A Shift in Pathotype Diversity and Complexity of Phytophthora sojae in Brazil.

Soybean root and stem rot caused by the oomycete Phytophthora sojae is a destructive disease worldwide that can affect plants at any growth stage. The use of resistant cultivars is the most effective method of controlling the disease. Therefore, monitoring changes in the population of P. sojae regarding the dynamics of avirulence genes capable of overcoming resistance genes (Rps) is important to reduce yield losses and to enhance the effectiveness of the Rps genes. Forty isolates of P. sojae sampled from a region of high incidence of soybean root and stem rot in Brazil were characterized using 14 soybean differentials, and 28 pathotypes were identified. Compared with a study conducted a decade ago, there was a major shift in pathotype diversity and complexity toward both higher numbers of different pathotypes and of avirulence genes in a given individual in the current population of P. sojae. Breeding programs aiming at developing soybean cultivars with resistance to root and stem rot should consider the high variability in the population of P. sojae and seek for strategic deployment of genes and germplasm.

The Population of Fusarium oxysporum f. sp. cubense in Brazil Is Not Structured by Vegetative Compatibility Group or by Geographic Origin.

Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), is considered one of the most destructive diseases of bananas in Brazil. In this study, a collection of 194 monosporic isolates from several banana-producing regions located in different climatic zones along a south-to-north transect in Brazil was formed to assess the genetic structure of the population of Foc. The isolates underwent pathogenicity tests, PCR diagnosis for the detection of tropical race 4, and screening of SIX homolog genes that produce putative effector proteins. The vegetative compatibility group (VCG) of 119 isolates was determined by pairing against 17 internationally known VCG-tester strains. A group of 158 isolates was selected for simple sequence repeat (SSR) genotyping. There was moderate diversity of Foc in Brazil. Eight VCGs were identified: 0120, 0122, 0124, 0125, 0128, 01215, 01220, and 01222, of which 78% of isolates belong to a single VCG, whereas 22% of isolates are assigned to multiple VCGs, belonging to complexes of VCGs. The distribution of VCGs is uneven and independent of the banana genotype. The isolates of a VCG shared a similar profile of SIX homologs, but there was no association with geographic region. Four SSR loci were polymorphic, and, on average, 7.5 alleles were detected per locus. Thirty-five multilocus genotypes (MLGs) were identified. There was no association between VCG and MLGs, and no genetic structure of the population of Foc in Brazil was detected.

The Population of Sclerotinia sclerotiorum in Brazil Is Structured by Mycelial Compatibility Groups.

The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil, and 68.5% of the isolates were assigned to either MCG 1 or MCG 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was because of differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). By contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs; lineages originating from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time, and affect many hosts, but there is evidence of some degree of outcrossing, which may lead to a more genetically variable population in the future.

Genetic Structure of Ralstonia solanacearum and Ralstonia pseudosolanacearum in Brazil.

Bacterial wilt-causing Ralstonia threaten numerous crops throughout the world. We studied the population structure of 196 isolates of Ralstonia solanacearum and 39 isolates of Ralstonia pseudosolanacearum, which were collected from potato- and tomato-growing areas in 19 states of Brazil. Regardless of the species, three groups of isolates were identified. One group encompassed R. pseudosolanacearum isolates. The other two groups comprise isolates of R. solanacearum (phylotype II) split according to geographic regions, one made of isolates from the North and Northeast and the other made of isolates from the Central, Southeast, and South regions (CSS). Among the isolates collected in CSS, those from tomato were genetically distinct from the potato isolates. The genetic variability in the population of R. pseudosolanacearum was lower than that of R. solanacearum, suggesting that the former was introduced in Brazil. Conversely, the high genetic variability of R. solanacearum in all regions, hosts, and times supports the hypothesis that this species is autochthonous in South America, more precisely in Brazil and Peru. For R. solanacearum, higher variability and lower migration rates were observed when tomato isolates were analyzed, indicating that the variability is caused mainly by the differences of the local, native soil population. The North subpopulation was distinct from all others, possibly because of differences in environmental features of this region. The proximity of some geographic regions and the movement of potato tubers could have facilitated migration and therefore low genetic differentiation between geographic regions. Finally, geography, which also influences host distribution, affects the structure of the population of R. solanacearum in Brazil. Despite quarantine procedures in Brazil, increasing levels of trade are a threat to biosecurity, and these results emphasize the need for improving our regional efforts to prevent the dispersal of pathogens.

