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Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

'Top Shelf' (Reg. no. CV‐380, PI 704478), experimental designation DH162310, is a two‐row winter barley (Hordeum vulgare L.) released by Oregon Agricultural Experiment Station in 2023. It is a malting cultivar that is known to be a non‐producer of glycosidic nitrile (GN0). GN0 is the precursor to a regulated compound (ethyl carbamate) in distilled spirits and thus, the GN0 trait is becoming a requisite for malting cultivars geared toward distilling. While GN0 spring cultivars have been available for over 20 years, Top Shelf is the first winter GN0 cultivar to be released in North America, and only the second globally. In addition to its GN0 status it exceeds contemporary agronomic and malt quality expectations. Over 5 years of field trials in Oregon it performed equal to or better than the check entries. It shows high yields, plump grains, and test weights. It also has good resistance to scald (caused by Rhynchosporium commune) and preliminary data suggest resistance to barley stripe rust (Puccinia striiformis f. sp. hordei). Results were confirmed in field trials in southern Idaho, a major malting barley production region, and a target environment for this cultivar. Under standard malting protocols Top Shelf meets the guidelines for malt and all‐malt and/or grain distilling, and has high extract, enzymatic activity, and free amino nitrogen. When malted under optimized conditions, mimicking commercial distilling malt production, it produced even better results. As one of only a handful of GN0 cultivars available in the United States with potential for mainstream production, Top Shelf provides an important option for the distilling supply chain. Core Ideas: 'Top Shelf' is a non‐producer of glycosidic nitrile.'Top Shelf' is the first GN0 winter barley released in the United States.'Top Shelf' is well adapted to the Pacific Northwest (Idaho, Oregon, Washington).'Top Shelf' produces exceptional malt quality for distilling purposes. [ABSTRACT FROM AUTHOR]

Abstract Background Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102) assembled at the start of the Barley Coordinated Agricultural Project (CAP). This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608. Results Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We then conducted association analyses - with SNP data only - in the larger germplasm arrays. For both vernalization sensitivity and inflorescence type, the most significant associations in the larger data sets were found with SNPs coincident with the synthetic markers used in the CAP Core and with SNPs detected via interaction analysis in the CAP Core. Conclusions Small and highly structured collections of germplasm, such as the CAP Core, are cost-effectively phenotyped and genotyped with high-throughput markers. They are also useful for characterizing allelic diversity at loci in germplasm of interest. Our results suggest that discovery-oriented exercises in AM in such small arrays may generate a large number of false-positives. However, if haplotypes in candidate genes are available, they may be used as anchors in an analysis of interactions to identify other candidate regions harboring genes determining target traits. Using larger germplasm arrays, genome regions where the principal genes determining vernalization sensitivity and row type are located were identified.

Abstract Background High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

'Lontra' (Reg. no. CV‐378, PI 702797), experimental designation DH142010, is a two‐row winter barley (Hordeum vulgare L.) released by Oregon Agricultural Experiment Station in 2023. It is well adapted to the US Pacific Northwest. Lontra is a doubled haploid produced via anther culture and was advanced through fall‐planted trials from 2016 to 2021. Lontra was developed with the goal of commercial production as a malting cultivar for the craft malting industry; therefore, it was not tested in the American Malting Barley Association Pilot Program due to the limited number of selections that can be accommodated. Lontra has a solid record of agronomic performance, malting quality, beer quality, and beer sensory. Core Ideas: Lontra malting barley meets the needs and expectations of craft maltsters and brewers.Lontra offers a new option for winter‐habit malting barley in the Klamath basin.Lontra malting barley was evaluated in an alternate pipeline to the existing AMBA evaluation. [ABSTRACT FROM AUTHOR]

Malting barley is an economically important crop, with strict quality standards. In some sectors of the industry, there is a bias against malting barley with blue aleurone. The rationale behind this bias is not clear. We therefore investigated the relationships between barley color and malting quality using a panel of fall-planted doubled haploid lines from the Oregon State University barley breeding program. The panel was assessed for malting and aleurone color traits using grain from the 2021 harvest and for aleurone color with grain from the 2022 harvest. The white and blue aleurone groups were found to be different for some malting traits across the entire panel of lines, but this was a result of selection history. When a biparental subset of the panel segregating for aleurone color was considered, differences between the color groups were minimal. A genome wide association study showed that the major QTL contributing to aleurone color (on the long arm of chromosome 4H) was independent of the malt quality QTL. It is concluded that there is no basis for a bias against blue aleurone: identifying new malting barley varieties should be based on their malting performance, not their color. The blues are all right – aleurone color and malting quality are controlled by different genes. Observed relationships between aleurone color and specific malting quality traits are due to breeding history. Barley varieties with specific malting quality profiles can be developed irrespective of aleurone color. [ABSTRACT FROM AUTHOR]

