New Male Specific Markers for Hop and Application in Breeding Program.

Male specific DNA sequences were selected from a Diversity Arrays Technology (DArT) mapping study to evaluate their suitability for determination of the sex phenotype among young seedlings in a hop (Humulus lupulus L.) breeding program. Ten male specific DArT markers showed complete linkage with male sex phenotype in three crossing families. Following optimization, four were successfully converted into PCR markers and a multiplex PCR approach for their use was developed. Among 197 plants (97 from the world collection; 100 from three segregating families), 94-100% positive correlation with sex phenotypic data was achieved for the single PCR amplification, whereas the multiplex approach showed 100% correlation. To develop a fast and low-cost method, crude sample multiplex PCR was evaluated in 253 progenies from 14 segregating populations without losing accuracy. The study describes, for the first time, the routine application of molecular markers linked to male sex in an intensive Slovenian hop breeding program. The methods described could be employed for screening of sex at the seedling stage in other hop programs worldwide, thereby saving resources for desirable female plants.

Assessment of the phytochemical profiles of novel hop (Humulus lupulus L.) cultivars: A potential route to beer crafting.

This study investigated the volatile phytochemical diversity of 30 samples obtained from experimental hybrid and commercial H. lupulus L. plants. Essential oils distilled from these samples were analysed by high resolution gas chromatography coupled with accurate mass time-of-flight mass spectrometry (GC-accTOFMS). A total of 58 secondary metabolites, mainly comprising 18 esters, 6 monoterpene hydrocarbons, 2 oxygenated monoterpenes, 20 sesquiterpene hydrocarbons, 7 oxygenated sesquiterpenes, and 4 ketones, were positively or tentatively identified. A total of 24 metabolites were detected in all samples, but commercial cultivars (selected for brewing performance) had fewer compounds identified compared to experimental genotypes. Chemometrics analyses enabled distinct differentiation of experimental hybrids from commercial cultivars, discussed in terms of the different classes of compounds present in different genotypes. Differences among the mono- and sesquiterpenoids, appear to be related to either: i) the genetic origin of the plants; or ii) the processes of bioaccumulation of the identified secondary metabolites.

Sequential Hybrid Three-Dimensional Gas Chromatography with Accurate Mass Spectrometry: A Novel Tool for High-Resolution Characterization of Multicomponent Samples.

A novel sequential three-dimensional gas chromatography-high-resolution time-of-flight mass spectrometry (3D GC-accTOFMS) approach for profiling secondary metabolites in complex plant extracts is described. This integrated system incorporates a nonpolar first-dimension (1Dnp) separation step, prior to a microfluidic heart-cut (H/C) of a targeted region(s) to a cryogenic trapping device, directly followed by the rapid reinjection of a trapped solute into a polar second-dimension (2DPEG) column for multidimensional separation (GCnp-GCPEG). For additional separation, the effluent from 2DPEG can then be modulated according to a comprehensive 2D GC process (GC×GC), using an ionic liquid phase as a third-dimension (3DIL) column, to produce a sequential GCnp-GCPEG×GCIL separation. Thus, the unresolved or poorly resolved components, or regions that require further separation, can be precisely selected and rapidly transferred for additional separation on 2D or 3D columns, based on the greater separation realized by these steps. The described integrated system can be used in a number of modes, but one useful approach is to target specific classes of compounds for improved resolution. This is demonstrated through the separation and detection of the oxygenated sesquiterpenes in hop ( Humulus lupulus L.) essential oil and agarwood ( Aquilaria malaccensis) oleoresin. Improved resolution and peak capacity were illustrated through the progressive comparison of the tentatively identified components for GCnp-GCPEG and GCnp-GCPEG×GCIL methods. Relative standard deviations of intraday retentions (1 tR, 2 tR,, and 3 tR) and peak areas of ≤0.01, 0.07, 0.71, and 7.5% were achieved. This analytical approach comprising three GC column selectivities, hyphenated with high-resolution TOFMS detection, should be a valuable adjunct for the improved characterization of complex plant samples, particularly in the area of plant metabolomics.

Chemotyping of new hop (Humulus lupulus L.) genotypes using comprehensive two-dimensional gas chromatography with quadrupole accurate mass time-of-flight mass spectrometry.

Comprehensive two-dimensional gas chromatography with quadrupole accurate mass time-of-flight mass spectrometry (GC×GC-Q-TOFMS) is employed to profile Humulus lupulus L. (hop) essential oils. Comparison of characterised essential oils allows discrimination among chemotypes. Experimental and commercial hop genotypes displayed distinguishable chemotypic patterns among the volatile secondary metabolites making up their essential oils. In total, 210-306 unique compounds were detected (depending on specific genotype), with 99 of these compounds either positively or tentatively identified. Identified volatile secondary metabolites were grouped into esters, monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes and ketones. Terpenoids were the dominant chemical families across all hop genotypes analysed, representing between 67% and 90% of the total ion count. The multidimensional chromatographic profiles of hop essential oils are extremely information-rich, making GC×GC-Q-TOFMS useful for fast screening of new hybrid hop genotypes, and therefore informing breeding strategies to derive new commercial hop cultivars for the development of distinctive and desirable beers.

Parallel comprehensive two-dimensional gas chromatography.