First report of Ralstonia solanacearum causing bacterial wilt of eucalyptus in Ecuador.

In January 2018, eucalyptus trees showing wilt symptoms were identified in a commercial plantation located in the Quevedo Cantón, Los Ríos province, Ecuador. Disease incidence reached 40% of the eucalyptus field and affected plants displayed reddening and wilting of the foliage, leaf drop, branch dieback, and reduced growth, resembling bacterial wilting symptoms (Santiago et al., 2014). Transverse sections made on trunks of wilted trees revealed vascular discoloration of the wood and bacterial ooze. Wood pieces taken from discoloured tissues were surface disinfected and macerated in sterilized distilled water. The resulting suspensions were spread on plates containing triphenyltetrazolium chloride medium (TZC) (Kelman, 1954) and incubated at 28°C for 48 h. Three mucoid white colonies with pinkish centers, characteristic of Ralstonia solanacearum, were purified (Figure S1C). The isolates were Gram negative in the KOH test, non-fluorescent on King's B medium, and formed cream colonies on yeat extract-dextrose-calcium carbonate (YDC) medium. Phylotype-specific multiplex PCR (PMX-PCR) (Fegan and Prior, 2005) and phylogenetic analysis based on partial endoglucanase (egl) gene sequences (Poussier et al. 2000) (Figure S2) identified the isolates as R. solanacearum Phylotype IIB sequevar 51. The isolates were preserved in the COAD culture collection of the Universidade Federal de Vicosa, Brazil (codes COAD 2586, 2587 and 2588) and the corresponding egl DNA sequences were deposited in the GenBank (accession numbers MH350031, MH350032 and MH350033). Pathogenicity tests were conducted with all three isolates. Twenty microliters of bacterial suspensions (108 CFU/mL of saline solution) were injected at the base of the stem of eucalyptus (Eucalyptus urograndis), banana (Musa sp. cv. Maçã) and tomato (Solanum lycopersicum cv. Santa Clara) plants kept in a greenhouse (28 ± 2 °C) (Fonseca et al., 2016). Three plants of each host species were inoculated per bacterial isolate and plants injected with distilled water were used as controls. Necrotic symptoms appeared at the inoculation site on eucalyptus plants after 10 days. Wilt symptoms started at the top and progressed towards the base of the plants (Figure S1A). Tomato plants died within one week, and eucalyptus seedlings died after three weeks. The inoculated banana seedlings and all plants from the control treatments remained asymptomatic. Bacterial ooze was observed on freshly-cut transverse sections made on wilted eucalyptus seedlings (Figure S1B) and typical colonies of R. solanacearum were isolated from inoculated plants, fulfilling Koch's postulates. The correct diagnosis of the pathogen is the first step in the long-term process of developing effective management tools for this disease in Ecuador.

Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus.

BACKGROUND: Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species. RESULTS: A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions. CONCLUSIONS: New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.

Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location.

The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.

Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases.

BACKGROUND: Sclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of several species. Transposons from the Tc1-Mariner superfamily are thought to be ubiquitous components of fungal genomes and are generally found in low copy numbers with large numbers of deleterious mutations in their transposase coding sequence. RESULTS: This study shows that the genome of S. sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3' regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation. CONCLUSIONS: Fourteen novel Tc1-Mariner families were characterized. Some families had evidence of introns, which might or might not be excised depending on the family or element in question, and this finding demonstrates a possible strategy for overcoming possible mutations that generate premature stop codons in a RNA sequence. Tc1-Mariner elements likely play an important role in the structure and evolution of the S. sclerotiorum genome.

Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato.

