Pathotype-specific QTL for stem rust resistance in Lolium perenne

A genetic map populated with RAD and SSR markers was created from F1 progeny of a stem rust-susceptible and stem rust-resistant parent of perennial ryegrass (Lolium perenne). The map supplements a previous map of this population by having markers in common with several other Lolium spp. maps including EST-SSR anchor markers from a consensus map published by other researchers. A QTL analysis was conducted with disease severity and infection type data obtained by controlled inoculation of the population with each of two previously characterized pathotypes of Puccinia graminis subsp. graminicola that differ in virulence to different host plant genotypes in the F1 population. Each pathotype activated a specific QTL on one linkage group (LG): qLpPg1 on LG7 for pathotype 101, or qLpPg2 on LG1 for pathotype 106. Both pathotypes also activated a third QTL in common, qLpPg3 on LG6. Anchor markers, present on a consensus map, were located in proximity to each of the three QTL. These QTL had been detected also in previous experiments in which a genetically heterogeneous inoculum of the stem rust pathogen activated all three QTL together. The results of this and a previous study are consistent with the involvement of the pathotype-specific QTL in pathogen recognition and the pathotype-nonspecific QTL in a generalized resistance response. By aligning the markers common to other published reports, it appears that two and possibly all three of the stem rust QTL reported here are in the same general genomic regions containing some of the L. perenne QTL reported to be activated in response to the crown rust pathogen (P. coronata).Keywords: Ryegrass population, Fescue festuca pratensis, Disease resistance, Puccinia coronata resistance, SSR markers, Multiflorum lam., Crown rust, Self incompatibility, F-SP Lolii, Linkage mapKeywords: Ryegrass population, Fescue festuca pratensis, Disease resistance, Puccinia coronata resistance, SSR markers, Multiflorum lam., Crown rust, Self incompatibility, F-SP Lolii, Linkage ma

Effects of the Mycoparasite Sphaerellopsis filum on Overwintering Survival of Stem Rust in Perennial Ryegrass

Sphaerellopsis filum is a mycoparasite of Puccinia graminis subsp. graminicola, a rust fungus that causes widespread crop damage on perennial ryegrass grown for seed. In observations taken over the winter months, S. filum was found naturally colonizing 2% of P. graminis subsp. graminicola uredinia on first-year plantings and 25% of the uredinia on second-year plantings of perennial ryegrass. In controlled experiments conducted in glasshouses and growth chambers, S. filum applied to rust-inoculated plants reduced the lifetime spore production of P. graminis subsp. graminicola pustules by half, from 39,000 to 18,000 spores/pustule. Mist duration, temperature, and P. graminis subsp. graminicola pustule age at the time of S. filum inoculation had significant effects on the proportion of P. graminis subsp. graminicola pustules infected by S. filum. Fifty percent of all P. graminis subsp. graminicola pustules were infected when S. filum was inoculated onto erumpent pustules and incubated above 5°C for 48 h while exposed to mist. Plants inoculated with both fungi under controlled conditions and then planted into the field had a significantly greater proportion of P. graminis subsp. graminicola pustules infected with S. filum, and a significantly reduced P. graminis subsp. graminicola overwintering population, compared with plants inoculated with P. graminis subsp. graminicola only. First-year stands of perennial ryegrass treated in the field with monthly applications of S. filum had more than 10 times the proportion of pustules infected with S. filum and 50% less P. graminis subsp. graminicola disease compared with the nontreated controls. In comparison, plants with one application of fungicide during the winter had 98% lower P. graminis subsp. graminicola severity than the P. graminis subsp. graminicola-only control There were no effects of S. filum or fungicide application on rust severity in 2- or 3-year-old perennial ryegrass stands

The strong thirteen spheres problem

The thirteen spheres problem is asking if 13 equal size nonoverlapping spheres in three dimensions can touch another sphere of the same size. This problem was the subject of the famous discussion between Isaac Newton and David Gregory in 1694. The problem was solved by Schutte and van der Waerden only in 1953. A natural extension of this problem is the strong thirteen spheres problem (or the Tammes problem for 13 points) which asks to find an arrangement and the maximum radius of 13 equal size nonoverlapping spheres touching the unit sphere. In the paper we give a solution of this long-standing open problem in geometry. Our computer-assisted proof is based on a enumeration of the so-called irreducible graphs.Comment: Modified lemma 2, 16 pages, 12 figures. Uploaded program packag

Impact of land use patterns and agricultural practices on water quality in the Calapooia River Basin of western Oregon

