1
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Clare SJ, King RM, Tawril AL, Havill JS, Muehlbauer GJ, Carey SB, Harkess A, Bassil N, Altendorf KR. An affordable and convenient diagnostic marker to identify male and female hop plants. G3 (BETHESDA, MD.) 2023; 14:jkad216. [PMID: 37963231 PMCID: PMC10755173 DOI: 10.1093/g3journal/jkad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/11/2023] [Indexed: 11/16/2023]
Abstract
Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.
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Affiliation(s)
- Shaun J Clare
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Ryan M King
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Anna L Tawril
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
| | - Joshua S Havill
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Nahla Bassil
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Kayla R Altendorf
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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3
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Features of Non-Alcoholic Beer on Cardiovascular Biomarkers. Can It Be a Substitute for Conventional Beer? Nutrients 2022; 15:nu15010173. [PMID: 36615830 PMCID: PMC9824297 DOI: 10.3390/nu15010173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Numerous studies have revealed the beneficial effects of moderate beer consumption on cardiovascular diseases. However, the presence of alcohol in beer can represent a matter of concern, since alcohol intake poses a risk to some individuals. Additionally, adults who are life-long abstainers should not be encouraged to consume alcohol for health purposes. Consequently, the benefits of beer consumption remain a controversial issue. In this scenario, the present review gathers the reported information concerning the cardiovascular effects of non-alcoholic beer, and makes a comparison between these effects and those of conventional beer. Despite the scarcity of published results to date describing the effects of non-alcoholic beer consumption, the available literature indicates that it is more effective than conventional beer in preventing oxidative stress (lower lipid and protein oxidation), preserving the endothelial function (lower endothelial dysfunction) and inhibiting thrombogenic activity (lowered oxidized LDL). By contrast, conventional beer has shown to induce greater increases in HDL-cholesterol levels (known as a cardiovascular protective factor) compared to non-alcoholic beer. This effect cannot be solely attributed to alcohol content, since the polyphenol content in conventional beer tends to be higher than that found in non-alcoholic beer.
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Cottrell MT. A Search for Diastatic Enzymes Endogenous to Humulus lupulus and Produced by Microbes Associated with Pellet Hops Driving “Hop Creep” of Dry Hopped Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Márquez Gutiérrez R, Cherubino Ribeiro TH, de Oliveira RR, Benedito VA, Chalfun-Junior A. Genome-Wide Analyses of MADS-Box Genes in Humulus lupulus L. Reveal Potential Participation in Plant Development, Floral Architecture, and Lupulin Gland Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091237. [PMID: 35567239 PMCID: PMC9100628 DOI: 10.3390/plants11091237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 05/14/2023]
Abstract
MADS-box transcription factors (TFs) are involved in multiple plant development processes and are most known during the reproductive transition and floral organ development. Very few genes have been characterized in the genome of Humulus lupulus L. (Cannabaceae), an important crop for the pharmaceutical and beverage industries. The MADS-box family has not been studied in this species yet. We identified 65 MADS-box genes in the hop genome, of which 29 encode type-II TFs (27 of subgroup MIKCC and 2 MIKC*) and 36 type-I proteins (26 α, 9 β, and 1 γ). Type-II MADS-box genes evolved more complex architectures than type-I genes. Interestingly, we did not find FLOWERING LOCUS C (FLC) homologs, a transcription factor that acts as a floral repressor and is negatively regulated by cold. This result provides a molecular explanation for a previous work showing that vernalization is not a requirement for hop flowering, which has implications for its cultivation in the tropics. Analysis of gene ontology and expression profiling revealed genes potentially involved in the development of male and female floral structures based on the differential expression of ABC homeotic genes in each whorl of the flower. We identified a gene exclusively expressed in lupulin glands, suggesting a role in specialized metabolism in these structures. In toto, this work contributes to understanding the evolutionary history of MADS-box genes in hop, and provides perspectives on functional genetic studies, biotechnology, and crop breeding.
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Affiliation(s)
- Robert Márquez Gutiérrez
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Vagner Augusto Benedito
- Laboratory of Plant Functional Genetics, Plant and Soil Sciences Division, 3425 Agricultural Sciences Building, West Virginia University, Morgantown, WV 26506-6108, USA
- Correspondence: (V.A.B.); (A.C.-J.)
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
- Correspondence: (V.A.B.); (A.C.-J.)
