Spread of Heterobasidion annosum in Christmas Tree Plantations of the United States Pacific Northwest

ABSTRACT The population structure of Heterobasidion annosum in the Pacific Northwest (PNW) Christmas tree plantations was estimated at two spatial scales to assess the relative importance of primary and secondary infection, colonization, and spread of the pathogen. Ninety-three isolates from single trees in 27 discrete mortality pockets and 104 isolates from 12 individual root systems of noble and Fraser fir trees were sampled near Mossyrock, Washington. Isolates were genotyped using somatic compatibility assays and microsatellite markers to determine the spatial scale at which dispersal of single genotypes (genets) was occurring. All isolates sampled from different trees in discrete mortality pockets had distinct genotypes, whereas the root systems of single trees were dominated by one or two genotypes. These results suggest that infection of PNW Christmas trees results from frequent primary infection events of adjacent stumps and localized secondary spread within root systems rather than clonal spread of the pathogen between adjacent trees. We hypothesize that mortality pockets may be due to availability of infection courts and/or variation in inoculum levels during selective harvesting of patches of mature trees.     

The effect of non-inversion tillage and light availability on dispersal and spatial growth of Cynodon dactylon

The invasive ability of Cynodon dactylon is dependent on self dispersal and on cultivation practices. Tillage can seriously change patch biomass and spatial structure, spreading vegetative propagules of the weed. The objectives of this study were: (i) to quantify the effect on non‐inversion tillage on dispersal, establishment and colonization of C. dactylon and (ii) to propose a simple model considering soil cultivation effects and light availability on spatial growth of weed patches. Two experiments were carried out, exploring different soils and environmental conditions. Spatial distribution of vegetative units differed when tillage was conducted with different non‐inversion implements and could be described by simple functions. A minimum patch biomass seems necessary before vegetative structures are vulnerable to movement by cultivation. Only a small proportion of the biomass dispersed from original patches was able to establish. However, simulation showed that the area colonized by C. dactylon mostly increased by means of tillage dispersal, both with and without crop competition, in one growing cycle. It appears sensible to consider changing cultivation practices to reduce weed dispersal and to use crop competition for light to create unsuitable habitats limiting weed colonization.     

Localized origins of herbicide resistance in Alopecurus myosuroides

The process of evolution of resistance to acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides was investigated in four distinct patches of Alopecurus myosuroides Huds. (black-grass) that occur within adjacent fields on a cereal farm in Nottinghamshire, UK. In one field, there was a `main' patch containing 96% resistant plants and two `satellite' patches containing ≈2.9% and 4.4% resistant plants, and in an adjacent field another patch contained 25% resistant plants. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction (PCR) was used to analyse variation at 30 genetic loci in at least 20 resistant and 20 sensitive individual plants from each patch, from additional resistant populations from Essex and Lincolnshire, and from a sensitive reference population. Banding patterns were found to be highly repeatable. Each patch contained a high level of genetic diversity, regardless of its resistance status, and there was evidence for genetic differences between the patches (Gst = 0.14, Nei's distances up to 0.26). There was no evidence that resistance had spread from the `main' patch to the others, as resistant and sensitive plants in the same patch were more closely related on average than were resistant plants from neighbouring patches. The most likely explanations of this distribution, and their implications, are discussed.     

Population Genetic Structure of Septoria passerinii in Northern Great Plains Barley

ABSTRACT The genetic structure of Septoria passerinii from nine field populations was examined at several scales (within lesions, among lesions in a leaf, among leaves in a field, and among fields in North Dakota and western Minnesota) by using amplified fragment length polymorphism (AFLP) markers. A total of 390 isolates were sampled from seven barley fields located in North Dakota and two barley fields located nearby in western Minnesota in 2003 and 2004. Based on 57 polymorphic AFLP markers, AFLP DNA fingerprints identified 176 different genotypes among 390 (non-clone-corrected) isolates in nine different fields. In two intensively sampled sites, ND16 (Williston, ND) and ND17 (Langdon, ND), only one to four different genotypes were found within a lesion. A higher level of genetic and genotypic diversity was found within a leaf in which six to nine different genotypes were found from lesions on a leaf. The genetic diversity within a leaf was similar to the genetic diversity within a field. The average genetic diversity (H) within a field across all AFLP loci was approximately 0.3, except at site ND12 (Carrington, ND) where it was 0.16. Genotypic diversity was high in all populations, and with the exception of ND15 (Rothsay, MN), very low multilocus linkage disequilibrium values ( r(d)) were found in all populations. The population differentiation, G(ST), was relatively high (G(ST) = 0.238) among the nine populations due to the high G(ST) in ND12, ND14 (Twin Valley, MN), and ND15. Population differentiation without those three populations was 0.09. A lack of correlation between geographical distance and genetic distance was found, suggesting the potential for a high level of gene flow between different geographical regions. The population genetic structure described in this study for S. passerinii in North Dakota and western Minnesota is consistent with that of a sexually reproducing fungus.     

