Genetic structure of Phaeosphaeria nodorum populations in the north-central and midwestern United States

Stagonospora nodorum blotch, caused by Phaeosphaeria nodorum, is considered one of the most destructive foliar diseases of wheat in the United States. However, relatively little is known about the population biology of this fungus in the major wheat-growing regions of the central United States. To rectify this situation, 308 single-spore isolates of P. nodorum were analyzed from 12 populations, five from hard red spring wheat cultivars in Minnesota and North Dakota and seven from soft red winter wheat in Indiana and Ohio. The genetic structure of the sampled populations was determined by analyzing polymorphisms at five microsatellite or simple-sequence repeat (SSR) loci and the mating type locus. Although a few clones were identified, most P. nodorum populations had high levels of gene (H(S) = 0.175 to 0.519) and genotype (D = 0.600 to 0.972) diversity. Gene diversity was higher among isolates collected from spring wheat cultivars in North Dakota and Minnesota (mean H(S) = 0.503) than in those from winter wheat cultivars in Indiana and Ohio (H(S) = 0.269). Analyses of clone-corrected data sets showed equal frequencies of both mating types in both regional and local populations, indicating that sexual recombination may occur regularly. However, significant gametic disequilibrium occurred in three of the four populations from North Dakota, and there was genetic differentiation both within and among locations. Genetic differentiation between the hard red spring and soft red winter wheat production regions was moderate (F(ST) = 0.168), but whether this is due to differences in wheat production or to geographical variation cannot be determined. These results suggest that sexual reproduction occurs in P. nodorum populations in the major wheat-growing regions of the central United States, and that geographically separated populations can be genetically differentiated, reflecting either restrictions on gene flow or selection.     

Indirect evidence for sexual reproduction in Cercospora beticola populations from sugar beet

Cercospora beticola is the main causal agent of cercospora leaf spot on sugar beet and has a large negative impact on the yield and quality of sugar beet production worldwide. Previous studies have shown that both mating type idiomorphs of C. beticola are present in natural populations, suggesting that C. beticola is heterothallic and may be reproducing sexually. Cercospora beticola isolates are diverse in the morphology of their conidia, onset of disease symptoms and fungicide resistance. To find the source of this diversity and to determine if sexual reproduction occurs in this fungus, C. beticola populations were collected from Western Europe, Iran and New Zealand. The mating types of these isolates were determined and AFLP analyses were used to study the genetic diversity in these populations. The mating type ratios did not deviate significantly from a 1:1 ratio in most of the populations and AFLP analyses showed high levels of genetic variation within and between the populations, with 86·4% of the isolates having unique genotypes. All populations were in significant linkage disequilibrium but levels of disequilibrium were low, and loci from only one primer pair were in significant gametic equilibrium in populations from the Netherlands and Italy. From these results there is the possibility that C. beticola reproduces sexually. High levels of gene flow among the samples from Europe demonstrated a single panmictic European population. This study confirms C. beticola to be a genetically highly diverse species, supporting the assumption that some populations are reproducing sexually.     

Population structure and mating system of Ascochyta rabiei in Tunisia: evidence for the recent introduction of mating type 2

The population structure of Ascochyta rabiei (teleomorph: Didymella rabiei ) in Tunisia was estimated among five populations sampled from the main chickpea growing regions using simple sequence repeat markers (SSR) and a mating type ( MAT ) marker. Mating type 2 isolates ( MAT1-2 ) had reduced genetic and genotypic diversity relative to mating type 1 isolates ( MAT1-1 ). This result, coupled with previous observations of lower overall frequency and restricted geographical distribution of MAT1-2 in Tunisia, and recent (2001) observation of the sexual stage, support the hypothesis of a recent introduction of MAT1-2 . Despite the presence of both mating types in Nabeul, Kef and Jendouba, the hypothesis of random mating was rejected in these locations with multilocus gametic disequilibrium tests. Highly significant genetic differentiation ( θ  = 0·32, G _ST = 0·28, P  < 0·001) was detected among populations and genetic distance and cluster analyses based on pooled allele frequencies revealed that populations from Nabeul and Kef were distinct from those in Beja, Bizerte and Jendouba. More than 70% of total gene diversity ( H _T = 0·55) detected was attributable to variation within populations compared to 28% among populations. This result, coupled with the occurrence of private alleles in each population, suggests that gene flow is currently limited among populations, even those separated by short geographic distances. The presence of two main genetic clusters was confirmed using Bayesian model-based population structure analyses of multilocus genotypes (MLGs) without regard to geographic origin of samples. The presence of MAT1-2 isolates in both clusters suggests at least two independent introductions of MAT1-2 into Tunisia that are likely to be the result of importation and planting of infected chickpea seeds.     

