Brewers consistently look for new and unique hop (Humulus lupulus L.) cultivars that possess excellent flavor profiles and are cost effective to produce and utilize. Proprietary aroma cultivars have in some cases met this need but are costly to produce due to susceptibility to major plant diseases and primary adaptation for high desert climates such as that found in the Yakima Valley, Washington. In order to fill this gap, the USDA-ARS hop breeding program developed and released 'USDA Triumph' (Reg. no. CV-30, PI 689549) to the public on 19 April 2019. The defining characteristics of this hop cultivar are high yields, broader adaptation across multiple environments, and excellence in brewing multiple beer styles. USDA Triumph arose from a cross made in 2000 between 'USDA Nugget' and 'USDA 21110M'. USDA Triumph has exhibited high yields and disease tolerance across multiple states. It has been utilized in lager, pilsner, pale ales, and amber ales along with IPA brewing with excellent consumer reviews. The release and registration of this new cultivar provides brewers with an exciting new high-yielding, widely adapted hop cultivar with excellent aroma and cost-effective superior flavor.

Hop with powdery mildew [HPM: caused by Podosphaera macularis (Wallr.) U. Braun & S. Takam.] results in significant losses in hop production by reducing yield and quality. One means of increasing yield and quality is the production of resistant hop lines. Breeding for resistance can be significantly improved and accelerated by use of marker-assisted selection. The objective of this preliminary study was to identify QTLs and markers for genetic resistance to HPM. A bi-parental mapping population between the resistant line "Newport'' and susceptible line '21110M'. Phenotypic data was scored under controlled greenhouse conditions. Significant differences among offspring were observed and disease resistance did not follow a distinct binomial distribution, suggesting quantitative genetic control. Genotyping-by-sequencing resulted in approximately 375 K SNP markers, which were filtered down to 2263 markers mapped to 10 linkage groups. Interval Mapping identified four QTLs with one on linkage group 1 and three located on linkage group 6. Composite interval mapping identified three QTLs, all located on linkage group 6. Mixed linear models identified 15 markers associated with expression of resistance to HPM. Three of these 15 SNPs were also identified in QTL-CIM analysis. Evaluation of the scaffolds containing the significant SNP markers identified seven putative genes-several of which appear involved in disease resistance in other plant species. The SNP markers identified in this study still require validation in unrelated populations prior to implementation in breeding programs.

Downy mildew (caused by Pseudoperonospora humuli) causes significant losses in hop (Humulus lupulus L.) cone yield and quality, and potential crown death. Breeding for resistance has proved difficult presumably because of the highly quantitative nature of genetic control over expression. The objective of this study was to utilize multiple environments to ascertain downy mildew resistance and identify molecular markers linked to resistance. A widely segregating population, ‘Teamaker’ × USDA 21422M was inoculated and evaluated for downy mildew in field studies (Corvallis, OR and Yakima, WA) and a greenhouse study. Next generation sequencing using an Illumina HiSeq 2000 was performed on this population. Resulting reads were imported into UNEAK TASSEL 4.0 pipeline for processing and SNP-calls. Approximately 120,435 unfiltered SNP markers were identified and of these markers, 9081 high quality markers chosen for association analysis. Data analyses for field studies in OR and WA were performed separately using trait values averaged across blocks. Differential trait associated marker sets were identified across each physical environment with partial overlap between field environments. Mixed linear model analyses identified 39 markers (21 from OR, 10 from WA and eight overlapping) associated with response to downy mildew infection (p < 1 × 10−4). The most significant 17 markers were validated using high-resolution melting curve analysis and the resistant allele identified. Four SNP markers, along with the respective “resistant” alleles, were classified as highly selective for resistance (model adjusted R2 = 0.437). Multiplexing studies are underway to develop a simple PCR tool for selecting downy mildew resistance.

Hop is one of the few dioecious plants with dimorphic sex chromosomes. Because the entire Cannabaceae family is dioecious, hop and other members of this family are thought to have a relatively older sex chromosomal system than other plant species. Hop cones are only produced in female hops with or without fertilization. This has lead to most genomic research being directed toward female plants. The work we present provides genomic resources surrounding male plants. We have produced a draft genome for the male hop line USDA 21422M using a novel genome assembly method. In addition, we identified a 1.3 Mb set of scaffolds, which appear to be the male specific region based upon specificity with male hop accessions. This set includes a smaller high confidence total length 18 Kb set of scaffolds, which are supported by over 500 individuals, including the USDA world collection of hop varieties and two mapping populations, with genotyping by sequencing. We also have identified a portion of the Teamaker × 21422M linkage map to be associated with the pseudo-autosomal region (PAR). Within the genomic scaffolds, we identified a set of genes that are sex-linked and likely located in the PAR.

