Genetic differentiation of the wheat leaf rust fungus Puccinia triticina in Europe

The objective of this study was to determine whether genetically differentiated groups of Puccinia triticina are present in Europe. In total, 133 isolates of P. triticina collected from western Europe, central Europe and Turkey were tested for virulence on 20 lines of wheat with single leaf rust resistance genes, and for molecular genotypes with 23 simple sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotype within countries, 121 isolates were retained for further analysis. Isolates were grouped based on SSR genotypes using a Bayesian approach and a genetic distance method. Both methods optimally placed the isolates into eight European (EU) groups of P. triticina SSR genotypes. Seven of the groups had virulence characteristics of isolates collected from common hexaploid wheat, and one of the groups had virulence characteristics of isolates from tetraploid durum wheat. There was a significant correlation between the SSR genotypes and virulence phenotypes of the isolates. All EU groups had observed values of heterozygosity greater than expected and significant fixation values, which indicated the clonal reproduction of urediniospores in the overall population. Linkage disequilibria for SSR genotypes were high across the entire population and within countries. The overall values of R_ST and F_ST were lower when isolates were grouped by country, which indicated the migration of isolates within Europe. The European population of P. triticina had higher levels of genetic differentiation compared to other continental populations.     

High genotype diversity and lack of isolation by distance in the Alternaria solani populations from China

A genomic library was used to develop seven SSR markers for studying the population genetics of Alternaria solani, a pathogenic fungus causing early blight disease of potato and tomato worldwide. Population genetic analysis of 268 isolates of A. solani sampled from four locations, each representing one of four potato production systems in China, indicates that these SSR markers are moderately diverse, selectively neutral and possibly unlinked. Population genetic analysis also indicated that genetic variation of A. solani in China is high. About 2/3 of 123 genotypes were detected only once and genotype diversity measured by the standardized Shannon index ranged between 0·82 and 0·92 in the populations. Although clones were detected in multiple populations separated by thousands of kilometres, random association among SSR loci was found in half of the populations assayed. On average, nearly six copies of genetic material were exchanged among these populations each generation and no isolation by distance was detected. It is hypothesized that the joint effects of cryptic sexual reproduction and human‐mediated gene flow may account for the observed population genetic structure of A. solani in China.     

Russian populations of Puccinia triticina in distant regions are not differentiated for virulence and molecular genotype

The objective of this study was to determine whether genetically distinct groups of Puccinia triticina are present in four regions of the Russian Federation. Collections of P. triticina were obtained from the Central, North Caucasus, Volga and West Siberia regions from 2006 to 2010. Ninety‐nine single uredinial isolates were tested for virulence phenotype with 20 Thatcher near‐isogenic lines of wheat. Forty‐one virulence phenotypes were found in the four regions, with eight in common between the widely separated Central and West Siberia regions. A total of 72 isolates were tested for molecular genotype with 23 simple sequence repeat (SSR) primer pairs, and 66 isolates were used for further analysis after clone correction for virulence and molecular genotype. Analysis of variation showed no overall differentiation of SSR genotypes or virulence phenotypes based on region of origin. Linkage disequilibria for SSR genotypes were high across the entire population. The regional populations had higher than expected levels of allelic heterozygosity that indicated clonal reproduction. Based on cluster analysis of SSR genotypes there were two groups of P. triticina isolates that were widely distributed across Russia. The two SSR groups also differed significantly for virulence. Puccinia triticina may be dispersed from a common source of inoculum in the European or Caucasus regions of Russia. The Russian P. triticina populations were highly differentiated for SSR genotype from populations in Tajikistan, Kyrgyzstan, Uzbekistan, Armenia, Georgia and Azerbaijan and more similar to populations from southern Kazakhstan and northern Kazakhstan.     