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Patzak J, Henychová A, Matoušek J. Developmental regulation of lupulin gland-associated genes in aromatic and bitter hops (Humulus lupulus L.). BMC PLANT BIOLOGY 2021; 21:534. [PMID: 34773975 PMCID: PMC8590222 DOI: 10.1186/s12870-021-03292-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Hop (Humulus lupulus L.) bitter acids are valuable metabolites for the brewing industry. They are biosynthesized and accumulate in glandular trichomes of the female inflorescence (hop cone). The content of alpha bitter acids, such as humulones, in hop cones can differentiate aromatic from bitter hop cultivars. These contents are subject to genetic and environmental control but significantly correlate with the number and size of glandular trichomes (lupulin glands). RESULTS We evaluated the expression levels of 37 genes involved in bitter acid biosynthesis and morphological and developmental differentiation of glandular trichomes to identify key regulatory factors involved in bitter acid content differences. For bitter acid biosynthesis genes, upregulation of humulone synthase genes, which are important for the biosynthesis of alpha bitter acids in lupulin glands, could explain the higher accumulation of alpha bitter acids in bitter hops. Several transcription factors, including HlETC1, HlMYB61 and HlMYB5 from the MYB family, as well as HlGLABRA2, HlCYCB2-4, HlZFP8 and HlYABBY1, were also more highly expressed in the bitter hop cultivars; therefore, these factors may be important for the higher density of lupulin glands also seen in the bitter hop cultivars. CONCLUSIONS Gene expression analyses enabled us to investigate the differences between aromatic and bitter hops. This study confirmed that the bitter acid content in glandular trichomes (lupulin glands) is dependent on the last step of alpha bitter acid biosynthesis and glandular trichome density.
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Affiliation(s)
- Josef Patzak
- Hop Research Institute Co., Ltd., Kadaňská 2525, 438 01, Žatec, Czech Republic.
| | - Alena Henychová
- Hop Research Institute Co., Ltd., Kadaňská 2525, 438 01, Žatec, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005, České Budějovice, Czech Republic
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7
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Patzak J, Henychová A, Krofta K, Svoboda P, Malířová I. The Influence of Hop Latent Viroid (HLVd) Infection on Gene Expression and Secondary Metabolite Contents in Hop ( Humulus lupulus L.) Glandular Trichomes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112297. [PMID: 34834660 PMCID: PMC8617911 DOI: 10.3390/plants10112297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/21/2021] [Indexed: 05/10/2023]
Abstract
Viroids are small infectious pathogens, composed of a short single-stranded circular RNA. Hop (Humulus lupulus L.) plants are hosts to four viroids from the family Pospiviroidae. Hop latent viroid (HLVd) is spread worldwide in all hop-growing regions without any visible symptoms on infected hop plants. In this study, we evaluated the influence of HLVd infection on the content and the composition of secondary metabolites in maturated hop cones, together with gene expression analyses of involved biosynthesis and regulation genes for Saaz, Sládek, Premiant and Agnus cultivars. We confirmed that the contents of alpha bitter acids were significantly reduced in the range from 8.8% to 34% by viroid infection. New, we found that viroid infection significantly reduced the contents of xanthohumol in the range from 3.9% to 23.5%. In essential oils of Saaz cultivar, the contents of monoterpenes, terpene epoxides and terpene alcohols were increased, but the contents of sesquiterpenes and terpene ketones were decreased. Secondary metabolites changes were supported by gene expression analyses, except essential oils. Last-step biosynthesis enzyme genes, namely humulone synthase 1 (HS1) and 2 (HS2) for alpha bitter acids and O-methytransferase 1 (OMT1) for xanthohumol, were down-regulated by viroid infection. We found that the expression of ribosomal protein L5 (RPL5) RPL5 and the splicing of transcription factor IIIA-7ZF were affected by viroid infection and a disbalance in proteosynthesis can influence transcriptions of biosynthesis and regulatory genes involved in of secondary metabolites biosynthesis. We suppose that RPL5/TFIIIA-7ZF regulatory cascade can be involved in HLVd replication as for other viroids of the family Pospiviroidae.
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8
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Kunej U, Jakše J, Radišek S, Štajner N. Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1883. [PMID: 34579416 PMCID: PMC8471970 DOI: 10.3390/plants10091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.