Viral diseases caused by begomoviruses are of economic importance due to their adverse effects on the production of tropical and subtropical crops. In Ecuador, despite reports of significant infestations of Bemisia tabaci in the late 1990s, only very recently has a begomovirus, tomato leaf deformation virus (ToLDeV, also present in Peru), been reported in tomato. ToLDeV is the first monopartite begomovirus discovered that originated in the Americas, and its presence in Ecuador highlights the need for a wider survey of tomato-infecting begomoviruses in this country. Tomato and weed samples were collected in 2010 and 2011 in six provinces of Ecuador, and begomovirus genomes were cloned and sequenced using a rolling-circle-amplification-based approach. Most tomato samples from the provinces of Guayas, Loja, Manabi and Santa Elena were infected with tomato leaf deformation virus (ToLDeV). One sample from Manabi had a triple infection with ToLDeV, rhynchosia golden mosaic Yucatan virus (RhGMYuV) and an isolate that was a recombinant between the two. A new begomovirus was detected in another tomato sample from Manabi. Samples of Rhynchosia sp. from the provinces of Guayas and Manabi were infected by RhGMYuV. These results indicate not only the prevalence of ToLDeV in tomato in Ecuador but also the presence of other viruses, albeit at a much lower frequency.

Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil.

The rust fungus, Puccinia psidii, is a devastating pathogen of introduced eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912. This pathogen is hypothesized to be endemic to South and Central America and to have first infected eucalypts via a host jump from native guava (Psidium guajava). Ten microsatellite markers were used to genotype 148 P. psidii samples from eucalypts and guava plus five additional myrtaceous hosts across a wide geographic range of south-eastern Brazil and Uruguay. Principal coordinates analysis, a Bayesian clustering analysis and a minimum-spanning network revealed two major genetic clusters among the sampled isolates, one associated with guava and another associated with eucalypts and three additional hosts. Multilocus genotypes infecting guava differed by multiple mutational steps at eight loci compared with those infecting eucalypts. Approximate Bayesian computation revealed that evolutionary scenarios involving a coalescence event between guava- and eucalypt-associated pathogen populations within the past 1000 years are highly unlikely. None of the analyses supported the hypothesis that eucalypt-infecting P. psidii in Brazil originated via host jump from guava following the introduction of eucalypts to Brazil approximately 185 years ago. The existence of host-associated biotypes of P. psidii in Brazil indicates that this diversity must be considered when assessing the invasive threat posed by this pathogen to myrtaceous hosts worldwide.

Mycosphaerella musicola Identified as the Only Pathogen of the Sigatoka Disease Complex Present in Minas Gerais State, Brazil.

A thorough assessment of the distribution of Mycosphaerella spp. associated with banana in Minas Gerais State, Brazil, was conducted after Mycosphaerella fijiensis was first reported to occur in this region in 2005. From 2009 to 2011, 80 fields located in 20 municipalities including the same fields where the disease was first reported were sampled. A total of 800 samples of leaf tissue with symptoms similar to those of yellow or black Sigatoka diseases were examined, and 239 isolates were obtained. The identification of the fungi was based on morphological characters combined with DNA sequences obtained after amplification with species-specific primers and phylogeny inferred from the internal transcribed spacer region of Mycosphaerella strains from banana. All 239 isolates were identified as Mycosphaerella musicola. The absence of M. fijiensis in the samples may have been due to misidentification of M. fijiensis or the displacement of M. fijiensis by M. musicola. It is now apparent that yellow Sigatoka caused by M. musicola is the prevailing leaf spot disease of bananas in Minas Gerais State and that regulatory/legislative control measures need to be revised based on our findings.

High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil.

Diseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.

Movement of genotypes of Ceratocystis fimbriata within and among Eucalyptus plantations in Brazil.

