select barley genotypes for salinity tolerance, it may be possible to replace all measurements of gas exchange and chlorophyll fluorescence by the simple use of a porometer.