Anastomosis of germ tubes and migration of nuclei in germ tube networks of the soybean rust pathogen, <Emphasis Type="BoldItalic">Phakopsora pachyrhizi</Emphasis>

An important mechanism for genetic diversity in filamentous fungi is hyphal anastomosis and the formation of heterokaryons. In this study, we observed fusion of germ tubes in germinating urediniospores of Phakopsora pachyrhizi resulting in a complex hyphal network. Staining of the germ tubes derived from P. pachyrhizi urediniospores with 4’, 6-diamidino-2-phenylindole (DAPI) showed migration of nuclei through the network resulting in multinucleate hyphae. Short bridges connecting the hyphal network tubes were also observed. Our study provides the first evidence of germ tube and hyphal anastomosis, and nuclear migration in P. pachyrhizi. Considering the lack of a known sexual stage of P. pachyrhizi, this hyphal anastomosis followed by the parasexual cycle may explain the genetic diversity in virulence among populations of P. pachyrhizi.     

Genotypic diversity and migration of clonal lineages of Botrytis cinerea from chickpea fields of Bangladesh inferred by microsatellite markers

An analysis of allelic diversity at nine microsatellite loci provided an insight into the population structure of Botrytis cinerea from four fields (sampled in 2003 and 2004) that represented important regional locations for chickpea production in Bangladesh. Although three populations were limited by sample size after clone‐correction, a total of 51 alleles were amplified among 146 B. cinerea isolates from Bangladesh, which revealed a high amount of within‐population and overall genetic diversity (H_S = 0·48 and H_T = 0·54, respectively). The percentage of maximal genotypic diversity (G) ranged between populations (G = 23–40), with a total of 69 haplotypes detected (G = 25). Bayesian cluster analysis depicted two major clusters distributed among the four Bangladesh populations, indicating population admixture from two origins that have spread throughout these regions. Genotype flow between regions was detected and indicated the spread of clonal lineages, consistent with relatively low differentiation among the four populations (mean G_ST = 0·1, P < 0·05). These results highlighted the potential threat of host resistance breakdown as a result of considerable genetic diversity, genotype flow and the evolutionary potential of B. cinerea.     

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.     

Pathotypic and genetic diversity in the population of Rhizoctonia solani AG1‐IA causing rice sheath blight in China

Sheath blight, caused by Rhizoctonia solani AG1‐IA, is one of the most serious diseases of rice. In this study, a total of 175 isolates of R. solani AG1‐IA were collected from five rice‐growing regions in China. Pathogenicity tests revealed that all isolates were virulent to five cultivars with different levels of resistance at the rice seedling stage in the greenhouse. There was considerable variation in aggressiveness, and the isolates were classified into three pathotypes based on disease severity, with moderately virulent isolates prevalent in the population. Forty‐three haplotypes were identified based on ITS sequencing, and 39 haplotypes were distinct among isolates. There were high levels of haplotype diversity and nucleotide diversity within the populations of R. solani AG1‐IA. High gene flow (Nm = 1·63–5·22) was detected, consistent with relatively low differentiation between pairs of populations. Five populations were divided into two distinct clusters by the unweighted pair group method with arithmetic mean (UPGMA), and no spatial population differentiation was discernible. The majority (97·8%) of genetic diversity was distributed among isolates within populations, with only 2·2% of the genetic diversity attributed to differences among populations. The star‐like shape of the haplotype network provided evidence of signatures of population expansion in recent history. No significant relationships were found between the genetic diversity and aggressiveness or geographic origin among populations of R. solani AG1‐IA. These results highlight that the population characteristics of R. solani AG1‐IA should be taken into account in evaluating the germplasm resistance of rice cultivars to sheath blight.     

Genetic diversity of Solanum elaeagnifolium,an invasive problematic weed in Jordan

Solanum elaeagnifolium (silverleaf nightshade) is a problematic weed that is common in Jordan and difficult to control. The weed exhibits distinct morphological variations in growth habit, leaf shape, leaf margins, flower colour and presence or absence of spines between individuals among and within populations suggesting genetic differences. Genetic variations among 61 samples of S. elaeagnifolium collected from heavily infested sites in the central Jordan Valley were investigated using six simple sequence repeat (SSR) markers and eight amplified fragment length polymorphism (AFLP) primer combinations. Results showed that 111 out of 675 AFLP bands were polymorphic generating polymorphism information content (PIC) of 38.0%, while 23 SSR polymorphic alleles were detected generating a PIC of 30.8%. Phylogenetic analysis using RaxML software identified four major clades with a clear clustering of the samples with their collection sites. Genetic analysis using both techniques revealed high level of genetic diversity among S. elaeagnifolium samples collected from a small geographical area indicating that a range of genetic diversity may be detected in weed populations across the country that may complicate its management.     

