Genetic variation in populations of the cacao wilt pathogen, Ceratocystis cacaofunesta

Ceratocystis cacaofunesta (=  Ceratocystis fimbriata ) causes a lethal wilt disease of cacao ( Theobroma cacao ) in Latin America. Polymorphic microsatellite markers, (CAT)₅ nuclear DNA fingerprints and Hae III mitochondrial DNA fingerprints were used to compare genetic diversity among isolates of C. cacaofunesta collected from populations in western Ecuador, Costa Rica, Colombia, and Rondônia and Bahia in Brazil. Microsatellite markers and nuclear DNA fingerprints separated Ecuadorian isolates from isolates of the other four populations, and these two major groups correspond to genetic lineages already identified from ITS-rDNA sequences and intersterility groupings. Mitochondrial DNA fingerprints also demonstrated substantial diversity and split the Ecuadorian isolates into two groups. All marker types showed limited variation in the Colombian, Costa Rican and Bahian populations, as might be expected for introduced populations that have gone through recent genetic bottlenecks. In contrast, the Rondonian and western Ecuadorian populations showed gene diversity values similar to natural populations of other Ceratocystis species. The Rondonian population was the only sampled population in the native range of T. cacao (the Upper Amazon), and the putatively introduced populations were more closely related to the Rondonian population than to the western Ecuadorian population. The Ecuadorian population is in an area with other native Theobroma species, which may serve as natural hosts.     

Resistance of kiwifruit cultivars to ceratocystis wilt: An approach considering the genetic diversity and variation in aggressiveness of the pathogen

Kiwifruit (Actinidia spp.) is native to southern China, but was first cultivated in New Zealand and then spread worldwide. Emerging diseases such as ceratocystis wilt have attracted the attention of kiwifruit growers due to the great losses observed in southern Brazil. Effective control can be achieved by screening for resistance, but the genetic variability of the pathogen must be considered. Thus, this study aimed to assess the genetic diversity and variation in aggressiveness of Ceratocystis isolates from kiwifruit in southern Brazil and then evaluate the resistance of kiwifruit cultivars with the most aggressive isolates. A collection of 46 isolates were obtained from southern Brazil and 14 simple-sequence repeat (SSR) markers was successfully used for genotyping. Out of 14 markers, 13 were polymorphic and identified 26 genotypes. Fourteen distinct genotypes were tested on a susceptible cultivar to select the most aggressive ones. Finally, inoculation with an equal mixture of five of the most aggressive isolates was used to evaluate the resistance of seven kiwifruit cultivars: Red Arguta, Green Arguta, Allison, Chieftain, Hayward, Monty, and Tomury. Cultivars varied in levels of susceptibility, with disease severity ranging from 40% to 100%. Considering the length of stem lesions, Chieftain showed the lowest level of severity at 40%, while no wilt symptoms were observed at 45 days after inoculation. In addition to the seven cultivars, a half-sibling progeny with 618 plants of the rootstock cv. Bruno was also assessed, but only seven individuals were resistant. These seven plants can be cloned and used as resistant rootstocks in commercial orchards.     

Variation in growth rates and aggressiveness of naturally occurring self‐fertile and self‐sterile isolates of the wilt pathogen Ceratocystis albifundus

Ceratocystis albifundus is the most important fungal pathogen of black wattle (Acacia mearnsii) grown in plantations in southern and eastern Africa. It is a homothallic fungus but also undergoes unidirectional mating type switching. As a result, the ascospore progeny can be either self‐fertile or self‐sterile. The only apparent difference between these mating types is the deletion of the MAT1‐2‐1 gene in self‐sterile isolates. There is some evidence suggesting that self‐sterile isolates grow more slowly than self‐fertile isolates, but this has not been tested rigorously. The aim of this study was to determine whether self‐sterile isolates are less fit by examining growth rate, relative germination rate and pathogenicity. Five self‐sterile isolates were generated from each of five self‐fertile isolates of C. albifundus and these 30 isolates were compared. The results showed that the self‐sterile isolates grew consistently slower and were less pathogenic than the self‐fertile isolates. The germination ratio of self‐fertile to self‐sterile isolates from single ascospores collected from the ascomata of five self‐fertile isolates was on average 7:3. This could be a consequence of the self‐sterile isolates having a lower germination rate. This observation, and the lower growth and pathogenicity levels, suggests that self‐sterile isolates are not likely to compete effectively in nature, raising intriguing questions regarding their role and value to C. albifundus and other fungi having a similar mating system.     

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.     

Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europe and South Africa), based on analysis of 293 isolates genotyped with nine microsatellite markers. High levels of haplotypic richness (R = 0·91–1) and absence of multilocus linkage disequilibrium among loci supported the preponderance of sexual reproduction in all regions examined. Nonetheless, the identification of identical multilocus haplotypes with identical vegetative compatibility groups, in some vineyards in California and South Africa, suggests that asexual dispersal of the fungus among neighbouring plants could be a rare means of disease spread. The greatest levels of allelic richness (A = 4·89–4·97) and gene diversity (H = 0·66–0·69) were found in Europe among geographic samples from coastal areas surrounding the Mediterranean Sea, whereas the lowest genetic diversity was found in South Africa and Australia (A = 2·78–3·74; H = 0·49–0·57). Samples from California, Australia and South Africa, which had lower genetic diversity than those of Europe, were also characterized by demographic disequilibrium and, thus, may represent founding populations of the pathogen. Low but significant levels of genetic differentiation among all samples (D_EST = 0·12, P = 0·001; F_ST = 0·03, P = 0·001) are consistent with historical gene flow preventing differentiation at continental scales. These findings suggest that global, human‐mediated spread of the fungus may have resulted in its current global distribution.     

Diversity and differentiation in two populations of Gibberella circinata in South Africa

Gibberella circinata [anamorph Fusarium circinatum (=  F. subglutinans f.sp. pini )] causes pitch canker and is an important pathogen in South African pine nurseries. The initial outbreak of the pitch canker fungus was limited to a single nursery at Ngodwana in Mpumalanga Province. Subsequently, several other pine nurseries in South Africa became infected. Most of these outbreaks were relatively small except for the outbreak in the Klipkraal nursery (Mpumalanga Province). The genetic diversity, population differentiation and relative frequencies of the sexual and asexual cycles among two South African subpopulations were determined to establish whether immigration, mutation and/or recombination contributed towards population structure. The allelic diversity of the initial population (Ngodwana) was observed to be lower (0·16) than that of the more recent Klipkraal population (0·25). Approximately 4% ( G _ST = 0·04) of total gene diversity could be attributed to differences among the subpopulations. Furthermore, six new vegetative compatibility groups (VCGs) have been identified since the initial outbreak of G. circinata in South Africa 10 years ago. The relatively low allelic diversity and low level of genetic differentiation suggest restricted gene flow among subpopulations, and indicate that the pathogen has been introduced recently. However, the amount of allelic and VCG diversity suggests that multiple genotypes have been introduced into South Africa. The increases in effective population number, allelic diversity and new VCGs over the past 10 years suggest that sexual reproduction might be occurring.     

Low genetic diversity and strong geographic structure in introduced populations of the Eucalyptus foliar pathogen Teratosphaeria destructans

The aggressive Eucalyptus leaf pathogen, Teratosphaeria destructans, causes widespread damage in tropical and subtropical Eucalyptus-growing regions of Indonesia, China, Thailand, East Timor, Vietnam, Lao, and South Africa. Little is known regarding the origin, pathways of dispersal, or reproductive biology of this pathogen. The aim of this study was to investigate the genetic structure of a global collection of T. destructans isolates. This was achieved by developing and using polymorphic microsatellite markers. Low genotypic diversity and a limited number of private alleles were found in all investigated populations, with the highest maximum diversity of 10.7% in isolates from South Sumatra. This supports the hypothesis that T. destructans was introduced to these regions. High levels of clonality were common in all populations, especially in isolates sampled from the recent disease outbreak in South Africa, which were all identical. The global collection of isolates grouped into three distinct clusters, corresponding largely to their sampled regions. Low levels of genotypic diversity, high levels of clonality, and strong geographic structure suggest independent introductions into all the sampled areas from an unknown source. The results imply that strict biosecurity measures are needed to avoid introductions of additional genotypes in these areas.     

High diversity and clonality are hallmarks of Fusarium circinatum in South Africa

Pitch canker on plantation-grown Pinus species, caused by the fungal pathogen Fusarium circinatum, first appeared in the western and southern Cape regions of South Africa. However, outbreaks have subsequently been reported from the major plantation growing regions of KwaZulu-Natal and Limpopo in the eastern, summer rainfall regions of the country. It is more than 10 years since the last detailed population genetics studies on F. circinatum in the region were conducted. To shed light on the population biology of F. circinatum in this region of South Africa, we used microsatellite markers and mating-type assays to study a collection of 296 isolates from different nurseries and plantation sites. Our results showed that populations in the region are highly diverse, but strongly interconnected, with various genotypes shared across nursery and plantation collection sites. In contrast to nursery populations, those associated with pitch canker outbreaks were characterized by the presence of relatively small numbers of dominant genotypes that were generally widespread across the region. Opposite mating-type individuals occurred in most of the isolate collections, but multilocus linkage disequilibrium analyses pointed towards clonality being the main reproductive mode of F. circinatum in the region. Most of the pathogen's genetic variation could probably have resulted from multiple different introductions into the country and more specifically, into the summer rainfall region. Because the spread and establishment of invasive pathogens are typically driven by aggressive clones, the results of this study provide important considerations for current and future Pinus disease management strategies.     

