Abstract Background Hops (Humulus lupulus L.) are a dioecious climbing perennial, with the dried mature “cones” (strobili) of the pistillate/female inflorescences being widely used as both a bittering agent and to enhance the flavour of beer. The glandular trichomes of the bract and bracteole flowering structures of the cones produce an abundance of secondary metabolites, such as terpenoids, bitter acids and prenylated phenolics depending on plant genetics, developmental stage and environment. More knowledge is required on the functional and allelic diversity of terpene synthase (TPS) genes responsible for the biosynthesis of volatile terpenes to assist in flavour-directed hop breeding. Results Major volatile terpene compounds were identified using gas chromatography–mass spectrometry (GC–MS) in the ripe cones of twenty-one hop cultivars grown in New Zealand. All cultivars produced the monoterpene β-myrcene and the sesquiterpenes α-humulene and β-caryophyllene, but the quantities varied broadly. Other terpenes were found in large quantities in only a smaller subset of cultivars, e.g. β-farnesene (in seven cultivars) and α-pinene (in four). In four contrasting cultivars (Wakatu™, Wai-iti™, Nelson Sauvin™, and ‘Nugget’), terpene production during cone development was investigated in detail, with concentrations of some of the major terpenes increasing up to 1000-fold during development and reaching maximal levels from 50–60 days after flowering. Utilising the published H. lupulus genome, 87 putative full-length and partial terpene synthase genes were identified. Alleles corresponding to seven TPS genes were amplified from ripe cone cDNA from multiple cultivars and subsequently functionally characterised by transient expression in planta. Alleles of the previously characterised HlSTS1 produced humulene/caryophyllene as the major terpenes. HlRLS alleles produced (R)-(-)-linalool, whilst alleles of two sesquiterpene synthase genes, HlAFS1 and HlAFS2 produced α-farnesene. Alleles of HlMTS1, HlMTS2 and HlTPS1 were inactive in all the hop cultivars studied. Conclusions Alleles of four TPS genes were identified and shown to produce key aroma volatiles in ripe hop cones. Multiple expressed but inactive TPS alleles were also identified, suggesting that extensive loss-of-function has occurred during domestication and breeding of hops. Our results can be used to develop hop cultivars with novel/improved terpene profiles using marker-assisted breeding strategies to select for, or against, specific TPS alleles.

Hop aroma characteristics originate from hop essential oils, which have complex chemical profiles that remain poorly understood, particularly for New Zealand hops. The aim of this study was to determine volatile compounds that distinguish New Zealand hop cultivars. Untargeted fingerprinting methods based on headspace gas chromatography mass spectrometry (GC-MS) were used to analyse nine hop cultivars. A total of 61 volatile compounds were identified as compounds that differentiated the commercial hop varieties using advanced chemometrics and feature selection techniques. Similarities in volatile composition were found between Wakatu, Wai-iti™ and Kohatu®, which are rich in alcohols. Another grouping was found between Waimea™ and Nelson Sauvin™, where ketones and esters were commonly found. Rakau™ was distinct from the other eight cultivars, distinguished by 2-methylbutyl 3-methylbutanoate and methanethiol hexanoate. Riwaka™ contained the greatest number of discriminating volatile compounds when compared to other cultivars, which was dominated by terpenoids, such as geranyl 2-methylbutanoate, perillene and D-limonene. The chemical fingerprinting approach successfully identified volatile compounds that had not been previously found in New Zealand hop cultivars and that discriminated the commercial cultivars. The data obtained in the present study further extend the knowledge of New Zealand hops and will help facilitate targeted breeding.

The main objective of the New Zealand hop breeding programme is to develop triploid cultivars with unique brewing properties. Created from crosses between diploid and tetraploid parents, these genotypes have the advantage of being seedless as well as high yielding. Population improvement procedures are used independently for both diploid and tetraploid populations. Restricted maximum likelihood statistical procedures are used for the selection of both male and female genotypes for tetraploid and diploid parental material. In this regard, particular emphasis is placed on identifying sexually derived tetraploids to widen the gene pool. Crosses using tetraploids, as both female and male parents, hybridised with diploid genotypes, are described. Gender segregation ratios from recent triploid seedling populations vary considerably. The statistical analysis of triploid seedling female genotypes from these populations for several key traits is presented. A summary of main chemistry features of New Zealand bred polyploid cultivars is presented. Future breeding strategies for triploid hops are discussed.

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.

The Pacific northwestern region of North America is known for production of raspberries for process markets. The industry is characterised by being highly mechanised and utilising latest technologies for growing, freezing and processing fruit. For developing new commercial cultivars, high machine-harvested yield is a key objective for this process crop but breeding for this is difficult. In this paper we summarise a recently developed strategy for breeding for high machine-harvested yield based on plant yield components. For high-yielding floricane-fruiting raspberries that ripen early in the season, breeders should place selection emphasis on large berry weight and high numbers of laterals while for late-season ripening, selection emphasis should be on long laterals and long cane length.