We introduce an information rich analytical approach called parallel comprehensive two-dimensional gas chromatography (2GC×2GC). This parallel chromatography approach splits injected samples into two independent two-dimensional column ensembles and provides two GC×GC separations by using contra-directional thermal modulation. The first-dimension (1D) and second-dimension (2D) columns are connected using planar three-port microchannel devices, which are supplied with supplementary flow via two pressure controller modules. Precise carrier gas flow control at the junction of the 1D and 2D columns permits independent control of flow conditions in each separation column. The 2GC×2GC approach provides two entirely independent GC×GC separations for each injection. Analysis of hop (Humulus lupulus L.) essential oils is used to demonstrate the capability of the approach. The analytical performance of each GC×GC separation in the 2GC×2GC experiment is comparable to individual GC×GC separation with matching column configurations. The peak capacity of 2GC×2GC is about 2 times than that of single GC×GC system. The dual 2D chromatograms produced by this single detector system provide complementary separations and additional identification information by harnessing different selectivity provided by the four separation columns.

Quantitative genetic parameters for yield, plant growth and cone chemical traits in hop (Humulus lupulus L.).

BACKGROUND: Most traits targeted in the genetic improvement of hop are quantitative in nature. Improvement based on selection of these traits requires a comprehensive understanding of their inheritance. This study estimated quantitative genetic parameters for 20 traits related to three key objectives for the genetic improvement of hop: cone chemistry, cone yield and agronomic characteristics. RESULTS: Significant heritable genetic variation was identified for α-acid and ß-acid, as well as their components and relative proportions. Estimates of narrow-sense heritability for these traits (h2 = 0.15 to 0.29) were lower than those reported in previous hop studies, but were based on a broader suite of families (108 from European, North American and hybrid origins). Narrow-sense heritabilities are reported for hop growth traits for the first time (h2 = 0.04 to 0.20), relating to important agronomic characteristics such as emergence, height and lateral morphology. Cone chemistry and growth traits were significantly genetically correlated, such that families with more vigorous vegetative growth were associated with lower α-acid and ß-acid levels. This trend may reflect the underlying population structure of founder genotypes (European and North American origins) as well as past selection in the Australian environment. Although male and female hop plants are thought to be indistinguishable until flowering, sex was found to influence variation in many growth traits, with male and female plants displaying differences in vegetative morphology from emergence to cone maturity. CONCLUSIONS: This study reveals important insights into the genetic control of quantitative hop traits. The information gained will provide hop breeders with a greater understanding of the additive genetic factors which affect selection of cone chemistry, yield and agronomic characteristics in hop, aiding in the future development of improved cultivars.

Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry.

BACKGROUND: Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. RESULTS: QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. CONCLUSIONS: Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS.

Molecular variation of hop mosaic virus isolates.

Hop mosaic virus (HpMV), a member of the genus Carlavirus, is importance to hop production worldwide. We identified variation in nucleic and amino acid sequences among 23 HpMV isolates from Australia, the USA, the Czech Republic, South Africa and Japan using a 1,455-bp fragment covering the 3' end of the virus genome including ORFs 4, 5 and 6. Three clusters of two or more isolates were identified in phylogenies of the total nucleotide sequence and the coat protein (ORF5) amino acid sequence. Two of these clusters combined in analyses of ORF4 and ORF6 amino acid sequences. Isolates from within and outside of Australia were found in each cluster, indicating that sequence variation was not associated with geographic source. Monitoring of HpMV variants in the field and evaluation of the impact of variants on vector association, rate of spread, and hop yield and quality can now be undertaken.

Varietal characterization of hop (Humulus lupulus L.) by GC-MS analysis of hop cone extracts.

An approach is described for use in the varietal characterization of hop (Humulus lupulus L.) varieties. The study focuses on commercial hop varieties and was timed to coincide with the 2008 commercial hop harvest in Tasmania, Australia. Analysis of hop extracts was performed using GC-MS. A 60 m capillary column was employed to increase efficiency to permit the use of a quadrupole mass spectrometer in place of a time of flight mass spectrometer that is more commonly used for this type of analysis. A set of characterization functions were derived from discriminant analysis which were highly suitable for varietal characterization of the eight commercial varieties included in the study, namely Willamette, Victoria, Pride of Ringwood, Cascade, Southern Hallertau, Millennium, Southern Saaz, and Super Pride.

DNA sequence and expression variation of hop (Humulus lupulus) valerophenone synthase (VPS), a key gene in bitter acid biosynthesis.

BACKGROUND: The hop plant (Humulus lupulus) is a source of many secondary metabolites, with bitter acids essential in the beer brewing industry and others having potential applications for human health. This study investigated variation in DNA sequence and gene expression of valerophenone synthase (VPS), a key gene in the bitter acid biosynthesis pathway of hop. METHODS: Sequence variation was studied in 12 varieties, and expression was analysed in four of the 12 varieties in a series across the development of the hop cone. RESULTS: Nine single nucleotide polymorphisms (SNPs) were detected in VPS, seven of which were synonymous. The two non-synonymous polymorphisms did not appear to be related to typical bitter acid profiles of the varieties studied. However, real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis of VPS expression during hop cone development showed a clear link with the bitter acid content. The highest levels of VPS expression were observed in two triploid varieties, 'Symphony' and 'Ember', which typically have high bitter acid levels. CONCLUSIONS: In all hop varieties studied, VPS expression was lowest in the leaves and an increase in expression was consistently observed during the early stages of cone development.