Denis A. Shah

Nonparametric Analysis of Ordinal Data in Designed Factorial Experiments

ABSTRACT Plant disease severity often is assessed using an ordinal rating scale rather than a continuous scale of measurement. Although such data usually should be analyzed with nonparametric methods, and not with the typical parametric techniques (such as analysis of variance), limitations in the statistical methodology available had meant that experimental designs generally could not be more complicated than a one-way layout. Very recent advancements in the theoretical formulation of hypotheses and associated test statistics within a nonparametric framework, together with development of software for implementing the methods, have made it possible for plant pathologists to analyze properly ordinal data from more complicated designs using nonparametric techniques. In this paper, we illustrate the nonparametric analysis of ordinal data obtained from two-way factorial designs, including a repeated measures design, and show how to quantify the effects of experimental factors on ratings through estimated relative marginal effects.

Spatial patterns of viable spore deposition of Gibberella zeae in wheat fields

ABSTRACT An increased understanding of the epidemiology of Gibberella zeae will contribute to a rational and informed approach to the management of Fusarium head blight (FHB). An integral phase of the FHB cycle is the deposition of airborne spores, yet there is no information available on the spatial pattern of spore deposition of G. zeae above wheat canopies. We examined spatial patterns of viable spore deposition of G. zeae over rotational (lacking cereal debris) wheat fields in New York in 2002 and 2004. Viable, airborne spores (ascospores and macroconidia) of G. zeae were collected above wheat spikes on petri plates containing a selective medium and the resulting colonies were counted. Spores of G. zeae were collected over a total of 68 field environments (three wheat fields during 54 day and night sample periods over 2 years) from spike emergence to kernel milk stages of local wheat. Spatial patterns of spore deposition were visualized by contour plots of spore counts over entire fields. The spatial pattern of spore deposition was unique for each field environment during each day and night sample period. Spore deposition patterns during individual sample periods were classified by spatial analysis by distance indices (SADIE) statistics and Mantel tests. Both analyses indicated that the majority (93%) of the spore deposition events were random, with the remainder being aggregated. All of the aggregated patterns were observed during the night. Observed patterns of spore deposition were independent of the mean number of viable spores deposited during individual sample periods. The spatial pattern for cumulative spore deposition during anthesis in both years became aggregated over time. Contour maps of daily and cumulative spore deposition could be compared with contour maps of FHB incidence to gain insights into inoculum thresholds and the timing of effective inoculum for infection.

Seasonal and Spatial Dynamics of Alate Aphid Dispersal in Snap Bean Fields in Proximity to Alfalfa and Implications for Virus Management

Abstract Alfalfa is a source for viruses that may be acquired by aphids and transmitted to snap bean, Phaseolus vulgaris L. Snap bean fields in proximity to alfalfa could have an increased risk of virus infection. Knowledge of the abundance and temporal and spatial dispersal patterns of commonly encountered aphids in commercial snap bean fields, varying in distance from alfalfa, could provide insight into this risk. Alate aphids were monitored using water pan traps in snap bean and alfalfa fields that were adjacent to or >1 km away from each other. The pea aphid, Acyrthosiphon pisum (Harris), was the most common aphid species captured in early-planted snap bean fields in 2002 and 2003 (56 and 23% of total, respectively), whereas the corn leaf aphid, Rhopalosiphum maidis (Fitch), also was common in 2003 (15% of total). In contrast, the yellow clover aphid, Therioaphis trifolii (Monell), and soybean aphid, Aphis glycines Matsumura, were the most abundant species trapped in late-planted snap bean fields in 2002 (77% of total) and 2003 (64% of total), respectively. These species were prevalent in traps in alfalfa as well. The abundance and temporal dispersal patterns of these species in snap beans adjacent to and >1 km away from alfalfa were similar, suggesting that the risk for virus infection may not be affected by proximity to alfalfa. A similar number of alate aphids also were captured along snap bean field edges and field centers, regardless of their proximity to alfalfa. This suggests that the aphids dispersed into snap bean randomly rather than directionally from the field edge. The implication of these results is that separating snap bean fields from alfalfa or using crop borders/barriers are not likely to be successful virus management strategies.