Hop downy mildew (DM) is an obligate parasite causing severe losses in hop if not controlled. Resistance to this pathogen is a primary goal for hop breeding programs. The objective of this study was to identify QTLs linked to DM resistance. Next-generation-sequencing was performed on a mapping population segregating for DM resistance levels. Cloned plants were grown in a RCBD with three replicates under three environments: greenhouse (GH), field plots in Oregon (OR), Corvallis field plots in Washington (WA), Yakima). The linkage map of 3,341 SNP markers was determined with a four-stage process using Rqtl, TMAP, Joinmap v 4.0 and MERGEMAP. QTL analysis was performed using JMP Genomics and TASSEL 5.0. SNP markers were distributed across 11 linkage groups (LGs) with an average distance between markers of 0.2 cM and total distance of 745.9 cM. QTLs for all three environments were identified using multiple interval mapping. Overall heritability across the three environments varied from h(2) = 0.38 (GH) to 0.57 (OR). A total of 22 QTLs across 8 LG were identified for DM resistance: 5 identified from OR field data, 12 using WA data and five from GH DM data. No epistasis was observed. This study points out the complexity of genetic control of DM resistance in hop and identifies several markers that can be potentially be used to select for DM resistance in hop. It also provides the first linkage map suitable for genome sequencing due to the high density of SNP markers.

The overall objective of the USDA-ARS hop (Humulus lupulus L.) is to develop and release disease resistant, superior hop germplasm and varieties for the USA hop industry using both traditional and molecular-based selection protocols. As part of this mission, USDA-ARS develops new means of breeding to increase selection efficiency in breeding new hop varieties. Conventional quantitative genetic studies were pursued from 1996-2004 while molecular approaches have been more recent. These molecular approaches have been used to quantify genetic diversity between male and female accessions, identifying superior parents and superior mating pairs and more recently to identify molecular markers to be used in selection. Most recently, the USDA-ARS along with researchers from several other countries, are pursuing the sequencing of the complete hop genome with hopes of identifying regions controlling important traits in hop production. These studies involve next generation sequencing coupled with modern biometrics to assemble and align the hop genome.

Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars.

Diversity Arrays Technology (DArT - www.diversityarrays.com) is a micro-array based DNA marker technique for genome wide discovery and genotyping of genetic variation. DArT potentially allows simultaneous scoring of thousands of restriction site polymorphisms between genotypes and does not require DNA sequence information or site specific oligonucleotides. An international consortium (Australia, USA, UK, Slovenia) screened 86 (cultivated, wild; female, male) accessions of hop from Europe, North America, Asia and Australia, including examples of Humulus lupulus var. lupuloides, H. lupulus var. pubescens and H. lupulus var. neomexicanus, using DArT. The accessions included key current and historical, high and low a-acid, aroma, triploid, dwarf, and powdery and downy mildew resistant and susceptible cultivars. DArT identified 730 polymorphic markers, with reproducibility approaching 100%, and a high call rate. Preliminary studies of the data indicate that a large proportion of the markers reflect differences between wild and cultivated material. Distinction can be made between and within material of European, North American and Asian origin, with related accessions, and accessions from a single cultivar known by several synonyms clustering together. Initial investigation suggests that the reproducibility of DArT markers, the level of genetic variation detected with this system in hop, and the resolution of known genetic affinities are positive signs that DArT will provide the platform for future exploration of marker-trait associations to develop marker assisted selection technologies in hop. Based on this study, the DArT platform provides a reproducible, accurate, high throughput genotyping tool for hop. In the future this work will be developed to increase the number of markers available for hop using DArT, and to generate linkage maps and identify quantitative trait loci for key traits in a number of families.