Population genetic structure of four regional populations of the barley pathogen Pyrenophora teres f. maculata in Iran is characterized by high genetic diversity and sexual recombination

The leaf spot form of the barley disease net blotch, caused by the fungus Pyrenophora teres f. maculata (PTM), is an increasingly important foliar disease of barley. Studies of population genetic structure and reproductive mode are necessary to make predictions of the evolutionary potential of the pathogen. Sources of resistance to PTM have been found in Iranian landraces, which may have the potential to improve plant breeding efforts. However, little is known about the population genetic structure of this fungus in Iran. In this study, we analysed the frequency of the mating type genes to assess the potential for sexual mating of PTM collected from four provinces—Khuzestan, Hamadan, Golestan, and East Azerbaijan—and we investigated the population genetic structure using seven simple sequence repeat markers. High genotype diversity, linkage equilibrium, and equal ratios of mating types frequencies in the PTM populations at Khuzestan and Hamadan support the occurrence of sexual reproduction in these populations, while in Golestan and East Azerbaijan populations, significant gametic disequilibrium and relatively low genotype diversity suggest a higher incidence of clonality or different demographic histories. Unequal mating type frequencies in Golestan confirm a predominance of asexual reproduction. Finally, we found significant evidence for strong population structure with most of the genetic variation represented within regional populations (89%). Overall, our study provides evidence for high genetic variation in Iranian PTM populations, which may be the basis for rapid adaptive evolution in this pathosystem. This highlights the need for integrated efforts to control the disease.     

Global Hierarchical Gene Diversity Analysis Suggests the Fertile Crescent Is Not the Center of Origin of the Barley Scald Pathogen Rhynchosporium secalis

A total of 1,366 Rhynchosporium secalis isolates causing scald on barley, rye, and wild barley (Hordeum spontaneum) were assayed for restriction fragment length polymorphism loci, DNA fingerprints, and mating type, to characterize global genetic structure. The isolates originated from 31 field populations on five continents. Hierarchical analysis revealed that more than 70% of the total genetic variation within regions was distributed within a barley field. At the global level, only 58% of the total genetic variation was distributed within fields, while 11% was distributed among fields within regions, and 31% was distributed among regions. A significant correlation was found between genetic and geographic distance. These findings suggest that gene flow is common at the local level while it is low between regions on the same continent, and rare between continents. Analyses of multilocus associations, genotype diversity, and mating type frequencies indicate that sexual recombination is occurring in most of the populations. We found the highest allele richness in Scandinavia followed by Switzerland. This suggests that R. secalis may not have originated at the center of origin of barley, the Fertile Crescent, nor in a secondary center of diversity of barley, Ethiopia.     

Random amplified polymorphic DNA (RAPD) analysis of Phytophthora infestans isolates collected in Canada during 1994 to 1996

Mating type, glucose-6-phosphate isomerase ( Gpi ) allozyme banding patterns, response to the fungicide metalaxyl and random amplified polymorphic DNA (RAPD) markers were used to characterize genetic variability among 141 Canadian isolates of Phytophthora infestans collected between 1994 and 1996. Multiple correspondence analysis of RAPD profiles separated isolates into 21 groups that were not correlated to groups defined by mating type, Gpi allozyme banding patterns or response to metalaxyl. Population subdivision analysis showed that 97% of the total genetic variation was found among individuals within populations, compared with 3% among populations. The average similarity coefficient among isolates was 80%. No significant differences in haplotypic diversity were observed among the years under study, but levels of genetic diversity among local populations of P. infestans were high (0.76). All classes of response to the fungicide metalaxyl were observed, with 55% of isolates displaying moderate levels of insensitivity. The high level of genetic diversity detected within populations indicates that migration and sexual recombination probably play important roles in the population biology of P. infestans in Canada.     