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Affiliation(s)
- Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia;
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
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Grassa CJ, Weiblen GD, Wenger JP, Dabney C, Poplawski SG, Timothy Motley S, Michael TP, Schwartz CJ. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana. THE NEW PHYTOLOGIST 2021; 230:1665-1679. [PMID: 33521943 PMCID: PMC8248131 DOI: 10.1111/nph.17243] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/18/2021] [Indexed: 05/20/2023]
Abstract
Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance. A nanopore-based assembly anchored to a high-resolution linkage map provided a chromosome-resolved genome for CBDRx, a potent CBD-type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed. Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD-type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio. Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.
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Affiliation(s)
| | - George D. Weiblen
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | - Jonathan P. Wenger
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | - Clemon Dabney
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | | | - S. Timothy Motley
- Department of InformaticsJ. Craig Venter InstituteLa JollaCA92037USA
| | - Todd P. Michael
- Department of InformaticsJ. Craig Venter InstituteLa JollaCA92037USA
- Present address:
Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCA92037USA
| | - C. J. Schwartz
- Sunrise Genetics Inc.Fort CollinsCO80525USA
- Present address:
Industrial Hemp Genetics LLCMadisonWI53705USA
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10
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Moderate Consumption of Beer and Its Effects on Cardiovascular and Metabolic Health: An Updated Review of Recent Scientific Evidence. Nutrients 2021; 13:nu13030879. [PMID: 33803089 PMCID: PMC8001413 DOI: 10.3390/nu13030879] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
There is growing interest in the potential health-related effects of moderate alcohol consumption and, specifically, of beer. This review provides an assessment of beer-associated effects on cardiovascular and metabolic risk factors to identify a consumption level that can be considered “moderate”. We identified all prospective clinical studies and systematic reviews that evaluated the health effects of beer published between January 2007 and April 2020. Five of six selected studies found a protective effect of moderate alcohol drinking on cardiovascular disease (beer up to 385 g/week) vs. abstainers or occasional drinkers. Four out of five papers showed an association between moderate alcohol consumption (beer intake of 84 g alcohol/week) and decreased mortality risk. We concluded that moderate beer consumption of up to 16 g alcohol/day (1 drink/day) for women and 28 g/day (1–2 drinks/day) for men is associated with decreased incidence of cardiovascular disease and overall mortality, among other metabolic health benefits.
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11
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Eriksen RL, Padgitt-Cobb LK, Townsend MS, Henning JA. Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress. Sci Rep 2021; 11:5138. [PMID: 33664420 PMCID: PMC7970847 DOI: 10.1038/s41598-021-84691-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Hops are valued for their secondary metabolites, including bitter acids, flavonoids, oils, and polyphenols, that impart flavor in beer. Previous studies have shown that hop yield and bitter acid content decline with increased temperatures and low-water stress. We looked at physiological traits and differential gene expression in leaf, stem, and root tissue from hop (Humulus lupulus) cv. USDA Cascade in plants exposed to high temperature stress, low-water stress, and a compound treatment of both high temperature and low-water stress for six weeks. The stress conditions imposed in these experiments caused substantial changes to the transcriptome, with significant reductions in the expression of numerous genes involved in secondary metabolite biosynthesis. Of the genes involved in bitter acid production, the critical gene valerophenone synthase (VPS) experienced significant reductions in expression levels across stress treatments, suggesting stress-induced lability in this gene and/or its regulatory elements may be at least partially responsible for previously reported declines in bitter acid content. We also identified a number of transcripts with homology to genes shown to affect abiotic stress tolerance in other plants that may be useful as markers for breeding improved abiotic stress tolerance in hop. Lastly, we provide the first transcriptome from hop root tissue.