Why was the work done: Floor malting maintains a small but notable market share due to its reputed contributions to beer flavour. These malts are viewed as premium products and are produced in both historic and contemporary floor maltings. Despite this, little work has been performed on floor malting to evaluate its effect on malt and subsequent beer quality and flavour. Accordingly, this work investigated whether floor malting produces distinct malts and beers relative to pneumatic maltings. How was the work done: A mini-floor malting protocol was developed to malt small quantities of grain in a repeatable system that produces malt comparable to the production scale. Two winter barley varieties (Lontra and Thunder) were used to understand whether there was a malting type by variety interaction effect on beer flavour. What are the main findings: Both floor and pneumatic malts produced similar malts and beers based on quality metrics and the differences found between malts were more attributable to variety and the respective rate of proteolysis. Sensory results showed that there was a significant malting type by variety interaction driving hedonic and descriptive sensory results. Why is the work important: These results suggest that while the different malting types produce analytically similar malt, selection of barley variety can be used to optimise the floor malting process to produce distinct beer flavour profiles. [ABSTRACT FROM AUTHOR]

Vernalization, the requirement of a period of low temperature to induce transition from the vegetative to reproductive state, is an evolutionarily and economically important trait in the Triticeae. The genetic basis of vernalization in cultivated barley (Hordeum vulgare subsp. vulgare) can be defined using the two-locus VRN-H1/VRN-H2 model. We analyzed the allelic characteristics of HvBM5A, the candidate gene for VRN-H1, from ten cultivated barley accessions and one wild progenitor accession (subsp. spontaneum), representing the three barley growth habits - winter, facultative, and spring. We present multiple lines of evidence, including sequence, linkage map location, and expression, that support HvBM5A being VRN-H1. While the predicted polypeptides from different growth habits are identical, spring accessions contain a deletion in the first intron of HvBM5A that may be important for regulation. While spring HvBM5A alleles are typified by the intron-localized deletion, in some cases, the promoter may also determine the allele type. The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and we conclude that one of the three ZCCT-H genes is VRN-H2. The VRN-H2 locus is present in winter genotypes and deleted from the facultative and spring genotypes analyzed in this study, suggesting the facultative growth habit (cold tolerant, vernalization unresponsive) is a result of deletion of the VRN-H2 locus and presence of a winter HvBM5A allele. All reported barley vernalization QTLs can be explained by the two-locus VRN-H1/VRN-H2 model based on the presence/absence of VRN-H2 and a winter vs. spring HvBM5A allele.

Understanding the role barley variety plays in the overall flavor profile of beer is an area of research of interest to barley breeders, maltsters, and brewers. Here we build on previous research on the effect of barley variety on beer flavor by focusing on commercial-type malts and beers. A selection of three winter-habit, elite malting lines – two released varieties and one experimental – were grown in three locations across Oregon and California and harvested in summer 2020. Each was malted to the specifications of Pilsner-style malt. Beers were produced to mimic offerings of the industry partner and utilized a small portion of specialty malt and higher hopping rates than previous work. All beers underwent descriptive sensory analysis and Projective Mapping (Napping®) to characterize and determine the magnitude of separation between samples. Malting and brewing performance differed among the nine entries, but sensory outcomes showed only minor separation and few significant differences in the descriptive analysis. The results here showed that there is correlation between malt modification and sensory outcomes and ultimately confirmed that barley variety and growing location contributes to beer flavor. However, the overall contributions are nuanced, particularly in commercial-ty3pe malts and beers. [ABSTRACT FROM AUTHOR]

Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgare Lo), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six-row and two-row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model-based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two-row spring, two six-row spring, and two six-row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long-range LD suggestive of admixture. Genetic distance (allele-sharing) between populations varied from 0.11 (six-row spring vs. six-row spring) to 0.45 (two-row spring vs. six-row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele-sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable. doi: 10.2135/cropsci2009.04.0198

Heirloom barley (Hordeum vulgare L.) varieties remain interesting to maltsters and brewers for their perceived unique flavor contributions to beer, despite not meeting contemporary agronomic and malting expectations. This study utilized crosses of the heirloom Maris Otter® and two contemporary genotypes to determine if "updated heirlooms" could be produced that would show improved agronomics and contemporary malt quality, while contributing uniquely to malt and beer sensory and chemical profiles. Using a recently established pipeline of malting; brewing; hot steep and beer sensory; and metabolomics to evaluate barley genotype contributions to malt and beer flavor, four experimental lines were compared to a control. The experimental lines were also assessed for their genomic contribution from their respective parents to further elucidate regions of the Maris Otter genome that may contribute to unique beer flavors. Results show improved agronomic outcomes relative to the heirloom parent and were comparable to the control. Malting quality met current recommendations. However, sensory properties attributable to the unique heirloom parent were not found. Further, chemical profiling did not explain the observed nuanced sensory differences, nor did it reveal unique metabolites not described by the sensory panels. Supplemental data for this article is available online at at http://doi:10.1080/03610470.2021.1952509. [ABSTRACT FROM AUTHOR]