Genetic diversity provides the cornerstone for kiwifruit plant improvement. The genus Actinidia is very diverse, containing nearly 60 species, which are native to East Asia, with the centre of diversity in southern China. The recent domestication and commercialisation of kiwifruit during the past century has meant there is little difference between commercial cultivars and some of the wild germplasm. The characterisation and reproductive biology of Actinidia germplasm is described. The genetic diversity of germplasm resources and ploidy races is discussed, along with recent breeding efforts to introgress traits from related Actinidia species into commercial species. Examples of the use of Actinidia germplasm for research into kiwifruit genomics and biotechnology are given (e.g., colour expression) in relation to their potential uses for genetic improvement.

Hops, Humulus lupulus, are grown worldwide for use in the brewing industry to impart characteristic flavor and aroma to finished beer. Breeders produce many varietal crosses with the aim of improving and diversifying commercial hops varieties. The large number of crosses critical to a successful breeding program imposes high demands on the supporting chemical analytical laboratories. With the aim of reducing the analysis time associated with hops breeding, quantitative partial least-squares regression (PLS-R) models have been produced, relating reference data acquired by the industrial standard HPLC and UV methods, to vibrational spectra of the same, chemically diverse hops sample set. These models, produced from rapidly acquired infrared (IR), near-infrared (NIR), and Raman spectra, were appraised using standard statistical metrics. Results demonstrated that all three spectroscopic methods could be used for screening hops for α-acid, total bitter acids, and cohumulone concentrations in powdered hops. Models generated from Raman and IR spectra also showed potential for use in screening hops varieties for xanthohumol concentrations. NIR analysis was performed using both a standard benchtop spectrometer and a portable NIR spectrometer, with comparable results obtained by both instruments. Finally, some important vibrational features of cohumulone, colupulone, and xanthohumol were assigned using DFT calculations, which allow more insightful interpretation of PLS-R latent variable plots.

Hops (Humulus lupulus) impart many of the specific flavours and aromas that define the style of beer. To develop hop selections that confer intense, desired or novel sensory characteristics to beer is a key objective of hop breeding research. This prompted investigations on the use of sensory evaluation of hop raw material, i.e. dried cones, as a tool for identifying promising cultivars early in the breeding and development process.In the first approach, dried hop cones from a large number of cultivars were evaluated by trained sensory panels for the intensity of citrus aroma. Data collected across two years showed a very large variation in intensity of that aroma across hop cultivars. While dried cones from most breeding cultivars exhibited relatively weak citrus aroma intensities, some attained higher scores than commercial selections included for comparison purposes. Overall, the sensory method provided robust information for selection of breeding plants with appropriate citrus-like aroma properties.In the second approach, dried cones from 41 hop cultivars were evaluated for the presence/absence of nine aroma traits (grapefruit, passionfruit, feijoa, banana, hay, ginger, onion/garlic, sweaty, and piney). The purpose was to identify cultivars with salient, specific aroma nuances that could be of interest to the brewing industry. Significant differences were established between hop cultivars in citation frequencies for grapefruit, passionfruit, hay, ginger, onion/garlic and sweaty aroma notes. Overall, the most salient aroma traits exhibited by each of the cultivars evaluated provided information for decision making regarding whether to pursue their development.

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.

For most small fruit-breeding programs, high yield is a key objective and breeders face a number of challenges breeding for high yield, including interaction of environmental influences and the high cost of yield measurements. Red raspberry ( Rubus idaeus ) yield is determined by a number of yield components (YC), including cane number, cane length, number of fruiting laterals, fruit numbers, and fruit size. The ultimate goal for breeders would be to be able to select for high-yield genotypes using key YC as early in the life of the plant as possible. In this study we set out to determine how individual components of yield are inherited, determine which components contribute the most to total yield, and investigate whether it is possible using key components to make selections for high-yielding genotypes on 1- and 2-year-old plants. We estimated variance components, heritabilities, phenotypic and genotypic correlations, and breeding values for yield and YC from 1008 genotypes based on 85 families derived from 45 parents harvested over three seasons in Washington state. Narrow-sense heritability estimates varied from moderately low [0.2 for number of canes (NCAN)] to moderately high [0.69 for berry weight (BWT)]. In general, all YCs were positively correlated with total yield (TYLD). The highest genetic correlation with TYLD was found for BWT (0.8), followed by cane length (CLEN) (0.54) and number of fruit per lateral (NFRT) (0.5). NCAN had the lowest genetic correlation with TYLD (–0.03). Genotype × year (G×Y) interaction was higher for some YCs than others. Berry weight, lateral length (LLEN), and NFRT were found to be the most stable overall seasons and the interaction was higher between the first and second years than between the second and third years of the study. To determine the most important YC, we calculated the correlations between the product of all combinations of subsets of the YC breeding values and TYLD. Berry weight, CLEN, and cane diameter (CDIA) were found to be the most important for 2009, 2010, and 2011, respectively. The two most important YCs were LLEN and BWT and this was consistent overall seasons. We demonstrate that it is possible to select high-yielding genotypes by measuring key components such as LLEN, CLEN, and BWT in the first and second fruiting seasons.