Genetic diversity of East and West African Striga hermonthica populations and virulence effects on a contrasting set of sorghum cultivars

The root hemiparasite Striga hermonthica causes very significant yield loss in its dryland staple cereal host, Sorghum bicolor. Striga‐resistant sorghum cultivars could be an important part of integrated S. hermonthica control. For effective resistance breeding, knowledge about the diversity of the parasite is essential. This study aimed (i) to determine the genetic diversity within and between seven S. hermonthica populations from East and West Africa using 15 microsatellite markers and (ii) to assess the virulence and host–parasite interactions of these Striga populations grown on 16 diverse sorghum genotypes in a glasshouse trial. Most of the genetic variance (91%) assessed with microsatellite markers occurred within S. hermonthica populations. Only a small portion (8%) occurred between regions of origin of the populations. A positive correlation (R² = 0.14) between pairwise geographic and genetic distances reflected the slightly increasing differentiation of S. hermonthica populations with increasing geographic distance. East African S. hermonthica populations, especially those from Sudan, had significantly greater average infestation success across all sorghum genotypes than West African populations. Some specific host–parasite interaction effects were observed. The high genetic variation among individuals of each S. hermonthica population underlines the high potential adaptability to different hosts and changing environments. This points to the need to manage sorghum resistance alleles in space and time and to employ resistant varieties as part of integrated S. hermonthica control, so as to hinder the parasite overcoming resistance.     

Genetic diversity and population structure of Plasmopara viticola in China

Grape downy mildew is a destructive oomycete disease worldwide for viticulture. A total of 440 infected leaf lesions were collected from nineteen vineyards distributing in the major viticulture regions in China. Six specific SSR markers were used to genetically characterize the Plasmopara viticola populations. A total of 60 alleles were generated and 324 distinct genotypes were identified based on these multi-locus markers. Most populations had high levels of genetic and genotypic diversity. AMOVA analysis showed that majority of the total genetic diversity was distributed within the vineyards while moderate to high genetic differentiation was also observed among some P. viticola populations. Three populations (BJ, GX, and GS2) were clearly separated from the rest of the populations by using PCA and Nei’s genetic distance analysis. Mantel test showed no significant correlation between unbiased Nei’s genetic distance and geographical distance.     

Microsatellite variability of sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides (Cyperaceae) in Kinki,Japan

Schoenoplectus juncoides is one of the most harmful weeds found in East Asian paddy fields. Recent emergence of biotypes that are resistant to the herbicide sulfonylurea (SU) has made weed control difficult. To examine the effect of the evolution of this herbicide resistance on genetic diversity within local populations, we investigated microsatellite variability within and among paddy field populations of S. juncoides in Kinki, Japan. In vivo assay of acetolactate synthase activity and root elongation assay in the presence of SU revealed that of 21 populations, five were sulfonylurea‐susceptible (SU‐S) and eight were completely sulfonylurea‐resistant (SU‐R). The remaining eight populations were a mixture of SU‐S and SU‐R individuals. The average gene diversity for SU‐R populations (H_S = 0.168) was lower than those for SU‐S (H_S = 0.256) and mixed (H_S = 0.209) populations, but the difference was not significant. This indicates that positive selection for SU‐R phenotype did not cause a genome‐wide reduction in genetic diversity. Genetic differentiation among S. juncoides populations was higher than that observed for most weed species studied previously. Although populations in neighbouring paddy fields showed a high level of differentiation, Bayesian clustering analyses suggested that some level of gene flow occurs among them and that the genetic exchange or colonisation between neighbouring populations could contribute to the geographical expansion of the resistant allele.     