Random amplified polymorphic DNA markers reveal low genetic variation and a single dominant genotype in Eichhornia crassipes populations throughout China

Genetic variation within and between 34 populations of Eichhornia crassipes (water hyacinth) in China was surveyed using random amplified polymorphic DNA (RAPD) markers. A total of 1009 individuals were analysed, for which 12 RAPD primers amplified 69 reproducible bands, with 22 (32%) being polymorphic. The percentage of polymorphic loci (p) within a population ranged from 4.4% to 17.4%, and the mean Nei's gene diversity (H_e) was 0.046 ± 0.0145, indicating a low genetic diversity of E. crassipes in China. Each population contained at least four RAPD phenotypes (genotypes), and the same particular genotype was invariably dominant in all the populations sampled. The mean proportion of distinguishable genotypes was 0.29. Analysis of molecular variance revealed a large proportion of genetic variation (83.9%) residing within populations and a slightly larger proportion (88.1%) within localities, indicating a low genetic differentiation of E. crassipes populations, both locally and regionally. Human-mediated dispersal, vigorous clonal growth, and a generally low level of sexual reproduction were thought to be responsible for such a pattern of genetic structure.     

The Genetic Structure of Australian Populations of Mycosphaerella musicola Suggests Restricted Gene Flow at the Continental Scale

ABSTRACT Mycosphaerella musicola causes Sigatoka disease of banana and is endemic to Australia. The population genetic structure of M. musicola in Australia was examined by applying single-copy restriction fragment length polymorphism probes to hierarchically sampled populations collected along the Australian east coast. The 363 isolates studied were from 16 plantations at 12 sites in four different regions, and comprised 11 populations. These populations displayed moderate levels of gene diversity (H = 0.142 to 0.369) and similar levels of genotypic richness and evenness. Populations were dominated by unique genotypes, but isolates sharing the same genotype (putative clones) were detected. Genotype distribution was highly localized within each population, and the majority of putative clones were detected for isolates sampled from different sporodochia in the same lesion or different lesions on a plant. Multilocus gametic disequilibrium tests provided further evidence of a degree of clonality within the populations at the plant scale. A complex pattern of population differentiation was detected for M. musicola in Australia. Populations sampled from plantations outside the two major production areas were genetically very different to all other populations. Differentiation was much lower between populations of the two major production areas, despite their geographic separation of over 1,000 km. These results suggest low gene flow at the continental scale due to limited spore dispersal and the movement of infected plant material.     

土壤中氮营养斑研究进展

由于自然和人为因素,营养斑(nutrient patch)在土壤中是普遍存在的。从70年代以来,国外就通过各种模拟方式对土壤中营养斑进行了大量的研究,尤其以对氮营养斑研究居多。研究表明:氮营养斑对新生根系的繁殖影响较为明显,但不同植物反应不一样,影响机理还不很清楚。营养斑也是生物活性较强、种群数量较多区域,在养分循环体系中起着特殊作用。营养斑对土壤的理化性质和生物性质可能有很大的影响,但这方面的研究很欠缺。本文主要对土壤中氮营养班的研究进展做一综述。     