Genetic structure of Mycosphaerella graminicola populations in Iran

To provide insight into the genetic structure of Mycosphaerella graminicola populations in Iran, a total of 221 isolates were collected from naturally infected wheat fields of five major wheat‐growing provinces and analysed using AFLP markers and mating‐type loci. All populations showed intermediate to high genotypic diversity. In the Golestan and Ardabil populations two mating types were found at near‐equal frequencies, whilst all populations were in gametic disequilibrium. Moreover, clonal haplotypes were identified in different sampling sites within a field in both the Khuzestan and Fars provinces, demonstrating that pycnidia are probably the primary source of inoculum. All five populations had low levels of gene diversity and had private bands. Low levels of gene flow and high genetic differentiation were observed among populations and different clustering methods revealed five genetically distinct groups in accordance with the sampling areas. The Golestan and East Azarbaijan populations were more genetically differentiated than the others. Random genetic drift, selection and geographic barriers may account for the differentiation of the populations. The results of this study indicate a population structure of M. graminicola in Iran contrasting to that of most other countries studied.     

Low diversity of vegetative compatibility types and mating type of Cryphonectria parasitica in the southern Balkans

The diversity of vegetative compatibility (vc) types and mating type was estimated in populations of the chestnut blight fungus, Cryphonectria parasitica , throughout Macedonia and from selected areas in Greece. Nearly all of the 786 isolates (94%) from Macedonia were in a single vc type, EU-12; all 379 isolates from Greece were EU-12. Only six of 20 populations in Macedonia had more than one vc type. The diversity of vc types in the most diverse populations of Macedonia was comparable with the least diverse populations found previously in Italy. All but six of the 313 isolates assayed had the same mating type, MAT-1 , and no perithecia of Cryphonectria parasitica were observed in any population. These results lead to the conclusion that sexual reproduction does not occur in these populations. The lack of vc type diversity may indicate a high potential for the spread of hypoviruses and successful biological control with transmissible hypovirulence. However, if sexual reproduction should occur in Macedonian populations, up to 32 vc types would be possible by recombination among vegetative incompatibility loci.     

Population structure and reproductive mode of Didymella fabae in Syria

Didymella fabae is a highly destructive fungal pathogen of faba bean (Vicia faba) that represents a significant yield‐limiting biotic constraint in all locations where the crop is grown. However, nothing is known about the population structure of this pathogen anywhere in the world. Population genetic analyses employing 18 sequence‐tagged microsatellite (STMS) markers covering eight genetic linkage groups and a PCR‐based mating type marker were used to elucidate the genetic structure and reproductive mode of the pathogen in three populations in Syria. High gene diversity within populations but low genetic differentiation among populations was observed and the entire collection of isolates was assigned to a single genetic population using a Bayesian clustering algorithm. Independent analyses were performed based on four unlinked sets of STMS markers to infer reproductive mode. A simulation approach was used to estimate which of the repeated multilocus genotypes were probably the result of asexual reproduction and should be clone‐corrected. A 1:1 ratio of mating types could not be rejected in any clone‐corrected population, probably due to small sample sizes. Likewise, frequency of clones and sample size, but not marker linkage, had strong effects on multilocus gametic disequilibrium. The null hypothesis of random mating was rejected in the majority of populations for both non‐clone‐corrected and clone‐corrected samples and with four sets of unlinked markers indicating a predominance of asexual reproduction in these populations. This represents the first detailed screening of clonal and genetic composition of D. fabae populations in Syria.     

Genetic diversity assessed by SSR markers and chemotyping of Fusarium culmorum causal agent of foot and root rot of wheat collected from two different fields in Tunisia

Fusarium culmorum is a major pathogen able to cause foot and root rot and the incitant of Fusarium head blight in wheat in Tunisia. The aims of the present study were to evaluate by PCR the type of mycotoxins produced, to determine the mating type and to analyse the genetic diversity by microsatellite markers of 82?F. culmorum isolates recovered from two separated Tunisian fields. Specific sequences in the Tri6-Tri5 intergenic region, Tri7 and Tri13 were used to identify 3-AcDON- or 15-AcDON-. All studied F. culmorum isolates, were of the 3-AcDON- type. No 15-AcDON- and NIV types were detected in this research. Both mating types MAT1-1 and MAT1-2 were recovered from the two fields in approximately equal proportions. Five polymorphic microsatellite markers were applied to F. culmorum isolates, to determine the genetic variation in and among populations. Sixty-four haplotypes were identified; the analysis of the population structure did not reveal a strong variation between fields. Total gene diversity (H _T ?=?0.505; H _S ?=?0.497) and analysis of molecular variance confirmed that most of the genetic variability was within populations (Φ _ST ?=?0.033; P?<?0.0039). Gene flow (N _m ?=?31.05) indicated little differentiation among populations. Based on these results, the F. culmorum isolates collected from different fields might be part of one large panmictic population and in addition the low linkage disequilibrium values with high genetic variation within populations suggest that the population is recombining sexually.     