Agricultural practices, including tillage, fertilization, and residue management, can affect surface runoff, soil erosion, and nutrient cycling. These processes, in turn, may adversely affect (1) quality of aquatic resources as habitat for amphibians, fish, and invertebrates, (2) costs of treating surface and ground water to meet drinking water standards, and (3) large-scale biogeochemistry. This study characterized the surface water sources of nitrogen (N) (total, nitrate [NO₃⁻], ammonium [NH₄⁺], and dissolved organic N) and sediment active within 40 subbasins of the Calapooia River Basin in western Oregon in monthly samples over three cropping years. The subbasins included both independent and nested drainages, with wide ranges in tree cover, agricultural practices, slopes, and soils. Sediment and N form concentrations were tested against weather and agricultural practice variables. Subbasin land use ranged from 96% forest to 100% agriculture. Average slopes varied from 1.3% to 18.9%, and surface water quality ranged from 0.5 to 43 mg L⁻¹ (ppm) total N maxima and 29 to 249 mg L⁻¹ suspended sediment maxima. Total N during the winter was positively related to percentage landcover of seven common agricultural crops (nongrass seed summer annuals, established seed crops of perennial ryegrass [Lolium perenne L.], tall fescue [Schedonorus phoenix {Scop.} Holub], orchardgrass [Dactylis glomerata L.], clover [Trifolium spp.], and newly planted stands of perennial ryegrass and clover) and negatively related to cover by trees and one seed crop, Italian (annual) ryegrass (Lolium multiflorum). Results for NO₃⁻ and total N were highly similar. Sediment concentrations were most strongly related to rainfall totals during periods of 4 and 14 days prior to sampling, with smaller effects of soil disturbance. Fourier analysis of total N over time identified four prominent groups of subbasins: those with (1) low, (2) medium, and (3) high impacts of N (up to 2, 8, and 21 mg L⁻¹, respectively) and a strong cyclical signal peaking in December and (4) those with very high impact of N (up to 43 mg L⁻¹) and a weak time series signal. Preponderance of N in streams draining agriculturally dominated subbasins was in the form of the NO₃⁻ ion, implying mineralization of N that had been incorporated within plant tissue following its initial application in the spring as urea-based fertilizer. Since mineralization is driven by seasonal rainfall and temperature patterns, changes in agronomic practices designed to reduce prompt runoff of fertilizer are unlikely to achieve to more than similar to ~24% reduction in N export to streams.This is the publisher’s final pdf. The published article is copyrighted by Soil and Water Conservation Society and can be found at: http://www.jswconline.org/Keywords: Ecosystem services, Geographically weighted regression, Water quality, Fourier time series analysi

Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control

Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety ‘Capitola’ and the genotype ‘CF1116’. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045–2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality

A Simulation Model for Epidemics of Stem Rust in Ryegrass Seed Crops

A simulation model (STEMRUST_G, named for stem rust of grasses) was created for stem rust (caused by Puccinia graminis subsp. graminicola) in perennial ryegrass grown to maturity as a seed crop. The model has a daily time step and is driven by weather data and an initial input of disease severity from field observation. Key aspects of plant growth are modeled. Disease severity is modeled as rust population growth, where individuals are pathogen colonies (pustules) grouped in cohorts defined by date of initiation and plant part infected. Infections due to either aerial spread or within-plant contact spread are modeled. Pathogen cohorts progress through life stages that are modeled as disease cycle components (colony establishment, latent period, infectious period, and sporulation) affected by daily weather variables, plant growth, and fungicide application. Fungicide effects on disease cycle components are modeled for two commonly used active ingredients, applied preinfection or postinfection. Previously validated submodels for certain disease cycle components formed the framework for integrating additional processes, and the complete model was calibrated with field data from 10 stem rust epidemics. Discrepancies between modeled outcomes and the calibration data (log₁₀[modeled] – log₁₀[observed]) had a mean near zero but considerable variance, with 1 standard deviation = 0.5 log₁₀ units (3.2-fold). It appears that a large proportion of the modeling error variance may be due to variability in field observations of disease severity. An action threshold for fungicide application was derived empirically, using a constructed weather input file favorable for disease development. The action threshold is a negative threshold, representing a level of disease (latent plus visible) below which damaging levels of disease are unable to develop before the yield-critical crop stage. The model is in the public domain and available on the Internet.Keywords: Lolium perenne, Decision aid, Azoxystrobin, Propiconazole, WheatKeywords: Lolium perenne, Decision aid, Azoxystrobin, Propiconazole, Whea

New applications of statistical tools in plant pathology

Citation: Garrett, K., Madden, L., Hughes, G., and Pfender, W. (2007). New Applications of Statistical Tools in Plant Pathology. Phytopathology, 94(9), 999-1003. https://doi.org/10.1094/PHYTO.2004.94.9.999The series of papers introduced by this one address a range of statistical applications in plant pathology, including survival analysis, nonparametric analysis of disease associations, multivariate analyses, neural networks, meta-analysis, and Bayesian statistics. Here we present an overview of additional applications of statistics in plant pathology. An analysis of variance based on the assumption of normally distributed responses with equal variances has been a standard approach in biology for decades. Advances in statistical theory and computation now make it convenient to appropriately deal with discrete responses using generalized linear models, with adjustments for overdispersion as needed. New nonparametric approaches are available for analysis of ordinal data such as disease ratings. Many experiments require the use of models with fixed and random effects for data analysis. New or expanded computing packages, such as SAS PROC MIXED, coupled with extensive advances in statistical theory, allow for appropriate analyses of normally distributed data using linear mixed models, and discrete data with generalized linear mixed models. Decision theory offers a framework in plant pathology for contexts such as the decision about whether to apply or withhold a treatment. Model selection can be performed using Akaike's information criterion. Plant pathologists studying pathogens at the population level have traditionally been the main consumers of statistical approaches in plant pathology, but new technologies such as microarrays supply estimates of gene expression for thousands of genes simultaneously and present challenges for statistical analysis. Applications to the study of the landscape of the field and of the genome share the risk of pseudoreplication, the problem of determining the appropriate scale of the experimental unit and of obtaining sufficient replication at that scale