Population Structure of Mycosphaerella graminicola: From Lesions to Continents

ABSTRACT The genetic structure of field populations of Mycosphaerella graminicola was determined across a hierarchy of spatial scales using restriction fragment length polymorphism markers. The hierarchical gene diversity analysis included 1,098 isolates from seven field populations. Spatial scales ranged from millimeters to thousands of kilometers, including comparisons within and among lesions, within and among fields, and within and among regions and continents. At the smallest spatial scale, microtransect sampling was used to determine the spatial distribution of 15 genotypes found among 158 isolates sampled from five individual lesions. Each lesion had two to six different genotypes including both mating types in four of the five lesions, but in most cases a lesion was composed of one or two genotypes that occupied the majority of the lesion, with other rare genotypes interspersed among the common genotypes. The majority (77%) of gene diversity was distributed within plots ranging from approximately 1 to 9 m(2) in size. Genotype diversity (G / N) within fields for the Swiss, Texas, and Israeli fields was high, ranging from 79 to 100% of maximum possible values. Low population differentiation was indicated by the low G(ST) values among populations, suggesting a corresponding high degree of gene flow among these populations. At the largest spatial scale, populations from Switzerland, Israel, Oregon, and Texas were compared. Population differentiation among these populations was low (G(ST) = 0.05), and genetic identity between populations was high. A low but significant correlation between genetic and geographic distance among populations was found (r = -0.47, P = 0.012), suggesting that these populations probably have not reached an equilibrium between gene flow and genetic drift. Gene flow on a regional level can be reduced by implementing strategies, such as improved stubble management that minimize the production of ascospores. The possibility of high levels of gene flow on a regional level indicates a significant potential risk for the regional spread of mutant alleles that enable fungicide resistance or the breakdown of resistance genes.     

Influence of spatial structure on pathogen colonization and extinction: a test using an experimental metapopulation

The Linum marginale–Melampsora lini plant–pathogen interaction has been studied extensively with regard to its epidemiology and population genetic structure (host resistance and pathogen virulence) in a natural metapopulation. In this study, this system was used in an experimental metapopulation approach to investigate explicitly how the distance (degree of isolation) between local population patches influences disease dynamics within a growing season, as well as the genetic structure of pathogen populations through stochastic colonization and extinction processes. The experimental design centred on four replicate sets of populations, within which patches were spaced at increasingly greater distances apart. Each patch consisted of an identical set of host and pathogen genotypes, with each pathogen genotype having the ability to attack only one of four host-resistance types. Over the 2 years of the experiment, the results showed clear 'boom-and-bust' epidemic patterns, with the strongest determinant of disease dynamics within a growing season being the identity of particular host–pathogen genotypic combinations. However, there were also significant effects of spatial structure, in that more isolated patches tended to exhibit lower levels of disease during epidemic peaks than patches that were close together. Extinction of pathogen genotypes from individual populations was positively related to the severity of disease during preceding epidemic peaks, but negatively related to the level of disease present at the final census prior to overwintering. The probability of recolonization of pathotypes into populations during the second growing season was most strongly related to the distance to the nearest neighbouring source population in which a given pathotype was present. Overall, these results highlight the importance of spatial scale in influencing the numerical and genetical dynamics of pathogen populations.     

High Genetic Similarity Among Populations of Phaeosphaeria nodorum Across Wheat Cultivars and Regions in Switzerland

ABSTRACT Phaeosphaeria nodorum was sampled from nine wheat fields across a 30-km transect representing three geographical regions in Switzerland to determine the scale of genetic differentiation among subpopulations. Three different wheat cultivars were sampled three times to determine whether differences in host genotype correlated with differences among corresponding pathogen populations. Seven restriction fragment length polymorphism (RFLP) loci and one DNA fingerprint were assayed for each of the 432 isolates in the collection. DNA fingerprints differentiated 426 unique genotypes. Though absolute differences were small, five RFLP loci exhibited significant differences in allele frequencies across the nine sub-populations. Gene diversity within all subpopulations was high (H(T) = 0.51), but only 3% of the total genetic variation was distributed among the nine subpopulations. When subpopulations were grouped according to geographical region or host cultivar, less than 1% of the genetic variation was distributed among groups, suggesting widespread gene flow and the absence of pathogen adaptation to specific wheat cultivars. Tests for gametic equilibrium within subpopulations and across the entire Swiss population supported the hypothesis of random mating.     

Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean

Simple sequence repeat (SSR) markers were used to classify 116 isolates of Phakopsora pachyrhizi, the cause of soyabean rust, collected from infected soyabean leaves in four agroecological zones in Nigeria. A high degree of genetic variation was observed within the sampled populations of P. pachyrhizi. Eighty‐four distinct genotypes were identified among three of the four agroecological zones. Nei’s average genetic diversity across geographical regions was 0·22. Hierarchical analysis of molecular variance showed low genetic differentiation among all populations of P. pachyrhizi. The majority (> 90%) of the genetic diversity was distributed within each soyabean field, while approximately 6% of the genetic diversity was distributed among fields within geographic regions. Low population differentiation was indicated by the low F_ST values among populations, suggesting a wide dispersal of identical genotypes on a regional scale. Phylogenetic analysis indicated a strictly clonal structure of the populations and five main groups were observed, with group II accounting for 30% of the entire population. Because of the asexual reproduction of P. pachyrhizi, single‐step mutations in SSR genotypes are likely to account for the genetic differences within each group.     

