Functional Variation of Plant-Pathogen Interactions: New Concept and Methods for Virulence Data Analyses.

Classical virulence analysis is based on discovering virulence phenotypes of isolates with regard to a composition of resistance genes in a differential set of host genotypes. With such a vision, virulence phenotypes are usually treated in a genetic manner as one of two possible alleles, either virulence or avirulence in a binary locus. Therefore, population genetics metrics and methods have become prevailing tools for analyzing virulence data at multiple loci. However, a basis for resolving binary virulence phenotypes is infection type (IT) data of host-pathogen interaction that express functional traits of each specific isolate in a given situation (particular host, environmental conditions, cultivation practice, and so on). IT is determined by symptoms and signs observed (e.g., lesion type, lesion size, coverage of leaf or leaf segments by mycelium, spore production and so on), and assessed by IT scores at a generally accepted scale for each plant-pathogen system. Thus, multiple IT profiles of isolates are obtained and can be subjected to analysis of functional variation within and among operational units of a pathogen. Such an approach may allow better utilization of the information available in the raw data, and reveal a functional (e.g., environmental) component of pathogen variation in addition to the genetic one. New methods for measuring functional variation of plant-pathogen interaction with IT data were developed. The methods need an appropriate assessment scale and expert estimations of dissimilarity between IT scores for each plant-pathogen system (an example is presented). Analyses of a few data sets at different hierarchical levels demonstrated discrepancies in results obtained with IT phenotypes versus binary virulence phenotypes. The ability to measure functional IT-based variation offers promise as an effective tool in the study of epidemics caused by plant pathogens.

Sperm competition and the evolution of gametic compatibility in externally fertilizing taxa.

Proteins expressed on the surface of sperm and egg mediate gametic compatibility and these proteins can be subject to intense positive selection. In this review, we discuss what is known about the patterns of adaptive evolution of gamete recognition proteins (GRPs). We focus on species that broadcast eggs and sperm into the environment for external fertilization, as the ease of observing and manipulating gamete interactions has allowed for greater advances in the understanding of GRP evolution, uncomplicated by confounding behavioral and physiological components that offer alternative evolutionary targets in internal fertilizers. We discuss whether interspecific mechanisms, such as selection to avoid fertilization between species (reinforcement selection), or intraspecific mechanisms, such as selection to increase (or decrease) the affinity between eggs and sperm based on the intensity of sperm competition, may be responsible for the pattern of GRP evolution observed. Variation in these proteins appears to influence gametic compatibility; GRP divergence among species is a better predictor of hybrid fertilization than neutral genetic markers and GRP variation within species predicts reproductive success among individuals within a population. Evidence suggests that sperm competition may play a large role in the evolution of gametic compatibility.

Comparative analysis of flexible two-parameter models of plant disease epidemics.

ABSTRACT Eleven previously published models of plant disease epidemics, given as differential equations with a rate and a shape parameter, are compared using general model characteristics as well as their usefulness in fitting observed data. Six out of the eleven models can be solved analytically resulting in epidemic growth functions, while the others can be solved only numerically. When all 11 differential equations were fitted to two data sets, all models showed a similar goodness of fit, although the shape parameter in some models could not be estimated very precisely. With respect to useful characteristics (exponential population growth at the beginning, ability to generate monomolecular disease progression, and flexibility of the inflection point), the models of Fleming, Kosman-Levy, Birch, Richards and Waggoner, and Rich are recommended. Formulas were established to calculate the point of inflection as well as the weighted absolute and relative rate, respectively, depending on the shape and rate parameter. These formulas allow transformation of the parameter values of one model into those of another model in many cases. If the two models are required to have the same temporal position of the disease progress curve, then the initial disease level at the start of the epidemic or the time when the inflection point is reached have to be transformed.

Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species.

Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)-vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well-founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals' phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.

Spore dimensions of Puccinia species of cereal hosts as determined by image analysis.

Digital image analysis was used to measure dimensions of spores produced by Puccinia coronata, P. graminis, P. hordei, P. recondita, P. striiformis and P. triticina. Included were teliospores, basidiospores, urediniospores and, except for P. striiformis, pycniospores and aeciospores. Length, width and projection area of spores were measured with NIH Image or Scion software. By using limits on size, spores were automatically selected and measured, except for teliospores, which required manual elimination of the pedicel and separation of images of adhering spores. Length and width were determined as the major and minor axes of the best fitting ellipse for each spore. This procedure gave values for length and width close to results obtained with an ocular micrometer. Projection area was determined as the number of pixels within spore boundaries multiplied by the area represented by each pixel, giving values that are not feasible to obtain accurately with an ocular micrometer. Of the species studied, spores of P. recondita had the largest dimensions, P. triticina had the smallest. The rank of the six species based on increasing width, length or projection area was almost the same, using each spore type except pycniospores. Generally, differences of 5% in a given spore dimension between two species were significant. Differences between species were greater with basidiospores and aeciospores than with other spore types. Teliospores were unique in that length and width were negatively correlated, resulting in less variation in area than in length or width. The results indicate that image analysis is useful for measuring spore dimensions, that projection area of spores is a useful added parameter for characterizing rust species and that dimensions of teliospores, basidiospores, aeciospores and urediniospores each are potentially useful for differentiating species.