Spatial genetic diversity and interregional spread of <Emphasis Type="Italic">Puccinia striiformis</Emphasis> f. sp. <Emphasis Type="Italic">tritici</Emphasis> in Northwest China

In China, wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat. The Longnan and Linxia regions in Gansu Province and Qinghai Province are the major over-summering regions for the pathogen and key epidemiological zones in Northwest China. Population genetic diversity and interregional long-distance spread of the wheat stripe rust pathogen in Northwest China were studied using SSR markers. The genetic diversity in the Longnan population was much higher than those in the Linxia and Qinghai populations. Therefore, the molecular data confirmed that the Longnan region is a center of genetic diversity for P. striiformis f. sp. tritici in Northwest China. The low genetic differentiation (Gst = 0.15) and the extensive gene flow (Nm = 1.37) were found among the three regions in Northwest China. The most important conclusion of this study is that the stripe rust inoculum in Qinghai can come from both Longnan and Linxia, but mainly from Longnan directly in the spring.     

Genetic diversity and population structure of Lasiodiplodia theobromae from different hosts in northeastern Brazil and Mexico

Lasiodiplodia theobromae is one of the most frequent fungal pathogens associated with dieback, gummosis, leaf spot, stem-end rot and fruit rot symptoms in cashew, mango, papaya and grapevine. In this study, the variation in the genetic diversity of 117 L. theobromae isolates from northeastern Brazil (n = 100) and Mexico (n = 17), which were collected from these four crops, was analysed using microsatellite markers. The results revealed low genetic diversity among L. theobromae populations and the existence of two genetic groups. All Mexican isolates were grouped with Brazilian isolates, suggesting a low level of differentiation between these populations. Furthermore, no evident host or climate-based population differentiation was observed for L. theobromae in Brazil. The populations studied were mostly clonal, but additional studies are needed to better understand the mode of reproduction of the pathogen. The low genetic diversity of L. theobromae populations in northeastern Brazil suggests that resistant cultivars could be used as a durable management strategy to reduce the impact of the diseases caused by this pathogen.     

Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp

ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P < 0.05) and populations from different host genotypes (P < 0.02). In the geographic populations, most of populations from cultivated and wild P. virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P < 0.02), except there was no differentiation between the Shubert Select and wild chokecherry populations (>P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow existed between populations from different regions and host species. Gene flow rates (Nm) varied from <1 to 12.5, with higher gene flow rates among population pairs from the same host species (P = 1.000). The analysis of molecular variance revealed that a major genetic variance source came from the genetic variation among isolates within populations regardless of the origin and host genotype of the population. Although some locations had a limited number of isolates, the results of this study clearly showed that the genetic diversity and population differentiation of A. morbosa were closely associated with host genotypes and geographic locations, but mostly with the former.     

Genetic variability of Pseudocercospora fijiensis,the black Sigatoka pathogen of banana (Musa spp.) in Mexico

Pseudocercospora (previously known as Mycosphaerella) fijiensis causes black Sigatoka disease in banana (Musa spp.) and is considered to be the most devastating pathogen of this crop worldwide. To improve knowledge of its evolutionary patterns, this study determined the genetic variability of populations from two regions of Mexico: Central Pacific (Colima and Michoacan) and Southern (Chiapas, Tabasco and Oaxaca), using 10 simple sequence repeat (SSR) loci and the MAT-specific PCR assay. Both mating types were present in all regions under study, with frequencies of 63% MAT1-1 and 37% MAT1-2. The SSR markers showed an average of three alleles per locus, resulting in 34 alleles in total. The genetic diversity (H_T) was 0.3308, but at the local level (H_S) ranged from 0.0976 (Colima) to 0.2228 (Oaxaca). However, the genotypic diversity was usually high (H′ > 2.4, S > 0.89). Cluster analysis grouped the isolates into five clusters with high statistical support (au > 80%), suggesting a geographic organization of the genetic variability of P. fijiensis; AMOVA, the minimum spanning tree and the population structure analysis supported this result, and all data indicated that the major genetic differences were between the different populations under analysis. Thus, the high level of genetic variability in P. fijiensis is attributed partly to a high rate of sexual reproduction, and also to a strong evolutionary capacity coupled with isolation due to limited genetic flow between distant populations. Both possibilities could be playing a relevant role in population differentiation of the pathogen.     