Genetic differentiation of Magnaporthe oryzae populations from scouting plots and commercial rice fields in Korea

A previous study of the diversity and population structure of the rice blast fungus, Magnaporthe oryzae, over a 20-year period in Korea, found novel fingerprint haplotypes each year, and the authors hypothesized that populations might experience annual bottlenecks. Based on this model, we predicted that M. oryzae populations would have little or no genetic differentiation among geographic regions because rice blast is commonly found throughout Korea each year and M. oryzae would have to disperse from small populations surviving annually between rice crops. To test this hypothesis, we sampled M. oryzae from rice fields in eight provinces in Korea in a single year (1999). In four provinces, we sampled from a set of rice cultivars commonly grown in commercial fields (group I); because of low disease incidence in four other provinces, we could not sample from commercial fields and instead sampled from scouting plots of different cultivars set up for detecting new pathotypes of M. oryzae (group II). All isolates were genotyped with DNA fingerprint probes MGR586 and MAGGY, a telomere-linked gene family member TLH1, the PWL2 host specificity gene and mating type. Fingerprint haplotypes clustered into two distinct lineages corresponding to the two sets of cultivars (groups I and II), with haplotype similarities of 71% between lineages and >76% within lineages. Isolates from the same cultivar within group I were genetically differentiated among locations, and isolates within the same location were differentiated among cultivars. Differentiation for TLH1 and PWL2 was significant (P < 0.03), but not as strong as for fingerprint markers. Similar analyses were not possible among group II isolates because too few isolates were available from any one cultivar. All isolates were in the same mating type, Mat1-1, ruling out sexual reproduction as a source of novel haplotypes. When the 1999 samples were compared with the historical samples from the previous study, haplotypes of group I formed a separate cluster, while those of group II clustered with haplotypes from the historical sample. Altogether, geographic subdivision, monomorphism of mating type, and correlation of haplotypes to sets of cultivars are not consistent with the hypothesis of repeated turnover of haplotypes. Instead, the previous correlations of haplotypes to year might have been caused by inadequate sampling of haplotypes each year, highlighting the need for studies of population genetics to be conducted with systematic samples collected to address specific questions.     

Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California

Sclerotinia trifoliorum, an important pathogen of cool season legumes, displays both homothallism and heterothallism in its life cycle, unique among members of the genus Sclerotinia. Very little is known about its genetic diversity and population structure. A sample of 129 isolates of S. trifoliorum from diseased chickpea in California was investigated for genetic diversity, population differentiation and reproductive mode. Genetic diversity was estimated using mycelial compatibility (MCG) phenotypes, rDNA intron variation, and allelic diversity at seven microsatellite loci. Genetic analysis revealed high levels of genotypic diversity demonstrated by high genotypic richness (0·88). Similarly, high levels of gene diversity (mean expected heterozygosity H_E = 0·68) were observed at the microsatellite loci. Geographic populations of S. trifoliorum were highly admixed as evident from low F_ST values (0–0·11), suggesting high contemporary or historical gene flow. Hierarchical analysis of molecular variance showed that more than 92% of the genetic variation occurred among isolates within populations. Bayesian clustering analysis identified four cryptic genetic populations that were not correlated to geographic location, and index of multilocus association was non‐significant in each of the four genetic populations. However, the presence of identical haplotypes within and among populations indicates clonal reproduction. The high levels of haplotype diversity and population heterogeneity, a lack of correspondence between MCG and microsatellite haplotype, and low levels of population differentiation suggest that populations of S. trifoliorum in chickpea have been undergoing extensive outcrossing and migration events probably shaped by human‐mediated dissemination, the underlying diverse cropping systems, and chickpea disease management practices.     