A USDA-sponsored plant collecting expedition in collaboration with the Vavilov Institute of Plant Industry (VIR), St. Petersburg, Russian Federation, and the Aral Sea Experiment Station for Plant Genetic Resources, Chelkar Town, Kazakhstan, was conducted in the fall of 2000. Hop (Humulus lupulus var. lupulus) cones were collected from wild plants growing on trees in a moist area about 50 km NE of Emba, Kazakhstan. A portion of the seeds were brought to the US and donated to the US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon. Of 74 seedlings that were germinated from Kazakhstani seedlots, four seedlings from PI 635262 demonstrated resistance to powdery mildew, caused by Podosphaera macularis (Braun and Takamatsu). One of these resistant seedlings, 'Kazak 2000', exhibited a hypersensitive response after challenge by powdery mildew, especially when incubated at temperatures greater than 29 degrees C post-infection. In greenhouse assays with an Oregon field population of P. macularis, macroscopic signs of powdery mildew were not observed following repeated inoculations. In laboratory assays at 18 degrees C, 'Kazak 2000' did not develop powdery mildew when challenged with a P. macularis isolate capable of overcoming resistance genes R-b, R-3, and R-5. Infection of 55% of detached leaves was observed when challenged with characterized isolates capable of overcoming R-b, R-3, R-4, R-5, R-6 or R-b, R-1, R-2, R-3, R-5, and R-6, respectively. In experimental field plots in Oregon from 2003 to 2007, only one powdery mildew colony was observed despite inoculation and exposure to natural inoculum sources each year. Infection of cones was not observed. `Kazak 2000' provides a novel source of powdery mildew resistance that is effective at high temperatures against multiple races of the pathogen. Limited quantities of cuttings of `Kazak 2000' are available for research or breeding. Requests should be made to the Hop Curator, USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333.

Eight genic SSR loci were evaluated for genetic diversity assessment and genotype identification in Humulus lupulus L. from Europe and North America. Genetic diversity, as measured by three diversity indices, was significantly lower in European cultivars than in North American wild accessions. Neighbor Joining cluster analysis separated the hop genotypes into European and North American groups. These eight SSRs were useful in uniquely identifying each accession with the exception of two sets of European landraces and a pair of Japanese cultivars, ‘Shinshuwase’ and ‘Kirin II’. An accession from Manitoba grouped with the European (EU) cluster reflecting the group’s genetic similarity to older Manitoba germplasm used to develop ‘Brewer's Gold’ and the gene pool arising from this cultivar. Cultivars grouped closely with one of their immediate parents. ‘Perle’ grouped with its parent ‘Northern Brewer and ‘Willamette’ grouped with its parent ‘Fuggle H’. Wild American accessions were divided into two subgroups: a North Central group containing mostly H. lupulus var. lupuloides and a Southwestern group containing H. lupulus var. neomexicanus accessions. These eight SSRs will be valuable for genotype identification in European and wild American germplasm and may potentially prove useful for marker-assisted selection in hop. PCR products from four previously reported primer pairs that amplify the same intronic SSR regions as do the genic SSRs in this study were compared in eight common cultivars. Different primer pairs generated robust markers at the chs 2 and chi loci. However, only the HLC-004B and HLC-006 primer pairs amplified successfully at the chs 3 and chs 4 loci.

Hop (Humulus lupulus L. var. lupulus) is grown worldwide for the production of the dried female inflorescence (strobulus), or cones, used principally for the bittering and flavoring of beer. Information is scant on the inheritance of traits of economic importance in hop, and present knowledge is based on historical data rather than designed experimental investigation. The objective of this study was to estimate the heritability of and genetic correlation among six traits: yield (YLD), α‐acid (ALP) concentration, β‐acid (BET) concentration, cohumulone (COH) percentage, colupulone (COL) percentage, and xanthohumol (XAN) concentration. Twenty‐five full‐sib families were developed by crossing five randomly chosen females and five randomly chosen males in a North Carolina Design II mating design. Plants were transplanted into the field in a randomized complete block (RCB) design with four replicates. Data were recorded for two years. Heritabilities for all traits were moderate to high using variance components estimated from males. With the exception of heritability estimates for YLD and ALP, all other traits were not significantly different from zero using female variance components as estimators. Pooled estimates of heritability yielded more reasonable estimates with lowest heritability for BET (h2 = 0.57 ± 0.19) and highest for COL (h2 = 0.89 ± 0.02). Pooled estimates of genetic correlations ranged from r = 0.28 (ALP and YLD) to r = 0.92 (YLD and XAN). Finally, correlations between coefficients of coancestry (COA) between pairs and their respective mean offspring data were significant for ALP, COL, and XAN suggesting that for these traits at least, COA values may be predictive of potential heterosis. On the basis of these data, selection for COL, ALP, and YLD would be successful using simple selection protocols such as phenotypic recurrent or mass selection. The likelihood of success when selecting for BET and XAN would be low, thus requiring one of the genotypic recurrent selection techniques. Selection against COH (a negative factor in brewing) appears problematic because of positive correlations with all other traits. The information presented in this study is the first published record of field‐based estimates of narrow‐sense heritability and genetic correlations in hop and will aid hop breeders working with these traits.