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Affiliation(s)
- Renée L. Eriksen
- grid.512836.b0000 0001 2205 063XUSDA Agricultural Research Service, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Lillian K. Padgitt-Cobb
- grid.4391.f0000 0001 2112 1969Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331 USA
| | - M. Shaun Townsend
- grid.4391.f0000 0001 2112 1969Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331 USA
| | - John A. Henning
- grid.512836.b0000 0001 2205 063XUSDA Agricultural Research Service, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97331 USA
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12
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Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. THE PLANT GENOME 2021; 14:e20072. [PMID: 33605092 DOI: 10.1002/tpg2.20072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/03/2020] [Indexed: 05/25/2023]
Abstract
Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sarah B Kingan
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Jackson Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | | | | | - Paul Peluso
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - David Rank
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | | | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
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13
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Easterling KA, Pitra NJ, Morcol TB, Aquino JR, Lopes LG, Bussey KC, Matthews PD, Bass HW. Identification of tandem repeat families from long-read sequences of Humulus lupulus. PLoS One 2020; 15:e0233971. [PMID: 32502183 PMCID: PMC7274563 DOI: 10.1371/journal.pone.0233971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/16/2020] [Indexed: 11/28/2022] Open
Abstract
Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. From this we identified 17 new and distinct tandem repeat sequence families, which represent candidates for FISH probe development. For two of these candidates, HuluTR120 and HuluTR225, we produced oligonucleotide FISH probes from conserved regions of and demonstrated their utility by staining meiotic chromosomes from wild hop, var. neomexicanus to address, for example, questions about hop transmission genetics. Collectively, these tandem repeat sequence families represent new resources suitable for development of additional cytogenomic tools for hop research.
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Affiliation(s)
- Katherine A. Easterling
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Nicholi J. Pitra
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Taylan B. Morcol
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, United States America
- The Graduate Center, City University of New York, New York, New York, United States America
| | - Jenna R. Aquino
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Lauren G. Lopes
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Kristin C. Bussey
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Paul D. Matthews
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
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14
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Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, Ashnest JR, Mau M, Schranz ME, Alcorn J, Laprairie RB, McKay JK, Burbridge C, Schneider D, Vergara D, Kane NC, Sharbel TF. The Genomics of Cannabis and Its Close Relatives. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:713-739. [PMID: 32155342 DOI: 10.1146/annurev-arplant-081519-040203] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.
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Affiliation(s)
- I Kovalchuk
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - M Pellino
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - P Rigault
- Gydle Inc., Québec, Québec G1S 1E7, Canada
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - R van Velzen
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
- Bedrocan International, 9640 CA Veendam, The Netherlands
| | - J Ebersbach
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - J R Ashnest
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M Mau
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M E Schranz
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
| | - J Alcorn
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - R B Laprairie
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department of Pharmacology, College of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - J K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - C Burbridge
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Schneider
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Vergara
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - N C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - T F Sharbel
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
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15
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McCallum JL, Nabuurs MH, Gallant ST, Kirby CW, Mills AAS. Phytochemical Characterization of Wild Hops ( Humulus lupulus ssp. lupuloides) Germplasm Resources From the Maritimes Region of Canada. FRONTIERS IN PLANT SCIENCE 2019; 10:1438. [PMID: 31921222 PMCID: PMC6917649 DOI: 10.3389/fpls.2019.01438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/16/2019] [Indexed: 05/06/2023]
Abstract
A survey was conducted in the Maritimes region of eastern Canada to measure the phytochemical diversity of prenylchalcone, soft resins (alpha & beta acids), and flavonol constituents from 30 unique wild-growing populations of hops (Humulus lupulus L.). Based on cone chemometrics, the majority of accessions (63.3%) are native Humulus lupulus ssp. lupoloides, with cones containing both xanthogalenol and 4'-O-methyl xanthohumol as chemotaxonomic indicator molecules. Interestingly, the leaves of all verified Humulus lupulus ssp. lupulus accessions accumulated high proportions (>0.20 total flavonols) of two acylated flavonol derivatives (kaempferol-3-O-(6''-O-malonyl)-β-D-glucopyranoside; quercetin-3-O-(6''-O-malonyl)-β-D-glucopyranoside), both previously unreported from hops leaves. The native lupuloides accessions examined possess only trace amounts of this compound in their leaves (<0.10 total flavonols), suggesting its potential utility as a novel, leaf-derived chemotaxonomic marker for subspecies identification purposes. A leaf-derived taxonomic marker is useful for identifying wild-growing accessions, as leaves are present throughout the entire growing season, whereas cones are only produced late in summer. Additionally, the collection of cones from 10-meter tall wild plants in overgrown riparian habitats is often difficult. The total levels of alpha acids, beta acids, and prenylchalcones in wild-collected Maritimes lupuloides cones are markedly higher than those previously reported for lupuloides individuals in the westernmost extent of its native range and show potentially valuable traits for future cultivar development, while some may be worthy of immediate commercial release. The accessions will be maintained as a core germplasm resource for future cultivar development.
