Precision QTL mapping of downy mildew resistance in hop (Humulus lupulus L.)

Henning, Jimmy C.; Gent, David H.; Twomey, Megan C.; Townsend, M. Shaun; Pitra, Nicholi J.; Matthews, Paul D.

doi:10.1007/s10681-015-1356-9

Cited by 33 publications

(36 citation statements)

References 30 publications

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“…Incorporating downy mildew resistance, appropriate agronomic characteristics, and aroma and flavor profiles desired by brewers is thus a long-term endeavor. Recently, quantitative trait loci (QTL) markers have been identified for downy mildew resistance that could be used to make marker-assisted selections for resistance and expedite identification of progeny with higher levels of resistance (Henning et al 2015).…”

Section: Discussion and Recommendationsmentioning

confidence: 99%

“…Commercial production of hops relies on sanitation, crown pruning, and fungicides as the main management tools for downy mildew (Skotland and Johnson 1983;Neve 1991;Gent and Ocamb 2009;Gent et al 2010;Gent et al 2012). While the most efficacious management tool is the production of resistant cultivars, no cultivars are completely immune to downy mildew and resistance appears to be highly quantitative and polygenic (Royle and Kremheller 1981;Neve 1991;Johnson et al 2009;Henning et al 2015). Some cultivars are highly susceptible to the crown rot phase of the disease (e.g., Cluster), while others can withstand some crown infection but are highly susceptible to the foliar phase of the disease (e.g., Nugget) (Coley-Smith 1964;Neve 1991;Johnson et al 2009).…”

Section: Introductionmentioning

confidence: 99%

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Susceptibility of Hop Cultivars to Downy Mildew: Associations with Chemical Characteristics and Region of Origin

Woods

Gent

2016

Plant Health Progress

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Hop downy mildew (caused by Pseudoperonospora humuli) is a yield-limiting disease in many hop-production regions of the world. In this research, 110 cultivars that are or were widely grown in the United States, Europe, or Australasia were evaluated in western Oregon over three years for their reaction to the shoot infection phase of downy mildew and vigor. There was a large range of downy mildew susceptibility and vigor amongst commercial cultivars, with some cultivars possessing a very high level of resistance. Overall, however, disease resistance and vigor were significantly greater in cultivars originating from Europe than those originating from the United States, Japan, and Australia/New Zealand. Amongst a subset of 79 cultivars, vigor was negatively correlated with levels, in cones, of cohumulone, a chemical constitute of bittering acids typically found in germplasm derived from North America. The generally poor vigor observed in cultivars derived outside of Europe likely is indicative of a lack of tolerance to the crown infection phase of the disease. Thus, the best sources of downy mildew resistance seems to be found in cultivars from the United Kingdom and continental Europe, and such cultivars are typically lower yielding and lack distinctive aroma and flavor characteristics presently desired by craft brewers. Introgression of downy mildew resistance into North American germplasm with high yield and desirable brewing characteristics is needed. Accepted for publication 3 March 2016. Published 7 March 2016.

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Section: Discussion and Recommendationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Susceptibility of Hop Cultivars to Downy Mildew: Associations with Chemical Characteristics and Region of Origin

Woods

Gent

2016

Plant Health Progress

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“…DMR in hops has been shown to be an inheritable and quantitative trait (Henning et al, 2015). Henning et al investigated resistance to primary infection with downy mildew in hop, while our study focused on the secondary infection event.…”

Section: Major Dmr Locus Likely Confers Resistance By Regulating Thmentioning

confidence: 99%

Downy mildew resistance is genetically mediated by prophylactic production of phenylpropanoids in hop

Feiner

Pitra²,

Matthews³

et al. 2020

Plant Cell & Environment

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Downy mildew in hop (Humulus lupulus L.) is caused by Pseudoperonospora humuli and generates significant losses in quality and yield. To identify the biochemical processes that confer natural downy mildew resistance (DMR), a metabolome-and genomewide association study was performed. Inoculation of a high density genotyped F1 hop population (n = 192) with the obligate biotrophic oomycete P. humuli led to variation in both the levels of thousands of specialized metabolites and DMR. We observed that metabolites of almost all major phytochemical classes were induced 48 hr after inoculation. But only a small number of metabolites were found to be correlated with DMR and these were enriched with phenylpropanoids. These metabolites were also correlated with DMR when measured from the non-infected control set. A genome-wide association study revealed co-localization of the major DMR loci and the phenylpropanoid pathway markers indicating that the major contribution to resistance is mediated by these metabolites in a heritable manner. The application of three putative prophylactic phenylpropanoids led to a reduced degree of leaf infection in susceptible genotypes, confirming their protective activity either directly or as precursors of active compounds.

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“…Powdery mildew reduces the quality and quantity of yield while increasing the cost of production [26]. Although Cascade has historically possessed disease resistance to fungal pathogens powdery mildew (Podosphaero macularis) [18] and downy mildew (Pseudoperonospora humuli) [27], there are still risks of damage by these fungal pathogens. A recent outbreak of powdery mildew affecting Cascade in the U.S. Pacific Northwest (PNW) was the result of a Cascade-adapted isolate of P. Macularis [18].…”

Section: Introductionmentioning

confidence: 99%

“…Very little management was required to grow Cascade until powdery mildew was introduced in the PNW in the mid-1990s [28], and the rise of PM infection corresponds to an increase in Cascade acreage [18]. Hop breeding with resistant cultivars [26, 27, 29] can result in new resistance, but given the inevitability of pathogen adaptation, an understanding of the genomic features underlying resistance and susceptibility is necessary to breed for hop that can withstand pathogen adaptations. Past efforts in the identification of alleles, genes, and regulatory genomic regions have been hindered by an incomplete draft assembly [26].…”

Section: Introductionmentioning

confidence: 99%

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

Padgitt-Cobb

Kingan

Wells

et al. 2019

Preprint

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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 around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid 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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Precision QTL mapping of downy mildew resistance in hop (Humulus lupulus L.)

Cited by 33 publications

References 30 publications

Susceptibility of Hop Cultivars to Downy Mildew: Associations with Chemical Characteristics and Region of Origin

Susceptibility of Hop Cultivars to Downy Mildew: Associations with Chemical Characteristics and Region of Origin

Downy mildew resistance is genetically mediated by prophylactic production of phenylpropanoids in hop

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

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