New commercial red raspberry ( Rubus idaeus ) cultivars suited to machine-harvesting and processing markets need to be high-yielding and have good fruit quality attributes, including fruit firmness, sugar content, acidity, flavor, and health properties. Combining many traits in one genotype is a challenge for breeders, especially for traits negatively correlated with yield. Despite its potential, the use of multiple-trait selection through selection indices has had limited application in fruit breeding. In this study, we estimated variance components, heritabilities, phenotypic and genetic correlations and breeding values for total yield (TYLD), harvest span, mid-harvest day and fruit quality traits, firmness (FIRM), soluble solids (SS), acidity (ACID), total anthocyanins (TACY), and total ellagitannins (TELG) from 1008 seedling genotypes based on 85 families derived from 45 parents harvested over three seasons in Washington state. Narrow-sense heritability estimates ranged from moderately low (0.22 for TYLD) to moderately high (0.73 for SS). All traits measured had positive genetic correlations with TYLD except for ACID (–0.35) and TACY (–0.28). Genotype × year (G×Y) interaction was high for TYLD and low for fruit quality attributes FIRM, SS, ACID, TACY, and TELG, and interactions were higher between the first (2009) and second (2010) seasons than between the second (2010) and third (2011) seasons. Using economic weights and breeding values derived from multivariate analysis for TYLD, FIRM, SS, and TACY, we constructed a selection index designed to assist with multiple-trait selection for population improvement and the development of commercial raspberry cultivars.

The Pacific northwestern (PNW) region of the United States is well known for production of machine- harvested red raspberries (Rubus idaeus) for process markets. The cultivar Meeker, developed in the 1960s, is well suited tothis area andfor machine-harvesting, butitis susceptible to raspberry bushy dwarfvirus and rootrot caused by Phytophthora rubi. Despite the efforts of several breeding programs, 'Meeker' is still the predominant cultivar for commercial production in the PNW. One of the major difficulties with breeding new berry fruit cultivars is the time- consumingnatureof collectingfruityieldandqualitydataonlargeseedlingpopulations.Forfruityield,visualscoring assessment methods are commonly used for seedling populations, but these may be poor predictors of yield. Consequently, visual scores for yield can result in less genetic improvement and thus can adversely affect successful cultivar development. Total yield measured by hand-harvesting is labor-intensive and does not assess machine- harvestability,butmachine-harvestingisnotpracticaltomeasureonindividualplants.Inthisstudywesetouttoseeif we could bulk machine-harvest full-sib family plots for among-family selection and use yield component data on individuals within the plots for within-family selection. Using best linear unbiased predictors, we estimated machine- harvest yield breeding values for our individual seedlings and found higher genetic gain per generation using estimated individual machine-harvest breeding values (7.6%) than using hand-harvested breeding values (6.5%). Implications for breeding machine-harvest red raspberries are discussed.

Hop powdery mildew [Podosphaera macularis (Wallr.) U. Braun & S. Takam.] is best controlled via the production of resistant varieties. Recent evidence supports selection against plant susceptibility genes to fungal pathogens as a more durable resistance mechanism than selection for resistance genes. The objective of this study was to identify molecular-based QTLs, their genetic effects and epistasis among QTLs associated with susceptibility to powdery mildew. Parents and offspring from the cross, ‘Perle’ × ‘USDA 19058M’, were clonally replicated and inoculated in a greenhouse using a CRD experimental design in Corvallis, OR. DNA was extracted, purified and analyzed via three different marker systems. Analysis of the resulting markers was based upon the “two-way pseudo-testcross” procedure. QTL mapping using multiple interval mapping and Bayesian interval mapping analyses were performed using WinQTL Cartographer 2.5_003. Comparison amongst mapping analyses identified three persistent QTLs on three linkage groups without significant epistatic effect upon expression. The persistent QTL on linkage group C7 had both additive and dominant effects controlling phenotype expression. The presence or absence of the two AFLP markers bordering the QTL on C7 defined susceptibility in offspring. This is the first report in hop identifying molecular markers linked to QTLs associated with disease susceptibility.