Defining the habitat niche of Alopecurus myosuroides at the field scale

The distribution of Alopecurus myosuroides (black‐grass) in fields is patchy. The locations of these patches can be influenced by the environment. This presents an opportunity for precision management through patch spraying. We surveyed five fields on various types of soil using a nested sampling design and recorded both A. myosuroides seedlings in autumn and seed heads in summer. We also measured soil properties at those sampling locations. We found that the patches of seed heads within a field were smaller than the seedling patches, suggesting that techniques for patch spraying based on maps of heads in the previous season could be inherently risky. We also found that the location of A. myosuroides patches within fields can be predicted through their relationship with environmental properties and that these relations are consistent across fields on different soil types. This improved understanding of the relations between soil properties and A. myosuroides seedlings could allow farmers to use pre‐existing or suitably supplemented soil maps already in use for the precision application of fertilisers as a starting point in the creation of herbicide application maps.     

Evolution of gene-for-gene systems in metapopulations: the effect of spatial scale of host and pathogen dispersal

The concept of gene-for-gene coevolution is a major model for research on disease resistance in crop plants. However, few theoretical or empirical studies have examined such systems in natural situations, and as a consequence, there is little knowledge of how spatial effects are likely to influence the evolution of host resistance and pathogen virulence in gene-for-gene interactions. In this work, a simulation approach was used to investigate the epidemiological and genetic consequences of varying host and pathogen dispersal in metapopulation situations. The results demonstrate clear impacts of dispersal distance on the total number of host and pathogen genotypes that are maintained, as well as on genetic variation at individual host resistance and pathogen virulence loci. Several other important results also emerged from this study. In contrast to the predictions of many earlier nonspatial models, so-called 'super-races' of pathogens do not always evolve and dominate, indicating that it is not necessary to assume costs of resistance or virulence to maintain high levels of polymorphism in biologically realistic situations. The rate of evolution of both resistance and virulence depend on the scale of dispersal, with greater mixing (as a function of dispersal scale) resulting in a faster approach to a dynamic endpoint. The model in this paper also predicts that, despite the greater total genotypic diversity of pathogens across the metapopulation, variation in host resistance will generally be greater than variation in pathogen virulence within local populations.     

黑龙江省大豆疫霉根腐病调查与病原分离

１９９６年对黑龙江省东部和中部大豆产区２３个市、县的大豆苗期疫霉根腐病进行了调查、研究,应用ＰＢＮＩＣ疫霉选择性培养基分离大豆疫霉根腐病病原菌,从牡丹江、穆棱、林口和佳木斯豆田具疫霉根腐症状的大豆植株上分离到大豆疫霉根腐病菌,并从根腐病株上单独或与大豆疫霉菌同时分离到终极腐霉菌,研究进一步证实我国黑龙江省有大豆疫霉根腐病。调查发现,大豆疫霉根腐病和终极腐霉根腐病主要发生在土质粘重、土壤含水量高或易积水的田块。     

Using Restriction Fragment Length Polymorphisms to Assess Temporal Variation and Estimate the Number of Ascospores that Initiate Epidemics in Field Populations of Mycosphaerella graminicola

ABSTRACT Restriction fragment length polymorphisms (RFLPs) and DNA fingerprints were used to assess temporal variation and estimate the effective population size of the wheat pathogen Mycosphaerella graminicola over a 6-year period. In each year, the fungal population was founded by ascospores originating from outside the sampled fields. A total of 605 fungal isolates were included in this study. Our results indicate that the genetic structure of these M. graminicola populations were stable over the 6-year period. The common alleles at each RFLP locus were present at similar frequencies each year. More than 99% of gene diversity was distributed within populations sampled from the same year and less than 1% was attributed to differences among years. The lack of population differentiation among collections taken in different years indicated that the effective size of the source population was sufficiently large that genetic drift was insignificant in this location. It also suggests that the initial colonists from ascospore founder populations were a fair reflection of the source population. We estimate that the effective sizes of these field populations ranged from 3,400 to 700,000 individuals, depending on the size of the field sampled and assumptions about mutation rates. Estimates of the number of ascospores initiating epidemics of leaf blotch disease in each field plot and factors that contribute to the large effective population size of M. graminicola are discussed.     