Transmission Efficiency of Cucumber mosaic virus by Aphids Associated with Virus Epidemics in Snap Bean

Cucumber mosaic virus (CMV) is a major component of the virus complex that has become more pronounced in snap bean in the midwestern and northeastern United States since 2001. Multiple-vector-transfer tests were done to estimate the CMV transmission efficiencies (p) of the main aphid species identified in commercial snap bean fields in New York and Pennsylvania. The four most efficient vectors (p > 0.05) were Aphis gossypii, A. glycines, Acyrthosiphon pisum, and Therioaphis trifolii, which were all significant species in the migratory aphid populations in snap bean. Moderately efficient vectors (0.01 < p < 0.04) were A. spiraecola, A. craccivora, Macrosiphum euphorbiae, and Rhopalosiphum maidis. Poor vectors (p < 0.01) included A. fabae, Nearctaphis bakeri, and Myzus persicae. Only one species, Sitobion avenae, failed to transmit CMV in replicated tests. Estimates of p were consistent between different clones of the same aphid species and among three different field isolates of CMV tested. Single-vector-transfer test results for a subset of the species supported those obtained via the multiple-vector-transfer approach. Our results are consistent with the notion that A. glycines is a major vector of recent CMV epidemics in snap bean, but that species is only one of several that are involved.

WEED SEEDBANK COMMUNITY RESPONSES TO CROP ROTATION SCHEMES

Abstract Improved weed management strategies may be possible through rotational schemes which alter the weed seedbank community. This study investigated the effects of 2-year crop rotations with alfalfa ( Medicago sativa L.), clover ( Trifolium pratense L.), rye ( Secale cereale L.), or sweet corn ( Zea mays L. var. rugosa Bonaf.) on weed seedbank density and diversity at three sites in New York. Weed seedbank density and diversity increased under all rotational schemes over the 2 years, but increases were generally lowest after sweet corn, in which tillage and herbicides were used. By the end of the second year, seed densities of individual weed species had changed to different extents in response to rotational crop. Most of the instances in which seed densities increased significantly were associated with rye. Although pre- and post-emergence herbicides plus tillage were used with sweet corn, weed seedbank densities were similar compared with the alfalfa and clover rotations, in which no herbicides nor tillage were used. Our results indicate that legumes could be a component in the sustainable management of weeds through manipulation of the seedbank. A rye cover crop did not appear to deter seed return nor recruitment to the seedbank as much as the legumes did.

Foci of stagonospora nodorum blotch in winter wheat before canopy development.

ABSTRACT Stagonospora nodorum blotch (SNB) often develops explosively on upper leaves and glumes of wheat. Inoculum for late season infections may arise from early disease foci in the lower canopy or from recent immigration of wind-dispersed ascospores. Research was conducted to determine if foci of SNB are present and secondary spread has occurred in fields before tiller elongation. We determined the incidence of infection by Stagonospora nodorum for plants sampled at the mid-tillering stage in 96 1-m(2) quadrats in each of two fields. Isolates of S. nodorum were recovered from 32 quadrats, one per infected plant where possible. Multilocus restriction fragment length polymorphism haplotypes were determined for each isolate. Of 55 isolates collected from one field, there were 22 distinct haplotypes. Diseased plants were aggregated in both fields; aggregates sometimes extended to adjacent quadrats. Plants within aggregates were often infected by the same haplotype, suggesting that secondary spread had occurred. Foci overlapped because some aggregates were infected by more than one haplotype. Our results show that genetically diverse populations of S. nodorum were already established in fields before canopy development and were comprised of sometimes overlapping foci undergoing clonal expansion.

Regional and varietal differences in the risk of wheat seed infection by fungal species associated with fusarium head blight in Italy

The incidence of seed infection by fungal species pertinent to the fusarium head blight complex was monitored from 1999 to 2002 in two soft and three durum wheat cultivars grown across the northern, central and southern production zones of Italy, in order to characterize the species composition at the seed level. The main species recovered were Fusariumgraminearum, F. poae and Microdochium nivale. There was a marked influence of production zone on seed infection incidence for both durum and soft wheat cultivars, with incidence of infection generally decreasing from the northern to the southern zone. Incidence of seed infection by different species of Fusarium was twice to four times higher in durum compared with the soft wheat cultivars in the study. There were no significant differences in terms of seed infection incidence between the two soft wheat cultivars, but the durum cultivars differed in their levels of seed infection for some of the pathogens. The results demonstrated that the durum cultivars were more at risk of seed infection by pathogens associated with fusarium head blight, and that wheat grown in northern Italy is at higher risk of seed infection by these species.