Genetic diversity and interfertility among highly differentiated populations of Ceratocystis fimbriata in Brazil

Mating studies showed that isolates of the insect‐associated wilt pathogen Ceratocystis fimbriata from Eucalyptus spp., mango, fig, inhame (Colocasia esculenta), Gmelina arborea and sweet potato were interfertile, and progeny from those crosses showed normal segregation for microsatellite markers. Genetic diversity was compared among 13 populations of C. fimbriata collected from six states in Brazil using 15 highly polymorphic microsatellite markers. The gene diversity values of most eucalyptus and mango populations from Minas Gerais, Bahia, Rio de Janeiro and São Paulo states were similar to putatively native populations of Ceratocystis platani and C. cacaofunesta, two other species in the C. fimbriata complex that are homothallic. Index of association values indicated substantial asexual reproduction or selfing in populations on mango and eucalyptus. Most of these eucalyptus and mango populations were not highly differentiated from each other, and these populations and genotypes appeared to be more closely related to each other than to other populations by upgma analyses. By contrast, the G. arborea population from Pará and the fig and inhame populations from São Paulo had relatively low levels of diversity and were highly differentiated from each other and all other studied populations, suggesting that they were from different origins and had gone through genetic bottlenecks. One of the eucalyptus populations in Bahia consisted of a single genotype and may have been introduced to the site in infected cuttings from another Bahia location. Similarly, a mango population from Mato Grosso do Sul consisted of a single genotype, which was identical to one of the genotypes found on mango in São Paulo. Aside from introductions by humans, mating studies and genetic analyses suggest that limited dispersal distance and a high degree of selfing or asexual reproduction lead to local populations of C. fimbriata that have limited diversity but are highly differentiated from other populations.     

采后胡萝卜腐烂病病原菌鉴定

In October 2012, infected post harvest carrot root were found with decay symptom in several farmer markets around Kunming city of Yunnan Province, China. The symptom was grey white initially, then became brown to black with visible perithecia. According pathogenicity, morphology and sequence of the rDNA internal transcribed spacer region ( ITSI-5.8S-ITS2 ), the pathogen was identified as Ceratocystis fimbriata. The disease has been reported only in Brazil before, this is the first report on C. fimbriata as the pathogen of carrot(Daucus carota) decay post harvest in China .     

Gummosis and wilt of Acacia mearnsii in South Africa caused by Ceratocystis fimbriata

A dieback of Acacia mearnsii trees was observed in the Mkomasi river valley, Natal Province, South Africa. A fungus, tentatively identified as Ceratocystis fimbriata , was consistently isolated from affected twigs and branches. Reinoculation of the pathogen resulted in the development of typical wilt and dieback of A. mearnsii seedlings and saplings and in a dieback of Protea cynaroides plants. This is the first report of this disease in South Africa.     

Genetic diversity of Phytophthora pluvialis,a pathogen of conifers,in New Zealand and the west coast of the United States of America

Phytophthora pluvialis is the causal agent of red needle cast on Pinus radiata in New Zealand. It was first isolated in 2008 but had previously been recovered from tanoak (Notholithocarpus densiflorus) and Douglas‐fir (Pseudotsuga menziesii) trees in Oregon, USA in 2002. Phytophthora pluvialis was subsequently described as a new species in 2013 and classified as a clade III Phytophthora species. The aim of this study was to gain a better understanding of the genetic diversity, population structure and origin of this pathogen. A total of 360 P. pluvialis isolates were collected from the USA and New Zealand. The genome sequences of two P. pluvialis isolates were used to identify 27 single nucleotide polymorphism (SNP) markers that were then used to genotype the two populations. The genotypic data showed that the USA population of P. pluvialis had twice the genetic diversity and a greater number of multilocus genotypes (MLGs) compared to the New Zealand population, with 126 and 24 MLGs, respectively. The majority of the subpopulations within the USA and New Zealand showed linkage disequilibrium. All subpopulations had a negative fixation index, indicating that clonal reproduction is prevalent in both countries. A minimum spanning network (MSN) showed two unique clusters of isolates in the New Zealand population, suggesting two potential introductions of P. pluvialis into New Zealand from the USA. There was no significant structure within the New Zealand or USA populations. This study provides novel insight into the genetic structure of P. pluvialis in New Zealand and the USA.     

