The epiphytic lichen Letharia vulpina has been commonly sampled in-situ for nitrogen (N) deposition biomonitoring studies but has never before been transplanted for this purpose. In the high-elevation wilderness areas of southern California Letharia vulpina is generally uncommon, making in-situ sampling difficult. In this study, we compared thallus N accumulation...
The role of small secreted peptides in plant defense responses to viruses has been seldom investigated. Here, we report a role for potato (Solanum tuberosum) PIP1, a gene predicted to encode a member of the PAMP-induced peptide (PIP) family, in the response of potato to potato virus Y infection (PVY)....
Biofortification of folates in staple crops is an important strategy to help eradicate human folate deficiencies. Folate biofortification using genetic engineering has shown great success in rice grain, tomato fruit, lettuce, and potato tuber. However, consumers’ skepticism, juridical hurdles, and lack of economic model have prevented the widespread adoption of...
The sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our...
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
In the Pacific Northwestern United States, the hop powdery mildew fungus, Podosphaera macularis, survives overwintering periods in association with living host tissue because the ascigerious stage of the pathogen is not known to occur in this region. Field experiments were conducted over a 5-year period to describe the overwintering process...
Shrubs, bunchgrasses and biological soil crusts (biocrusts) are believed to contribute to site resistance to plant invasions in the presence of cattle grazing. Although fire is a concomitant disturbance with grazing, little is known regarding their combined impacts on invasion resistance. We are the first to date to test the...
A new species belonging to the lichen genus Physconia is described from Alaska and the Canadian and American Rocky Mountains and adjacent forested regions. It is also reported from China, Nepal, India and Siberia. The new species, Physconia labrata, is superficially similar to P. perisidiosa, but can be distinguished by...
Thiamine diphosphate (vitamin B1) plays a fundamental role as an enzymatic cofactor in universal metabolic pathways including glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle. In addition, thiamine diphosphate has recently been shown to have functions other than as a cofactor in response to abiotic and biotic stress...
Thiamine pyrophosphate (vitamin B1) is an essential nutrient in the human diet, and is often referred as the energy vitamin. Potato contains modest amounts of thiamine. However, the genetic variation of thiamine concentrations in potato has never been investigated. In this study, we determined thiamine concentrations in freshly-harvested unpeeled tubers...
Biofortification of staple crops like potato via breeding is an attractive strategy to reduce human micronutrient deficiencies. A prerequisite is metabolic phenotyping of genetically diverse material which can potentially be used as parents in breeding programs. Thus, the natural genetic diversity of thiamine and folate contents was investigated in indigenous...
Malnutrition is one of the world’s largest health concerns. Folate (a.k.a. vitamin B9) is essential in the human diet and without adequate folate intake several serious health concerns such as congenital birth defects and an increased risk of stroke and heart disease can occur. Most people’s folate intake remains sub-optimal...
Background
Potato Virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genotype, the PVY strain, and the environmental conditions. A potato cultivar can induce resistance to a...
Thiamin is an essential nutrient in the human diet. Severe thiamin deficiency leads to beriberi, a lethal disease which is common in developing countries. Thiamin biofortification of staple food crops is a possible strategy to alleviate thiamin deficiency-related diseases. In plants, thiamin plays a role in the response to abiotic...
Thiamin diphosphate (ThDP), also known as vitamin B1, serves as an enzymatic cofactor in glucose metabolism, the Krebs cycle, and branched-chain amino acid biosynthesis in all living organisms. Unlike plants and microorganisms, humans are not able to synthesize ThDP de novo and must obtain it from their diet. Staple crops...
Thiamin is essential for human health. While plants are the ultimate source of thiamin in most human diets, staple foods like white rice have low thiamin content. Therefore, populations whose diets are mainly based on low-thiamin staple crops suffer from thiamin deficiency. Biofortification of rice grain by engineering the thiamin...