Predicting Fusarium Head Blight Epidemics With Weather-Driven Pre- and Post-Anthesis Logistic Regression Models

Our objective was to identify weather-based variables in pre- and post-anthesis time windows for predicting major Fusarium head blight (FHB) epidemics (defined as FHB severity ≥ 10%) in the United States. A binary indicator of major epidemics for 527 unique observations (31% of which were major epidemics) was linked to 380 predictor variables summarizing temperature, relative humidity, and rainfall in 5-, 7-, 10-, 14-, or 15-day-long windows either pre- or post-anthesis. Logistic regression models were built with a training data set (70% of the 527 observations) using the leaps-and-bounds algorithm, coupled with bootstrap variable and model selection methods. Misclassification rates were estimated on the training and remaining (test) data. The predictive performance of models with indicator variables for cultivar resistance, wheat type (spring or winter), and corn residue presence was improved by adding up to four weather-based predictors. Because weather variables were intercorrelated, no single model or subset of predictor variables was best based on accuracy, model fit, and complexity. Weather-based predictors in the 15 final empirical models selected were all derivatives of relative humidity or temperature, except for one rainfall-based predictor, suggesting that relative humidity was better at characterizing moisture effects on FHB than other variables. The average test misclassification rate of the final models was 19% lower than that of models currently used in a national FHB prediction system.

Effect of weed growth stage and adjuvant on the efficacy of fomesafen and bentazon

Abstract The efficacies of bentazon and fomesafen in controlling annual weeds in dry and edible pod beans in New York State were investigated in greenhouse and field experiments. Dose responses to bentazon and fomesafen were studied for four weed species (ragweed, velvetleaf, eastern black nightshade, and hairy nightshade) under greenhouse conditions. Herbicides were applied at cotyledon to two-, two- to four-, and four- to six–true leaf stages, both with and without a crop oil concentrate (bentazon) or a nonionic surfactant (fomesafen). Field studies were conducted for 2 yr for all weed species except eastern black nightshade, for which no adequate field populations were found. Field studies confirmed greenhouse results, indicating that weed control could be improved by the use of an adjuvant, but there were exceptions. In general, adjuvant usage improved the efficacy of fomesafen more than it did with bentazon. The minimum rates of herbicide required for effective and consistent control was dependent on the particular combination of weed species, herbicide and its rate of application, growth stage at which the application was made, and adjuvant usage. Nomenclature: Bentazon; fomesafen; common ragweed, Ambrosia artemisiifolia L. AMBEL; eastern black nightshade, Solanum ptycanthum Dun. SOLPT; hairy nightshade, Solanum sarrachoides Sendt. SOLSA; velvetleaf, Abutilon theophrasti Medic. ABUTH; dry and snap bean, Phaseolus vulgaris L.

Community structure of the Fusarium complex on wheat seed in Italy

The objective was to quantitatively document the pathogen community associated with the Fusarium head blight complex in Italian wheat. The observational study was prompted by increased concerns about mycotoxin contamination coupled with a surge in organically grown wheat. During the three-year survey (2004 to 2006) in three geopolitically defined zones (north, centre, south), seedborne pathogens associated with Fusarium head blight in organic bread and durum wheat were assayed by the freezing blotter method and identified to species based on morphological features. The four most abundant species overall, in order from highest to lowest, were Fusarium poae, Microdochium nivale, F. verticillioides and F. graminearum. Environment was more influential than wheat cultivar in determining the variances in seed infestation counts. Counts of infested seeds were higher (and more variable) in the north and centre zones than in the south zone. The odds of observing any seed infestation was significantly higher in both the north and centre zones (compared with the south zone) for F. avenaceum, F. graminearum, F. poae, and M. nivale in durum wheat. There was a significant nonlinear relationship between seed infestation prevalence and incidence, with evident separation of species along the prevalence-incidence curve. Species co occurrence was observed, but associations shifted with wheat type, over years, and among zones. F. poae was not positively associated with any other species.