The gene diversity pattern of Diplocarpon rosae populations is shaped by the age,diversity and fungicide treatment of their host populations

Black spot disease caused by the hemibiotrophic ascomycete Diplocarpon rosae is the most devastating disease of field‐grown roses. Although resistance to black spot is an important trait for rose breeding, little information on the diversity of the pathogen is currently available. To date, a number of single‐spore isolates have been characterized based on a set of test genotypes of the host. In this study, six polymorphic simple sequence repeat (SSR) markers for D. rosae were developed and their potential application to single‐spore isolates collected from a wide range of geographic locations within and outside Europe discussed. Populations of the fungus were then analysed in different German rose collections/populations. Gene diversity was highest in older rose collections managed without fungicide application, and lowest in the two‐ to three‐year‐old testing sites of German rose breeders. Additional analyses of a global collection of single samples and populations revealed no unique alleles from any of the locations, indicating that global trading of rose varieties has led to an admixture of the pathogen.     

甘肃省苹果蠹蛾不同地理种群遗传多样性分析

为探明苹果蠹蛾不同地理种群的遗传变异、种群分化及传播扩散情况,利用9对微卫星引物对甘肃9个不同苹果蠹蛾地理种群的遗传多样性进行了研究。应用POPGENE 1.32和NTSYSpc 2.1软件分析表明:9对引物共检测到21个多样性位点,多态性百分比为95.45%;9个不同地理种群的观测等位基因为1.954 5,有效等位基因为1.741 3,Nei氏指数为0.411 3,Shannon指数为0.592 7±0.147 2;遗传相似度在0.325 8~0.817 0范围内。UPGMA聚类分析表明甘州、金塔种群聚为一支,与肃州种群合为一支;临泽种群与总寨种群聚为一支;七里河与敦煌种群聚为一支;高台与民勤种群聚为一支,各分支间的遗传分化系数Fst分别为0.795 0、0.531 4、0.857 9、0.598 0。Mantel检测表明,种群间的遗传距离与地理距离无显著相关性。研究表明,甘肃苹果蠹蛾种群的遗传多样性较低,遗传变异主要来自种群内部,种群之间的基因交流较少,在甘肃省的传播以人为被动传播扩散为主。     

Population genetic diversity and structure of the pecan scab pathogen,Venturia effusa,on cv. Desirable and native seedlings,and the impact of marker number

Scab (Venturia effusa) is the major cause of economic loss in pecan in the south-eastern USA. We explored population genetic diversity and structure among orchards of cv. Desirable and native seedlings, and within-orchard variability among trees of all cultivars sampled. We compared the ability of 30, 15 and 7 previously developed microsatellites to characterize the population genetic diversity and structure of V. effusa. Analyses of molecular variance (AMOVA) provided little evidence of structure dependent on cultivar, but there was some evidence of structure between orchards of a cultivar based on distance. Individual orchard AMOVA showed that three of 11 orchards had between-tree population structure. Among six populations from cv. Desirable, a Mantel test showed that geographic distance was related to the pairwise genetic divergence (R² = 0.84). Among 11 orchards of various cultivars there was little difference in diversity using 30, 15 or 7 markers, or population structure based on AMOVA. Some minor differences in population structure were seen based on discriminant analysis of principal components, or dendrograms. Thus, depending on the objectives, future studies may use as few as 15 or 7 markers without losing ability to discern population genetic diversity or structure. More populations exhibited linkage disequilibrium when using 15 or 30 markers compared to when using seven markers. Knowledge of population genetics of V. effusa in relation to host genotype is needed to understand pathogen population interactions and gene flow, knowledge that will help underpin future breeding efforts to develop durable resistance in this long-lived orchard tree.     

Genetic structure of the grapevine fungal pathogen Phaeomoniella chlamydospora in southeastern Australia and southern France

In this study, 18 microsatellite loci were used to examine the genetic structure and mode of reproduction of Phaeomoniella chlamydospora, the fungus that causes Petri disease of grapevine and is involved in another grapevine disease, esca. A total of 60 southeastern Australian isolates were tested and compared with 64 isolates from southern France. The French population possessed relatively high genotypic diversity (G = 29·2) whilst the Australian population showed low genotypic diversity (G = 11·1), consistent with a limited founder population. Haplotypes from four different grapevine cultivars were not significantly differentiated (Φpt values effectively zero). Likewise, genetic differentiation of haplotypes from different regions within each country was not significant, although small but significant genetic differentiation (9%) was identified between Australia and France. Based on bootstrapped cluster analysis, there did not appear to be any genetic groups within the overall sample of isolates. Significant linkage disequilibrium identified in both countries, together with overrepresented, widespread identical haplotypes, indicated limited genetic recombination and a largely clonal structure consistent with the absence of an observed sexual cycle in this species.     