Pathogenicity variation and DNA polymorphism of Bipolaris sorokiniana infecting winter wheat in the Huanghuai floodplain of China

Wheat root rot, caused by Bipolaris sorokiniana, has led to severe losses of wheat products worldwide. To evaluate the pathogenicity and genetic variation of B. sorokiniana, diseased wheat samples were collected from 97 locations in the Huanghuai floodplain of China in 2014 and 2015 for analysis. A total of 673 isolates were obtained, 262 of which were identified as B. sorokiniana. Pathogenicity analysis of the isolates revealed variation in pathogenicity, which was not directly correlated with geographic region. Large variations in pathogenicity were also found within geographic groups. To determine the genetic structure of the populations, PCR was performed with universal rice primers (URP). Cluster analysis based on amplification patterns showed that the classified groups were correlated with geographical regions. Thus, analysis of the genetic diversity of the population indicated a negative correlation with geographic origin, that is, the greater the distance between sites, the lower the genetic variation similarity coefficient. Identification of wheat germplasm resistance showed that resistant cultivars accounted for a low percentage, while susceptible and highly susceptible cultivars were in the majority. Overall, these results are meaningful for developing strategies to prevent and control wheat root rot.     

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.     

Diversity of vegetative compatibility types and mating types of Cryphonectria parasitica in Slovenia and occurrence of associated Cryphonectria hypovirus 1

Cryphonectria parasitica, the causal agent of chestnut blight, has been present in Slovenia since at least 1950. To improve understanding of its diversity, 254 isolates of the fungus from 11 Slovenian populations were sampled. Fifteen vegetative compatibility (vc) types were identified. The dominant vc type was EU‐13, comprising 40·1% of all isolates tested, followed by EU‐1 (19·7%), EU‐2 (12·2%) and EU‐12 (9%). The vc type diversity in the most diverse population sampled in Slovenia was higher than in the populations found previously in northern Italy and Croatia. Both mating types and perithecia were observed in surveyed populations. Natural hypovirulence was found in six out of seven populations tested, with frequencies ranging from 72·2% in the population sampled near the Croatian border to 11·1% in the population sampled near the Austrian border. All identified hypoviral isolates (21) belonged to the Italian subtype of Cryphonectria hypovirus 1 and were closely related to the hypoviruses found in other European countries. Despite the high vc type diversity, incidence of hypovirulence was also high, indicating widespread natural biological control of the disease.     

Population Structure of Phytophthora cinnamomi in South Africa

ABSTRACT Phytophthora cinnamomi isolates collected from 1977 to 1986 and 1991 to 1993 in two regions in South Africa were analyzed using isozymes. A total of 135 isolates was analyzed for 14 enzymes representing 20 putative loci, of which four were polymorphic. This led to the identification of nine different multilocus isozyme genotypes. Both mating types of P. cinnamomi occurred commonly in the Cape region, whereas, predominantly, the A2 mating type occurred in the Mpumalanga region of South Africa. A2 mating type isolates could be resolved into seven multilocus isozyme genotypes, compared with only two multilocus isozyme genotypes for the A1 mating type isolates. Low levels of gene (0.115) and genotypic (2.4%) diversity and a low number of alleles per locus (1.43) were observed for the South African P. cinnamomi population. The genetic distance between the Cape and Mpumalanga P. cinnamomi populations was relatively low (D(m) = 0.165), and no specific pattern in regional distribution of multilocus isozyme genotypes could be observed. The genetic distance between the "old" (isolated between 1977 and 1986) and "new" (isolated between 1991 and 1993) P. cinnamomi populations from the Cape was low (D(m) = 0.164), indicating a stable population over time. Three of the nine multilocus isozyme genotypes were specific to the "old" population, and only one multilocus isozyme genotype was specific to the "new" population. Significant differences in allele frequencies, a high genetic distance (D(m) = 0.581) between the Cape A1 and A2 mating type isolates, significant deviations from Hardy-Weinberg equilibrium, a low overall level of heterozygosity, and a high fixation index (0.71) all indicate that sexual reproduction occurs rarely, if at all, in the South African P. cinnamomi population.     