Potato virus Y (PVY) is a major potato pathogen affecting potato yields worldwide. Thiamin, a water-soluble B vitamin (vitamin B1) has been shown to boost the plant’s immunity, thereby increasing resistance against pathogens. In this study, we tested different concentrations of thiamin (1 mM, 10 mM, 50 mM, 100 mM)...
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide...
Micronutrient malnutrition, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crop in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in potatoes could help alleviate worldwide micronutrient...
Explaining restoration failure can be as important as touting success. We used a series of studies to understand the failure of techniques commonly used to restore wetland prairies in the Willamette Valley of western Oregon. Burning, fallowing, and solarization (covering tilled plots with plastic sheeting to heat the soil) had...
Question: Most results of restoration efforts are species-specific and/or site-specific and therefore are not general enough to be easily applied to other species and other sites. Our research addresses the issue of species-specific results by investigating the feasibility of using plant traits instead of taxonomic species to characterize species responses...
Questions: Are traits related to the performance of plant species in restoration? Are the relationships between traits and performance consistent across the functional groups of annual forbs, perennial forbs, and grasses? Do the relationships between traits and performance depend on neighboring functional groups? Location: A former agricultural field, being restored...
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were...
Host resistance, both quantitative and qualitative, is the preferred long-term approach for disease management in many pathosystems, including powdery mildew of hop (Podosphaera macularis). In 2012, an epidemic of powdery mildew occurred in Washington and Idaho on previously resistant cultivars whose resistance was putatively based on the gene designated R6....
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The...
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
Nitrogen-fixing lichens (cyanolichens) are an important source of nitrogen (N) in Pacific Northwest forests, but limitation of lichen growth by elements essential for N fixation is poorly understood. To investigate how nutrient limitation may affect cyanolichen growth rates, we fertilized a tripartite cyanobacterial lichen (Lobaria pulmonaria) and a green algal...
Optimum timing and use of fungicides for disease control are improved by an understanding of the characteristics of fungicide physical mode of action. Greenhouse and field experiments were conducted to quantify and model the duration of pre- and postinfection activity of fungicides most commonly used for control of hop downy...
Results of 28 field trials conducted over a 12-year period investigating management of hop powdery mildew caused by Podosphaera macularis were quantitatively summarized by meta-analysis to compare product efficacy and use patterns by mode of action as defined by Fungicide Resistance Action Committee (FRAC) groups. Availability of original observations enabled...
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013,...
Correction:
21 Jan 2015: The PLOS ONE Staff (2015) Correction: Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages. PLOS ONE 10(1): e0117735. https://doi.org/10.1371/journal.pone.0117735
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles in the specific infection steps have not been addressed. Here we...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms...
Impact and relevance are valued by both plant pathologists and
the supporters of research and extension. Impact has been characterized
as the “So what?” of research results, and in applied research
in agriculture typically involves some change in human
behavior. This might involve, for instance, avoidance of broad
spectrum pesticides,...
Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus,
some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model
predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with...
Introduction: Biotic soil crust communities contribute valuable ecosystem services and biodiversity in steppe ecosystems. The uncommon crust lichens Acarospora schleicheri, Fuscopannaria cyanolepra, Rhizocarpon diploschistidina, and Texosporium sancti-jacobi are associated with fine-textured soils along rivers of the Columbia Basin. A. schleicheri and R. diploschistidina indicate late-successional habitat and may serve as...
Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms
describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The
widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth...
The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into
a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began
during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics...
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop,
maintain and use a set of structured, controlled
vocabularies for the annotation of genes, gene
products and sequences. The GO ontologies
are expanding both in content and in structure.
Several new relationship types have been introduced
and used, along with...
Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops
and a community resource for rice. We are populating and curating Gramene with
annotated rice (Oryza sativa) genomic sequence data and associated biological information
including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait
Loci (QTL). In order to support queries...
The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative
effort among several plant databases and experts in plant systematics, botany
and genomics. A primary goal of the POC is to develop simple yet robust
and extensible controlled vocabularies that accurately reflect the biology of plant
structures and developmental stages. These...
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require
uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative
studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is
used to describe...