Genetic differentiation in populations of Exserohilum turcicum from maize and sorghum in South Africa

Exserohilum turcicum is the causal agent of northern leaf blight, a devastating foliar disease of maize and sorghum. Specificity of E. turcicum to either maize or sorghum has been observed previously, but molecular evidence supporting host specialization is lacking. The aim of this study was to compare the genetic structure of E. turcicum isolates collected from adjacent maize and sorghum fields in Delmas and Greytown in South Africa. In addition, the mode of reproduction of this pathogen was investigated. Isolates from maize (N = 62) and sorghum (N = 64) were screened with 12 microsatellite markers as well as a multiplex mating type PCR assay. No shared haplotypes were observed between isolates from different hosts, although shared haplotypes were detected between isolates from maize from Delmas and Greytown. Population structure and principal coordinate analyses revealed genetic differentiation between E. turcicum isolates from maize and sorghum. Analysis of molecular variance indicated higher among‐population variation when comparing populations from different hosts, than comparing populations from different locations. Lack of shared haplotypes, high proportion of private alleles, greater among‐population variance between hosts than locations and significant pairwise population differentiation indicates genetic separation between isolates from maize and sorghum. The high haplotypic diversity in combination with unequal mating type ratios and significant linkage equilibrium indicates that both sexual and asexual reproduction contributes to the population genetic structure of E. turcicum in South Africa.     

山西玉米丝黑穗病菌SSR遗传多样性与群体结构分析

为明确山西省玉米丝黑穗病菌群体的遗传结构,为该病害的综合防控提供理论依据.采用SSR标记方法对山西省不同地区玉米丝黑穗病菌进行检测.结果显示,12个SSR分子标记在118株玉米丝黑穗病菌中共检测出30个等位基因,平均等位基因数(Na)、有效等位基因数(Ne)、Shannon's信息指数(I)、等位基因丰度(Ar)分别为...     

苹果黑星病菌遗传多样性的SSR分析

 Apple scab caused by Venturia inaequalis has a tendency to spread and threatens the development of apple production in recent years in China. The genetic diversity and population structure were investigated by using simple sequence repeat (SSR) markers. 51 strains were classified into 3 groups by UPGMA method as Xunyi, Xingping and U. K. population, each of them mainly including strains from its original place. A relatively high level of genetic diversity was revealed:H=0.425 3, I=0.675 8, PPL=66.67% (at species level); H=0.149 1, I=0.228 0, PPL=44.44% (at population level). A high level of genetic differentia-tion was detected among/within populations with Nei's Gst analysis and AMOVA. Molecular genetic variance within populations was greater than that among populations. Genetic variance among populations might result from barriers to gene flow (Nm=0.675 8). Genetic variance within populations might result from sexual propagation of V. inaequalis.     

Populations of Ceratocystis fimbriata on Colocasia esculenta and other hosts in the Mata Atlântica region in Brazil

Ceratocystis fimbriata is native to Brazil, where it is able to cause serious diseases on numerous hosts, especially on non‐native plants. Because C. fimbriata is soilborne and not wind dispersed, highly differentiated populations are found in different regions of Brazil. The present study compared populations of C. fimbriata on taro, mango, eucalyptus and kiwifruit from the coastal Mata Atlântica region with native populations of the fungus from the Cerrado‐transition region in Brazil by using 14 SSR markers and DNA sequences of ITS and mating type genes. Microsatellite and phylogenetic analyses were performed to test the hypothesis that populations on different hosts from the Mata Atlântica region are related to each other and are native to the region. The ITS sequences varied greatly among the taro isolates, with six sequences identified, from which two had not been previously reported. For mating type genes, four sequences were identified among the isolates on taro, mango, eucalyptus and kiwifruit. Phylogenetic analyses showed that Mata Atlântica populations formed a monophyletic group distinct from Cerrado‐transition region populations, although earlier studies had shown that isolates from the two regions are interfertile and are considered as a single biological species. Microsatellite analysis revealed low gene diversity for each of the three Mata Atlântica populations on taro, mango and kiwifruit, suggesting that these populations had gone through genetic bottlenecks, probably by dispersal of select genotypes in vegetative propagation material. Also, microsatellite markers showed that two microsatellite genotypes from taro are widely spread in Brazil, probably by infected corms.