Genetic Variation and Virulence on Lr26 in Puccinia triticina.

ABSTRACT The genetic relationships between isolates of Puccinia triticina virulent on wheat with the Lr26 resistance gene were studied. The diversity within and between isolates of P. triticina from Israel, Europe, and the United States was determined by virulence on near-isogenic Thatcher lines and by random amplified polymorphic DNA. According to the molecular markers, isolates that were virulent on Lr26 had diversity levels similar to those of Lr26 nonpathogenic isolates. Distances between subpopulations of isolates virulent and avirulent on Lr26 varied and were unrelated to the Lr26 virulence phenotype. Cluster analysis suggested four groups, three of which were closely associated with the geographical origin of the isolates-Israel, the United States, and Europe. All four groups included both Lr26 virulent and avirulent pathotypes. The results showed that Lr26 virulent rust pathotypes are as genetically dissimilar as the rest of the population. The cluster analysis showed that the rust population in Israel includes at least two different subpopulations, both of which contain Lr26 virulent and Lr26 avirulent isolates.

PF-IND: probability algorithm and software for separation of plant and fungal sequences.

The separation of plant and fungal sequences in EST pools by bioinformatic methods is difficult because of sequence similarities between plants and fungi, lack of enough sequence information, and the short length of the isolated fragments. An algorithm and software that utilize the differences in codon usage bias to discriminate between plant and fungal sequences are described. The software (PF-IND) includes five pairs of fungi and their host plants that can be used to analyze a large number of related species. Analysis of a sequence provides an arbitrary value that defines the likelihood that a sequence will be a fungal or a plant gene. The software can distinguish between homologous fungal and plant genes and it helps identify the correct reading frame of unknown expressed sequence tags (ESTs) for which BLAST analyses do not provide clear information. Short sequences of 100-150 bp can be analyzed with high confidence. PF-IND analysis of 100 sequences derived from fungal infected plants identified the origin of 94 sequences. Only 66 sequences were identified by a BLASTX analysis of the same 100 ESTs. Overall, PF-IND is a novel bioinformatic tool aimed at assisting the research of fungus-plant interactions.

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2001.

Collections of Puccinia triticina were obtained from rust-infected wheat leaves by cooperators throughout the United States and from surveys of wheat fields and nurseries in the Great Plains, Ohio Valley, Gulf Coast, California, Pacific Northwest, and Atlantic Coast States in order to determine the virulence of the wheat leaf rust fungus in 2001. Single uredinial isolates (477 in total) were derived from the wheat leaf rust collections and tested for virulence phenotype on lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17, Lr30, LrB, Lr10, Lr14a, and Lr18. The isolates also were tested for virulence on adult plants with leaf rust resistance genes Lr12, Lr13, Lr22a, Lr22b, Lr34, Lr35, and Lr37. In the United States in 2001, 44 virulence phenotypes of P. triticina were found. Virulence phenotype MBDS, which is virulent to resistance gene Lr17, was the most common phenotype in the United States. MBDS was found in the Southeast, Great Plains, and Ohio Valley regions. Virulence phenotype THBJ, which is virulent to Lr16 and Lr26, was the second most common phenotype, and occurred almost exclusively in the north-central Great Plains region. Phenotype MCDS, which is virulent to Lr17 and Lr26, was the third most common phenotype and was found primarily in the Southeast, Ohio Valley, and Great Plains regions. The Southeast and Ohio Valley regions differed from the Great Plains region for predominant virulence phenotypes, which indicate that populations of P. triticina in those areas are not closely connected. The northern and southern areas of the Great Plains region differed for phenotypes with virulence to Lr16; however, the two areas had other phenotypes in common. Virulence to the adult plant resistance genes Lr35 and Lr37 was detected for the first time in North America in the MBDS, MCJS, and MCDS phenotypes.

Measure of multilocus correlation as a new parameter for study of plant pathogen populations.

ABSTRACT The measure of multilocus correlation for diallelic loci was developed to augment use of other diversity indices in the study of multilocus structure of populations. This measure provides information not revealed by other parameters for measuring multilocus association and linkage disequilibrium among pairs of loci. Relationships between the measures of multilocus correlation and association and all commonly used indices for diversity within populations are also described. A number of hypothetical examples demonstrate that the measure of multilocus correlation describes unique aspects of multilocus structure of populations compared with the measure of multilocus association and phi coefficient of association. The measure of multilocus correlation can be used for analysis of independence of differentiating characters for a given population-the necessary condition of valid applications of the bootstrap method across differentials. Comparisons of the measures of multilocus correlation and association with the measures of diversity within population show that they reveal different aspects of population structure. As an adjunct to standard diversity indices, the measure of multilocus correlation may reveal subtle differences in diversity within populations even if the standard index fails to distinguish between the populations. A new measure of population uniformity also was developed to characterize another aspect of diversity within populations not detected by standard indices.

Comparative Analysis of Indices in the Study of Virulence Diversity Between and Within Populations of Puccinia recondita f. sp. tritici in Israel.

