This study contributes new knowledge on quantitative trait loci (QTLs) and candidate genes for adaptive traits and yield in two-rowed spring barley. A meta-analysis of a network of field trials, varying in latitude and sowing date, with 151 cultivars across several European countries, increased QTL detection power compared to single-trial analyses. The traits analysed were heading date (HD), plant height (PH), thousand-grain weight (TGW), and grain yield (GY). Breaking down the analysis by the main genotype-by-environment trends revealed QTLs and candidate genes specific to conditions like sowing date and latitude. A historical look on the evolution of QTL frequencies revealed that early selection focused on PH and TGW, likely due to their high heritability. GY selection occurred later, facilitated by reduced variance in other traits. The study observed that favourable alleles for plant height were often fixed before those for grain yield and TGW. Some regions showed linkage in repulsion, suggesting targets for future breeding. Several candidate genes were identified, including known genes and new candidates based on orthology with rice. Remarkably, the deficiens allele of gene Vrs1 , appears associated to higher GY. These findings provide valuable insights for barley breeders aiming to improve yield, and other agronomic traits. Highlight A dense genome-wide meta-analysis provides new QTLs, reveals breeding history trends and identifies new candidate genes for yield, plant height, grain weight and heading time of spring barley. ### Competing Interest Statement The authors have declared no competing interest.

A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.

Background Barley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal timing of flowering. Therefore, regulation of flowering time is of extraordinary importance to meet future food and feed demands. We developed the first barley nested association mapping (NAM) population, HEB-25, by crossing 25 wild barleys with one elite barley cultivar, and used it to dissect the genetic architecture of flowering time. Results Upon cultivation of 1,420 lines in multi-field trials and applying a genome-wide association study, eight major quantitative trait loci (QTL) were identified as main determinants to control flowering time in barley. These QTL accounted for 64% of the cross-validated proportion of explained genotypic variance (p G ). The strongest single QTL effect corresponded to the known photoperiod response gene Ppd-H1 . After sequencing the causative part of Ppd-H1 , we differentiated twelve haplotypes in HEB-25, whereof the strongest exotic haplotype accelerated flowering time by 11 days compared to the elite barley haplotype. Applying a whole genome prediction model including main effects and epistatic interactions allowed predicting flowering time with an unmatched accuracy of 77% of cross-validated p G . Conclusions The elaborated causal models represent a fundamental step to explain flowering time in barley. In addition, our study confirms that the exotic biodiversity present in HEB-25 is a valuable toolbox to dissect the genetic architecture of important agronomic traits and to replenish the elite barley breeding pool with favorable, trait-improving exotic alleles.

We suggest multi-parental nested association mapping as a valuable innovation in barley genetics, which increases the power to map quantitative trait loci and assists in extending genetic diversity of the elite barley gene pool.

Two hundred sixteen barley (Hordeum vulgare L.) cultivars were selected to represent the diversity and history of European spring two‐row barley breeding and to search for alleles controlling agronomic traits by association genetics. The germplasm was genotyped with 7864 gene‐based single nucleotide polymorphism markers and corresponding field trial trait data relating to growth and straw strength were obtained at multiple European sites. Analysis of the marker data by statistical population genetics approaches revealed two important trends in the genetic diversity of European two‐row spring barley, namely, i) directional selection for approximately 14% of total genetic variation of the population in the last approximately 50 yr and ii) highly uneven genomic distribution of genetic diversity. Association analysis of the phenotypic and genotypic data identified multiple loci affecting the traits investigated, some of which co‐map with selected regions. Collectively, these data show that the genetic makeup of European two‐row spring barley is evolving under breeder selection, with signs of extinction of diversity in some genomic regions, suggesting that “breeding the best with the best” is leading towards fixation of some breeder targets. Nevertheless, modern germplasm also retains many regions of high diversity, suggesting that site‐specific genetic approaches for allele identification and crop improvement such as association genetics are likely to be successful.