A method was developed to identify microsatellite-containing sequences from existing Humulus lupulus L. entries in the Nucleotide GenBank database. We screened 45 genomic, mRNA and expressed sequence tag (EST) Humulus nuclear sequences and identified 7 that contained simple sequence repeats (SSRs). Primer pairs were designed for 15 sequences and the optimum annealing temperature was determined by gradient PCR. SSR primers were screened for polymorphism in 24 wild accessions of hops. Ten primer pairs generated repeatable polymorphic bands and seemed to amplify single loci. These 10 polymorphic loci will be useful for genotype identification and for estimation of genetic diversity in the hop collection maintained at the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon.

Hop (Humulus lupulus L.) is a perennial, dioecious species in which the female inflorescence (cones) are harvested and used in the beer‐brewing process to impart bittering and/or flavoring to beer. Hop breeders have typically utilized clonal selection and hybridization to develop new cultivars. The use of genetically diverse parents for the purpose of capturing heterosis in the offspring has received little attention from hop breeders. The objective of this research was to assign male (N = 80) and female (N = 26) hop genotypes into potential heterotic groups using AFLP‐generated molecular markers. The six AFLP primers used in this study amplified 550 total fragments, of which 490 (89.1%) were polymorphic. A genetic distance (GD) matrix was computed from the binary data matrix, and groupings and summary statistics were calculated from the GD matrix. Two major clusters were observed, one composed primarily of European hops, while the second group was composed primarily of European–wild American hybrids. The two major clusters were further subdivided into 13 smaller clusters (two female, nine male, two male and female) based on a qualitative analysis. These results suggest potential parental combinations for hop researchers and breeders to study heterosis in hop.

Hop is a dioecious perennial with female plants grown commercially for brewing purposes. Parent selection in hop breeding on the basis of heterotic potential has not been reported in literature even though dominance has been reported in hops for several economically important traits. The objectives of this study were to determine if amplified fragment length polymorphism (AFLP)-based genetic distance among mate and female accessions accurately reflect pedigree relationships and present information on potential heterotic crosses in hop. Nineteen cultivars were analyzed for genetic distance to 82 male accessions representing the assumed diversity of U.S. hops. Genetic distances (GD) between male/female pairs were estimated using AFLP (490 polymorphic bands). Distance estimates comparing males with females ranged from 0.169 to 0.62 with an overall average of 0.306. For each hop female, the 10 most genetically diverse and 10 most genetically similar males were identified and grouped. Coefficients of coancestry (COA) for each male/female pair within these groups were calculated using pedigree analysis. Values of COA for the genetically similar pairs (COA(avg) = 0.046) were significantly higher than the COA for the diverse pairs (COA(avg) = 0.013), suggesting that choosing male/female pairs on the basis of AFLP-based genetic distance may predict heterotic potential in crosses when GD >0.36.

The presence of glandular trichomes may protect alfalfa (Medicago sativa L.) against certain stem-, leaf-, and fruit-eating insect pests. In order to determine appropriate breeding methods to select for this trait, this study characterized quantitative genetic parameters of erect glandular trichome density in `KS94GH6' diploid (2n=2x=16) alfalfa. Eight female and five male plants were crossed in a Design II mating to produce 40 full-sib families. Glandular trichome density was determined on these families under replicated greenhouse conditions in Las Cruces and Los Lunas, New Mexico, U.S.A. The effect of males was significant (p≤ 0.10) across the two environments. Variation among females was not significant within either location or across locations. The dominance genetic variance (σ2D = 0.210) was greater than the additive genetic variance (σ2A = 0.111). The average degree of dominance exceeded a value of `1' indicating that erect glandular trichome density in KS94GH6 may be influenced by digenic epistasis, and/or repulsion phase linkage disequilibrium. The large contribution of non-additiveeffects was reflected by a low narrow-sense heritability estimate (h2n = 0.25). The results indicate that further improvements in erect glandular trichome density in KS94GH6 alfalfa will require replicated progeny testing. Approaches to introgress this trait into cultivated tetraploid alfalfa are discussed.