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Affiliation(s)
- Jason L. McCallum
- Agriculture and Agri-Food Canada, Charlottetown Research and Development Centre, Charlottetown, Canada
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16
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Ma X, Meng Y, Wang P, Tang Z, Wang H, Xie T. Bioinformatics-assisted, integrated omics studies on medicinal plants. Brief Bioinform 2019; 21:1857-1874. [PMID: 32706024 DOI: 10.1093/bib/bbz132] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.
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Affiliation(s)
- Xiaoxia Ma
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Yijun Meng
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China
| | - Huizhong Wang
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Tian Xie
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
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17
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Undas AK, Weihrauch F, Lutz A, van Tol R, Delatte T, Verstappen F, Bouwmeester H. The Use of Metabolomics to Elucidate Resistance Markers against Damson-Hop Aphid. J Chem Ecol 2018; 44:711-726. [PMID: 29978430 PMCID: PMC6096525 DOI: 10.1007/s10886-018-0980-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/17/2018] [Accepted: 06/25/2018] [Indexed: 11/24/2022]
Abstract
Phorodon humuli (Damson-hop aphid) is one of the major pests of hops in the northern hemisphere. It causes significant yield losses and reduces hop quality and economic value. Damson-hop aphid is currently controlled with insecticides, but the number of approved pesticides is steadily decreasing. In addition, the use of insecticides almost inevitably results in the development of resistant aphid genotypes. An integrated approach to pest management in hop cultivation is therefore badly needed in order to break this cycle and to prevent the selection of strains resistant to the few remaining registered insecticides. The backbone of such an integrated strategy is the breeding of hop cultivars that are resistant to Damson-hop aphid. However, up to date mechanisms of hops resistance towards Damson-hop aphids have not yet been unraveled. In the experiments presented here, we used metabolite profiling followed by multivariate analysis and show that metabolites responsible for hop aroma and flavor (sesquiterpenes) in the cones can also be found in the leaves, long before the hop cones develop, and may play a role in resistance against aphids. In addition, aphid feeding induced a change in the metabolome of all hop genotypes particularly an increase in a number of oxidized compounds, which suggests this may be part of a resistance mechanism.
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Affiliation(s)
- Anna K Undas
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- RIKILT, Wageningen University & Research, Akkermaalsboss 2, 6708, WB, Wageningen, The Netherlands
| | - Florian Weihrauch
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Hop Research Center Huell, Wolnzach, Germany
| | - Anton Lutz
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Hop Research Center Huell, Wolnzach, Germany
| | - Rob van Tol
- Wageningen Plant Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Thierry Delatte
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
| | - Francel Verstappen
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Swammerdam Institute for Life Sciences, Plant Hormone Biology group, University of Amsterdam, Science Park 904, 1098, XH, Amsterdam, The Netherlands
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18
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Progar V, Jakše J, Štajner N, Radišek S, Javornik B, Berne S. Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae. PLANT CELL REPORTS 2017; 36:1599-1613. [PMID: 28698905 PMCID: PMC5602066 DOI: 10.1007/s00299-017-2177-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/04/2017] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. Hop (Humulus lupulus L.) production is hampered by Verticillium wilt, a disease predominantly caused by the soil-borne fungus Verticillium nonalfalfae. Only a few hop cultivars exhibit resistance towards it and mechanisms of this resistance have not been discovered. In this study, we compared global transcriptional responses in roots and shoots of resistant and susceptible hop plants infected by a lethal strain of V. nonalfalfae. Time-series differential gene expression profiles between infected and mock inoculated plants were determined and subjected to network-based analysis of functional enrichment. In the resistant hop cultivar, a remarkably low number of genes were differentially expressed in roots in response to V. nonalfalfae infection, while the majority of differentially expressed genes were down-regulated in shoots. The most significantly affected genes were related to cutin biosynthesis, cell wall biogenesis, lateral root development and terpenoid biosynthesis. On the other hand, susceptible hop exhibited a strong defence response in shoots and roots, including increased expression of genes associated with plant responses, such as innate immunity, wounding, jasmonic acid pathway and chitinase activity. Strong induction of defence-associated genes in susceptible hop and a low number of infection-responsive genes in the roots of resistant hop are consistent with previous findings, confirming the pattern of excessive response of the susceptible cultivar, which ultimately fails to protect the plant from V. nonalfalfae. This research offers a multifaceted overview of transcriptional responses of susceptible and resistant hop cultivars to V. nonalfalfae infection and represents a valuable resource in the study of this plant-pathogen interaction.
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Affiliation(s)
- Vasja Progar
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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