ABSTRACT Isolates of Puccinia recondita f. sp. tritici (n = 260) obtained from bread, durum, and wild emmer wheat leaf collections throughout Israel during 1993 to 1997 were analyzed for virulence on a set of wheat differentials. The overall frequency of virulence increased on differentials possessing resistance genes Lr1, Lr2a, Lr3, and Lr26 and decreased on Lr17, Lr21, and Lr30. Genes Lr9 and Lr24 were resistant, while Lr18 was susceptible (98% in 1996) to all tested leaf rust isolates and Lr10 and Lr23 were susceptible to more than 78% of the isolates. Diversity between populations (years) was assessed using Kosman's H(KB) (based on degrees of similarity among distinct phenotypes) and H(KDis) (based on frequencies of individual virulences) and Nei's and Rogers' distances. The greatest difference occurred between the 1993 and 1994 populations. Phenotypic diversity within each population (year) was analyzed using the Shannon's, Simpson's, and Kosman's indices. The highest diversity within years was recorded in 1994 and significantly increased from 1993 to 1994 for all indices. The variance in the diversity between populations can be only partially explained by differences between corresponding diversities within population. The comparative analysis of diversity between and within populations over the 5 years enabled a detailed study of changes in the pathogen population. The results show that the different measures do not yield the same rank order of diversity.

Emergency room visits of asthmatic children, relation to air pollution, weather, and airborne allergens.

BACKGROUND: The worldwide increase in the incidence, prevalence, and severity of asthma may suggest that environmental factors play a role in these epidemiologic changes. OBJECTIVE: To examine the correlations between air pollutants, weather conditions, airborne allergens, and the incidence of emergency room (ER) visits of children with acute asthma attacks. DESIGN: One-year prospective study. Data of daily concentration of air pollutants, weather conditions, and selective airborne allergens were collected and compared with the number of ER visits of asthmatic children. SUBJECTS: 1076 asthmatic children (aged 1 to 18 years) who presented at the Pediatric ER between January 1 and December 31, 1993. RESULTS: Correlations between fluctuations in ER visits of asthmatic children and various environmental parameters were more relevant for weekly than for daily values. Emergency room visits correlated positively with concentrations of NOx, SO2 and with high barometric pressure; and negatively with O3 concentration and minimal and maximal temperature. There were no significant correlations with concentrations of particulates, humidity, or airborne pollen and spores. An exceptionally high incidence of ER visits of asthmatic children was observed during September. This peak coincided with the beginning of the school year and the Jewish holidays. The correlations between ER visits and the environmental factors increased significantly when the September peak was excluded, revealing that 61% of the variance in ER visits was explained by NOx, SO2, and 03 concentrations, 46% by weather parameters, 66% by NOx, SO2 and barometric pressure, and 69% by the combination of air pollutants and weather parameters. CONCLUSION: The major factors found to be associated with ER visits of asthmatic children were high NOx, high SO2, and high barometric pressure. Negative correlation was found between ER visits of asthmatic children and ozone concentrations. The particularly high number of ER visits at the beginning of the school year and the Jewish holidays was probably associated with an increase in the number of viral infections and/or emotional stress.

The 'traveling salesman problem': a new approach for identification of differences among pollen allergens.

BACKGROUND: It is not easy to identify the specific plant species that causes an allergic response in a certain patient at a certain time. This is further complicated by the fact that closely related plant species cause similar allergic responses. A novel mathematical technique is used for analysis of skin responses of a large number of patients to several groups of allergens for improvement of the understanding of their similarity or dissimilarity and their status regarding cross-reactivity. METHODS: The responses of 153 atopic patients to 42 different pollen extracts were tested by skin prick tests. Among the responses of patients to various extracts, a measure of dissimilarity was introduced and calculated for all pairs of allergens. A matrix-structuring technique, based on a solution of the 'Travelling Salesman Problem', was used for clustering of the investigated allergens into groups according to patients' responses. The discrimination among clusters was confirmed by statistical analysis. RESULTS: Sub groups can be discerned even among allergens of closely related plants, i.e. allergens that are usually regarded as fully cross-reactive. A few such cases are demonstrated for various cultivars of olives and pecans and for various sources of date palms, turf grasses, three wild chenopods and an amaranth. CONCLUSION: The usefulness of the proposed approach for the understanding of similarity and dissimilarity among various pollen allergens is demonstrated.

Clustering of allergenic pollen on the basis of skin responses of atopic patients by matrix analysis.

The responses of 148 atopic patients to some 43 different extracts of allergenic pollen were tested by prick tests. The measure of dissimilarity was introduced and calculated for all pairs of allergens. The investigated allergens were clustered into groups, according to their unbiased greatest similarity, by a matrix-structuring method. Results indicate that subgroups of allergens can be distinguished even within groups of closely related pollen allergens that were believed to be fully cross-reactive. A few cases are demonstrated for various varieties of olives, pecans, date palms, and turf grasses and for some wild chenopods and amaranths. The usefulness of the suggested solution for allergy research and for clinical practice is discussed.