Genetic diversity of Puccinia striiformis from cereals in Alberta,Canada

Stripe rust of wheat caused by Puccinia striiformis f. sp. tritici has recently become a production problem on wheat in Alberta, Canada, and stripe rust of barley caused by P. striiformis f. sp. hordei occurs regularly. A total of 261 isolates of P. striiformis were collected from wheat, barley, Hordeum jubatum and triticale plants in Alberta, Canada from 2007 to 2012, and compared to isolates from other provinces and the USA. The genetic diversity of the pathogen was assessed using 11 simple sequence repeat (SSR) markers and by examining a length polymorphism in the ribosomal DNA (rDNA) intergenic spacer 1 (IGS1) region. A total of 28 SSR genotypes were detected within Alberta. The 13 genotypes common on wheat (P. striiformis f. sp. tritici) were distinct from the 15 genotypes common on barley (P. striiformis f. sp. hordei). Four SSR genotypes, two within each forma specialis, represented 85% of the isolates recovered. Genotypic diversity was low, population genetic analysis indicated a clonal structure, and the genotypes were widely dispersed. In both formae speciales, the dominant genotype varied between years. The second most common P. striiformis f. sp. hordei genotype was found to be more closely related to older P. striiformis f. sp. tritici genotypes from the USA than to other P. striiformis f. sp. hordei genotypes.     

Genetic diversity within and between sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides in Japan

To reveal the effects of herbicide selection on genetic diversity in the outcrossing weed species Schoenoplectus juncoides, six sulfonylurea‐resistant (SU‐R) and eight sulfonylurea‐susceptible (SU‐S) populations were analysed using 40 polymorphic inter‐simple sequence repeat loci. The plants were collected from three widely separated regions: the Tohoku, Kanto and Kyushu districts of Japan. Genetic diversity values (Nei's gene diversity, h) within each SU‐S population ranged from h = 0.125 to h = 0.235. The average genetic diversity within the SU‐S populations was H_S = 0.161, and the total genetic diversity was H_T = 0.271. Although the H_S of the SU‐R populations (0.051) was lower than that of the SU‐S populations, the H_T of the SU‐R populations (0.202) was comparable with that of the SU‐S populations. Most of the genetic variation was found within the region for both the SU‐S and SU‐R populations (88% of the genetic variation respectively). Two of the SU‐R populations showed relatively high genetic diversity (h = 0.117 and 0.161), which were comparable with those of the SU‐S populations. In contrast, the genetic diversity within four SU‐R populations was much lower (from h = 0 to 0.018) than in the SU‐S populations. The results suggest that selection by sulfonylurea herbicides has decreased genetic diversity within some SU‐R populations of S. juncoides. The different level of genetic diversity in the SU‐R populations is most likely due to different levels of inbreeding in the populations.     

Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = ?0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.     

西藏林芝与内地小麦条锈菌分子群体遗传结构及菌源关系

 2009-2010年春季,先后从甘肃、四川、陕西和西藏四省的29个县(市)采集到1 391份小麦条锈病标样,繁殖获得961个菌株,利用SSR分子标记进行群体遗传分析结果表明:甘肃天水、平凉和陇南,陕西宝鸡及汉中,四川阿坝和广元等地条锈菌的遗传多样性比较丰富,而四川宜宾及凉山、西藏林芝的遗传多样性水平相对较低。利用Arlequin软件中的AMOVA方法分析结果表明,小麦条锈菌的遗传变异主要存在于群体内部。内地各种群之间菌源交流频繁(Nm＞4),西藏与内地菌源交流很少(Nm＜1)。采用Structure及聚类分析表明,陕西宝鸡与甘肃平凉间,陕西汉中、甘肃陇南、甘肃天水及四川广元间,存在着频繁的菌源交流关系,四川宜宾和凉山与四川阿坝、陕西汉中和甘肃陇南间存在着菌源交流关系。而西藏与内地间几乎没有菌源交流。初步认为西藏林芝小麦条锈菌可能是一个相对独立的遗传群体。