Characterizing the spatial pattern of Abutilon theophrasti seedling patches

Spatial biology of weed populations is the study of weed patches and their relevant patch-level processes. In this context, a patch was defined as an area in which individuals are aggregated into discrete subdivided populations. Four Abutilon theophrasti seedling patches in two continuous maize production fields were surveyed using a contiguous grid of quadrats between 1995 and 1997. Surveyed area was dependent on patch size and ranged from 96 m² to 1134 m². Within each area, all seedlings were counted in each 1 m × 0.75 m quadrat in June, just before post-emergence weed control, and in mid-July after all weed control practices were completed. The spatial pattern observed in the seedling distribution maps was single or multiple focal points of high seedling density that decreased with distance from the focal point. Two-directional correlograms corroborated this visual observation, such that A. theophrasti seedling density in neighbouring quadrats was spatially autocorrelated, and correlation strength decreased with distance separating quadrats. Autocorrelation coefficients decreased at a greater rate across crop rows than parallel to crop rows. Visually, patch shape was elliptical and oriented in the direction of field traffic. Factors affecting patch-level processes of spatial aggregation, stability and edge dynamics were considered.     

Genotypic diversity in Fusarium pseudograminearum populations in Australian wheat fields

Despite being closely related to Fusarium graminearum, which has been extensively characterized in many countries around the world, the population biology of Fusarium pseudograminearum, the main causal agent of crown rot of wheat in Australia and many other wheat‐growing regions, has been comparatively poorly studied to date. A simple sequence repeat analysis of 163 F. pseudograminearum isolates from three field sites in NSW, Australia identified 128 distinct multilocus genotypes. Observed genetic diversity within fields was high, whilst genetic variation between fields was low. Across all fields genetic linkage disequilibrium was detected, but of the three individual fields, only one also displayed linkage disequilibrium. These results indicate that the isolates obtained were part of the same, highly diverse, population. However, this population may not be freely interbreeding. Whilst isolation incidence of F. pseudograminearum was found to be spatially aggregated within fields, spatial aggregation of genotypes within fields was weak. The study suggests that processes influencing population dynamics may operate at a scale larger than the narrow geographical scale covered in the fields sampled.     

Spatial aggregation in Fusarium pseudograminearum populations from the Australian grain belt

Previous studies have evaluated the overall structure of populations of Fusarium pseudograminearum (teleomorph, Gibberella coronicola ), causal agent of cereal crown rot, but there is no information available on spatial relationships of genetic variation in field populations. Three 1-m-row sections in crown-rot-affected wheat fields in the Australian grain belt were intensively sampled to estimate population genetic parameters and the spatial aggregation, or clustering, of disease aggregates and genotypes. Estimates of population genetic parameters based on amplified fragment length polymorphisms (AFLPs) indicated that the genetic diversity in isolates from the 1-m-row populations described a significant portion of the diversity recorded for corresponding field and regional populations. In point pattern analysis, there was physical clustering and aggregation of F. pseudograminearum isolates from two of the three sites. Analysis of the spatial distribution of clonal haplotypes (DICE similarity ≥ 97%) indicated significant aggregation of clones in all three 1-m-row populations. Based on matrix comparison tests, both mating types and genetic distances had significant spatial aggregation for at least two of the three 1-m-row populations. This is consistent with the presence of non-random spatial genetic structure due to clonal aggregation. High levels of genetic diversity and spatial structuring of disease and genotypes in at least two of the three 1-m-row populations is consistent with the hypothesis that stubble is a primary inoculum source in no-tillage farming systems, resulting in aggregated patterns of disease and allowing for haplotypes to be maintained in the field over a number of annual cropping cycles.     

Spatial and temporal patterns of Lolium rigidum–Avena sterilis mixed populations in a cereal field

Through a detailed case study of a two‐species (Lolium rigidum and Avena sterilis) weed community at contrasting scales, this paper examined factors that affect weed distribution across space and time in a commercial wheat field in north‐east Spain. A. sterilis showed relatively stable spatial distribution and spatial structure of its population over time at large scale, with well‐defined patches, although weed density rose quickly. L. rigidum showed poorly defined patches that were not stable across time. Interaction between species could explain to some degree the spatial distribution at large scale: a negative relationship was detected between the spatial structures of both weed populations. At fine scale, both species showed a clear interaction effect from primary dispersal (more important in A. sterilis) and secondary dispersal from combine harvesting (more important in L. rigidum).