Gene Flow and Sexual Reproduction in the Wheat Glume Blotch Pathogen Phaeosphaeria nodorum (Anamorph Stagonospora nodorum)

ABSTRACT Restriction fragment length polymorphisms (RFLPs) were used to characterize the genetic structures of three field populations of Phaeosphaeria nodorum from Texas, Oregon, and Switzerland. Data from seven nuclear RFLP loci were used to estimate gene diversity and genetic distances and to make indirect measures of gene flow between populations. Three of the seven RFLP loci differed significantly in allele frequencies across populations. On average, 96% of the total gene diversity was found within populations. There was little evidence for population subdivision, suggesting that gene flow was not restricted among populations. Based on an average population differentiation of 0.04, we estimated that the exchange of 11 migrants among populations per generation would be needed to account for the present level of population subdivision. Genotype diversity based on DNA fingerprints was at a maximum for the Swiss population, whereas populations in Texas and Oregon had lower genotype diversities. Many multilocus haplotypes were found in each population. Ninety-five percent of RFLP allele pairs were in gametic equilibrium. The data were consistent with random mating within each population.     

Population structure of Phytophthora infestans in China – geographic clusters and presence of the EU genotype Blue_13

The population structure of Phytophthora infestans in China was studied and three mitochondrial haplotypes (Ia, IIa, IIb) were observed. Genetic analysis with 10 highly informative SSR markers identified 68 different genotypes, including three dominant clonal lineages. In the Chinese P. infestans population, the genotypes were strongly clustered according to their geographic origin. One of dominant clonal lineages was genetically similar to Blue_13, a dominant clonal lineage found in Europe since 2004. This is the first report of Blue_13 outside Europe. Only one mating type (A1) was found in the northern and southeastern provinces, but in southern and northwestern China both mating types were observed. The mating type ratio and SSR allele frequencies indicate that in China the sexual cycle of P. infestans is rare. These results emphasize that the migration of asexual propagules and the generation of subclonal variation are the dominant driving factors of the population structure of P. infestans in China. They may also have implications for the role of monitoring P. infestans populations in potato late blight management strategies in China.     

Genetic Structure of Rhynchosporium secalis in Australia

ABSTRACT Restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Australian field populations of the barley scald pathogen Rhynchosporium secalis. Fungal isolates were collected by hierarchical sampling from five naturally infected barley fields in different geographic locations during a single growing season. Genetic variation was high in Australian R. secalis populations. Among the 265 fungal isolates analyzed, 214 distinct genotypes were identified. Average genotype diversity within a field population was 65% of its theoretical maximum. Nei's average gene diversity across seven RFLP loci was 0.54. The majority (76%) of gene diversity was distributed within sampling site areas measuring 1 m(2); 19% of gene diversity was distributed among sampling sites within fields; and 5% of gene diversity was distributed among fields. Fungal populations from different locations differed significantly both in allele frequencies and genotype diversities. The degree of genetic differentiation was significantly correlated with geographic distance between populations. Our results suggest that the R. secalis population in Western Australia has a different genetic structure than populations in Victoria and South Australia.     

Molecular evidence supports hypervariability in Phytophthora colocasiae associated with leaf blight of taro

The oomycete Phytophthora colocasiae that causes taro leaf blight is the most devastating disease of taro and is widely distributed worldwide. Molecular and phenotypic techniques were employed for assessing and exploiting the genetic variability among four populations of P. colocasiae obtained from a fine spatial scale (multiple leaf blight lesions on single taro leaf). Phenotypic characters such as virulence, morphology and mating type showed no variation. ITS characterization revealed detectable polymorphism among isolates of P. colocasiae. The mean number of haplotypes (H), haplotype diversity (HD), nucleotide diversity (π), and nucleotide substitution rate (θ) among analyzed sequences were 6.75, 1.00, 0.069, and 0.088 respectively. High levels of inter and intra specific variation were detected by random amplified polymorphic DNA (RAPD) assays. Moderate genetic diversity (H?=?0.2651) was observed among populations of P. colocasiae. Analysis of molecular variance (AMOVA) confirmed that most of the genetic variability was confined to within a population (63.54 %). The coefficient of genetic differentiation among populations (G _ST ) was 0.2007 and estimates of gene flow (Nm) among populations was 1.991 migrants per generation. Cluster analysis using UPGMA revealed that individuals from the same population failed to cluster in one distinct group. The results of the study reveal considerable genetic diversity among and within populations of P. colocasiae obtained from fine spatial scale. The possible mechanisms and implications of this genetic variation are discussed.