Hop (Humulus lupulus L.) is an important cash crop in the U.S. Pacific Northwest. Classifying groups of hop accessions presently held in the USDA‐ARS world collection is vital toward categorizing newly imported accessions and identifying closely related (if not identical) cultivars. The objective of this study was to identify hop germplasm diversity pools on the basis on morphological and chemical data by cluster analysis. Eight hop quality characteristics including yield (YLD), α acids, β acids, hop‐storage index (HSI), cohumulone (CoH), myrcene (M), caryophyllene (C), and humulene (H) were obtained from historical databases for 129 accessions from the USDA‐ARS hop germplasm field collection located near Corvallis, OR. Three distinct genetic diversity pools were identified and named: (i) European, (ii) Wild North American, and (iii) Hybrids. The European pool was divided into English and Continental European subgroups distinguished by their α‐acids and CoH contents. The Hybrid pool was divided into five subgroups distinguished by their geographic origins. The variables YLD and CoH content differentiated these five subgroups (r = 0.92; P ≤ 0.05). The information presented in our study will help categorize newly imported accessions into the current U.S. hop germplasm collection and will help in identifying closely related or similar accessions.

Crop ScienceVolume 44, Issue 3 p. 1018-1019 Registration of Cultivar Registration of ‘Newport’ Hop J. Henning, Corresponding Author J. Henning John.Henning@orst.edu USDA-ARS-NFSPRC, Oregon State Univ., Corvallis, OR, 97331Corresponding author (John.Henning@orst.edu)Search for more papers by this authorS. Townsend, S. Townsend Crop and Soil Sci. Dep., Oregon State Univ., Corvallis, OR, 97331Search for more papers by this authorW. Mahaffee, W. Mahaffee USDA-ARS-HRCL, Oregon State Univ., Corvallis, OR, 97331Search for more papers by this authorS. Kenny, S. Kenny Washington State Univ.—IAREC, Prosser, WA, 99350Search for more papers by this authorA. Haunold, A. Haunold USDA-ARS-NFSPRC, Oregon State Univ., Corvallis, OR, 97331Search for more papers by this author J. Henning, Corresponding Author J. Henning John.Henning@orst.edu USDA-ARS-NFSPRC, Oregon State Univ., Corvallis, OR, 97331Corresponding author (John.Henning@orst.edu)Search for more papers by this authorS. Townsend, S. Townsend Crop and Soil Sci. Dep., Oregon State Univ., Corvallis, OR, 97331Search for more papers by this authorW. Mahaffee, W. Mahaffee USDA-ARS-HRCL, Oregon State Univ., Corvallis, OR, 97331Search for more papers by this authorS. Kenny, S. Kenny Washington State Univ.—IAREC, Prosser, WA, 99350Search for more papers by this authorA. Haunold, A. Haunold USDA-ARS-NFSPRC, Oregon State Univ., Corvallis, OR, 97331Search for more papers by this author First published: 01 May 2004 https://doi.org/10.2135/cropsci2004.1018a Registration by CSSA. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Volume44, Issue3May–June 2004Pages 1018-1019 RelatedInformation

The agricultural by-products of the hop plant (Humulus lupulus L.) were investigated to determine their potential for use in the removal of heavy lead(II) ions from contaminated aqueous solutions. Separate batch laboratory experiments were performed to establish the optimal binding pH, time exposures, and capacity of the metal adsorption for lead(II) ions by dried and ground hop leaves and stems biomass. Results from these studies have shown a pH dependent binding trend from pH 2–6, with optimum binding occurring around pH 5.0. Time dependency experiments showed a rapid adsorption of lead(II) ions within the first 5min of contact. Binding capacity experiments demonstrated that 74.2mg of lead(II) were bound per gram of leaf biomass. Similarly overall capacity was seen for the leaves and stems. Desorption of 99% of the bound lead(II) ions was achieved by exposing the metal laden biomass to 0.5M sodium citrate. Further experiments were performed with silica-immobilized hop tissues to determine the lead(II) binding ability under flow conditions. Comparison studies were performed with ion-exchange resins to evaluate the binding ability and to gain further insight into the metal binding mechanism. X-ray absorption spectroscopy experiments were also utilized to gain further insight into the possible lead(II) binding mechanism by the hop plant tissue. Results from these studies indicate that carboxyl ligands are involved in the binding of lead(II) from aqueous solution. These findings show that the use of hop agricultural waste products may be a viable alternative, for the removal and recovery of aqueous lead(II) ions from contaminated waters.