Nitrogen (N) is one of the most important plant nutrients, controlling growth and, ultimately, yield of a cultivar. Hordeum vulgare ssp. spontaneum, the wild barley progenitor of cultivated barley, is known to possess genes that can improve tolerance against biotic and abiotic stresses. A quantitative trait locus (QTL) study with two levels of N fertilization was conducted under glasshouse in order to locate wild barley alleles that improve N stress tolerance in the genetic background of an elite barley cultivar. For this, a set of 28 barley introgression lines (S42ILs), which originate from the cross ‘Scarlett’ × ‘ISR42-8’, was studied. The S42ILs, containing single or multiple wild barley introgressions, and ‘Scarlett’ were evaluated in regard to a total of 15 traits, related to morphological parameters, grain parameters as well as to carbon (C) and N content parameters. A mixed model analysis and a subsequent Dunnett test was conducted to identify S42ILs that significantly deviate from the recurrent parent ‘Scarlett’, either tested separately for each N level, or simultaneously across both N levels. In total, 65 QTLs were detected for the S42IL set. Most QTLs were found for chlorophyll content during heading (10 QTLs) and the fewest for C/N ratio of straw (1 QTL). The individual S42ILs possessed different numbers of QTLs. For S42IL-108, a maximum of eight QTLs were found whereas S42IL-145 did not show any significant difference from ‘Scarlett’. Wild barley alleles revealed decreasing effects at 32 QTLs and increasing effects at 33 QTLs. Although 25 QTLs exhibited similar effects across both N levels, 18 and 22 QTLs exhibited effects that were only detected under N0 or N1, respectively. We, thus, conclude that it may be worth to select improved barley cultivars for N stress tolerance separately under low N fertilization, rather than extrapolating trait performances from experiments carried out under standard N fertilization conditions. A number of wild barley QTL alleles improved N stress tolerance. For example, a wild barley QTL allele on chromosome 4H, present in the Hsp introgression of S42IL-119, was associated with a 13.0 % increase of thousand grain weight across both N levels and a 20 % increase under low N supply. QTLs detected in the present study were compared with those of previous field studies of the same cross and with other QTL studies in barley and other small grains. Accordance between QTL studies (QTLs showing similar effects at the same map location) is documented and discussed. Based on our study, promising wild barley QTL alleles are available in S42ILs, which can be readily utilized to select for improved N use efficiency in barley breeding.

In connection with crop improvement strategies for marginal regions it has been proposed to increase the outcrossing rate in barley which would presuppose high and persistent pollen viability to ensure successful cross fertilisation. The present study was designed to investigate the viability of mature pollen from extruded and non-extruded anthers of cultivated and wild barley (Hordeum vulgare ssp vulgare and ssp spontaneum, respectively) in comparison with the closely related but obligatory outcrossing species H. bulbosum. Pollen viability (PV) was assessed employing the p-phenylenediamine-peroxidase-test on pollen derived from spikes or anthers immediately after collection and after treatment at 20, 30 and 40 ∘C for 1, 2, 4, 8 and 16 h. The latter treatment was interposed after 8 h by a 10 h period of darkness at 12 ∘C and thus called 26 h treatment, consecutively. Initial PV was high with 98% across all genotypes and even at 40 ∘C did not fall below 80% after 8 h. After the 26 h treatment, PV of two H. vulgare genotypes originating from semi-arid regions and of H. bulbosum fell below 60% while the other genotypes retained a PV of > 80%. Viability of pollen of extruded anthers in H. vulgare ssp. spontaneum was on average slightly but significantly lower than PV of non-extruded anthers but still remained above 90%, even after the 26 h treatment at 40 ∘C. Pollen viability of the outcrossing species H. bulbosum ranged on a very similar level as PV of H. vulgare. Results indicate that pollen of H. vulgare retains a sufficiently high level of viability to ensure successful cross-fertilisation over a period of at least 26 h even at high temperatures of up to 40 ∘C.