The genus Actinidia contains many species that have an array of novel traits of potential commercial interest. We have initiated an interspecific hybridisation programme to introgress some of these novel traits into commercial kiwifruit. Thus we need to have an understanding of the genetic behaviour of interspecific hybrids. We report on the fruiting characteristics of two interspecific Actinidia hybrid populations. Plants were harvested over five seasons (2006-2010). Key traits measured included average fruit weight, estimated yield, dry matter, soluble solids, fruit firmness, titratable acidity and vitamin C content. A mixed modelling approach for the analysis of data was used to derive estimates of narrow sense heritability for four traits and the genetic correlations between them. In addition, empirical breeding values were obtained for each genotype and selection indices developed. The implications of these estimates in breeding for improved commercial cultivars of Actinidia species are discussed.

Breeding for high yield is a major objective of most small fruit breeding programs worldwide. In recent years, research associated with health benefits of berry fruit has resulted in some breeding programs looking for material with improved health properties with the goal of incorporating these into genotypes with high yield and other favorable agronomic characters. In this study, we estimated variance components, heritabilities, and phenotypic and genotypic correlations for yield components and phytochemicals [total phenolics (TPH), antioxidant activity (FRAP), and total anthocyanins (TACY)] from 828 genotypes in a red raspberry ( Rubus idaeus ) factorial mating design based on 42 full-sib families derived from seven female and six male parents harvested in one season in New Zealand. Narrow sense heritability estimates varied from moderately low [0.23 for percent budburst (PCBB)] to high [0.82 for mean berry weight (BWT)]. Highest genotypic correlations with total yield (TYLD) were found for mean cane length (0.60) followed by moderate correlations for PCBB (0.38), BWT (0.34) and fruit number per unit lateral (0.31). For these four components, the correlation between the product of the empirical breeding values (eBV) and TYLD was as good (0.67) as the correlation between the product of the seven yield components measured (0.68). Moderately high negative genotypic correlations were found between TYLD and TPH (–0.67), FRAP (–0.68), and TACY (–0.64), suggesting that breeding for high-yielding genotypes may result in reduced phytochemical levels. A pigment-deficient R. parvifolius × R. idaeus hybrid derivative parent ( R. parv deriv) had the most influence on berry weight as a yield component. Removal of the R. parv deriv progeny from the analysis increased the contribution of berry weight to total yield. Heritability estimates were generally lower when the R. parv deriv crosses were omitted, particularly for number of canes BWT, TYLD, and the phytochemicals. Implications of R. parv deriv crosses on these results are discussed. Of the 828 genotypes, only five had an eBV for total yield greater than that of the best yielding parent, whereas 49 had larger berries than the best parent. None of the 828 genotypes had an eBV for yield components or phytochemicals less than that of the lowest parent, whereas 13 had a higher eBV associated with phytochemicals than that of the highest parent.

A study was conducted on the use of best linear unbiased predictors (BLUP) to estimate breeding values (BV) as a breeding tool to aid the development of seedless triploid aroma hop genotypes. BLUP is well suited to perennial crop breeding programmes where trials often involve unbalanced data sets conducted on the same plants across multiple environments. Parental material included noble aroma cultivars 'Saazer', 'Hallertauer Mittelfrueh' and 'Fuggle' crossed to three New Zealand bred male selections. The populations derived from these crosses were grown at different times over a five year period. The resulting BV thus allows the breeder to utilise all of the combined trial data available no matter what the stage of selection development. They also take into consideration genetic correlations, genetic relatedness and heritability estimates. The use of the BLUP procedure to estimate genetic gain for important commercial characters and to derive suitable selection indices is discussed.

Viruses pose a significant constraint to hop (Humulus lupulus) production worldwide. The incidence of Hop latent carlavirus (HpLV), Hop mosaic carlavirus (HpMV), American hop latent carlavirus (AHLV), Arabis mosaic nepovirus-hop strain (ArMV-H), and Apple mosaic ilarvirus (hop ApMV-H and intermediate ApMV-I serotypes) was assessed in 60 gardens at 11 locations (farms) in the Motueka province of New Zealand. The survey included 10 New Zealand-bred hop cultivars. Within each garden, one basal shoot was sampled from each of 50-75 plants and bulk-tested in groups of five by enzyme linked immunosorbent assay (ELISA). Viruses were prevalent, with HpLV, ApMV (H+I), ArMV-H, HpMV, and AHLV occurring in 55, 41, 37, 37, and 17 of the 60 gardens, respectively. ApMV and HpLV occurred at highest incidence, with 22 and 15 gardens, respectively, having >50% incidence. HpMV, ArMV-H, and AHLV occurred at lower incidence with only four, two, and one gardens, respectively, having >50% incidence. Results suggested the prevalence and incidence of viruses was high and of concern to the continued production of high yields in New Zealand.