Ceratocystis wilt on eucalyptus, caused by Ceratocystis fimbriata, was first recognized in 1997 in the state of Bahia, Brazil, but is now known in five other states and in four other countries. C. fimbriata is a native, soilborne pathogen in some parts of Brazil but we hypothesized that genotypes of the pathogen have been moved among plantations in rooted cuttings collected from diseased trees and within plantations on cutting tools. We used six microsatellite markers to identify 78 genotypes of C. fimbriata among 177 isolates from individual trees in 20 eucalyptus plantations. The highest gene and genotypic diversity values were found in plantations on formerly wild Cerrado forest in Minas Gerais, suggesting that the fungus was in the soil prior to planting eucalyptus. In contrast, one or only a few genotypes were found in plantations on previous pastureland (with no woody hosts) in Bahia and São Paulo, and most of these genotypes were found in a Bahian nursery or in one of two Bahian plantations that were sources for rooted cuttings. Sources of cuttings tended to be dominated by one or a few genotypes that may have been spread within the plantation on cutting tools.

Weevil Borers Affect the Spatio-Temporal Dynamics of Banana Fusarium Wilt.

Dispersal of propagules of a pathogen has remarkable effects on the development of epidemics. Previous studies suggested that insect pests play a role in the development of Fusarium wilt (FW) epidemics in banana fields. We provided complementary evidence for the involvement of two insect pests of banana, the weevil borer (Cosmopolites sordidus L., WB) and the false weevil borer (Metamasius hemipterus L., FWB), in the dispersal of Fusarium oxysporum f. sp. cubense (Foc) using a comparative epidemiology approach under field conditions. Two banana plots located in a field with historical records of FW epidemics were used; one was managed with Beauveria bassiana to reduce the population of weevils, and the other was left without B. bassiana applications. The number of WB and FWB was monitored biweekly and the FW incidence was quantified bimonthly during two years. The population of WB and the incidence (6.7%) of FW in the plot managed with B. bassiana were lower than in the plot left unmanaged (13%). The monomolecular model best fitted the FW disease progress data, and as expected, the average estimated disease progress rate was lower in the plot managed with the entomopathogenic fungus (r = 0.002) compared to the unmanaged plot (r = 0.006). Aggregation of FW was higher in the field with WB management. WB affected the spatial and temporal dynamics of FW epidemics under field conditions. Management of the insects may reduce yield loss due to FW.

Incidence, Spatial Pattern and Temporal Progress of Fusarium Wilt of Bananas.

The effective management of Fusarium wilt of bananas (FWB) depends on the knowledge of the disease dynamics in time and space. The objectives of this work were: to estimate disease intensity and impact, and to investigate the spatial and temporal dynamics of FWB. Fields planted with Silk (n = 10), Pome (n = 17), or Cavendish (n = 3) banana subgroups were surveyed in Brazil, totaling 95 ha. In each field, all plants were visually assessed, and diseased plants were georeferenced. The incidence of FWB and the impact of the disease on the yield on a regional scale were estimated. Spatial patterns were analyzed using quadrat- and distance-based methods. FWB incidence ranged from 0.09% to 41.42%, being higher in Silk fields (median = 14.26%). Impacts of epidemics on yield ranged from 18.4 to 8192.5 kg ha-1 year-1, with an average of 1856.7 kg ha-1 year-1. The higher economic impact of the disease was observed on Silk cultivar with an average loss of USD 1974.2 ha-1 year-1. Overall, estimated losses increased on average by USD 109.8 ha-1 year-1 at each 1% of incidence. Aggregation of FWB was detected by all analytical methods in 13 fields (1 of Cavendish, 11 of Pome, and 1 of Silk). In the other 17 fields, at least one analytical method did not reject the null hypothesis of randomness. One field (5 ha), composed of six plots, was selected for spatial and temporal studies during two years with bi-monthly assessments. A sigmoidal curve represented the FWB progress and the Gompertz model best-fitted disease progress. The level of aggregation varied over time, and evidence of secondary infection to neighboring and distant plants was detected. FWB is a widespread problem in Brazil and yield losses can be of high magnitude. Epidemiology-based management strategies can now be better established.

Experimental evolution of cowpea mild mottle virus reveals recombination-driven reduction in virulence accompanied by increases in diversity and viral fitness.

Major themes in pathogen evolution are emergence, evolution of virulence, host adaptation and the processes that underlie them. RNA viruses are of particular interest due to their rapid evolution. The in vivo molecular evolution of an RNA plant virus was demonstrated here using a necrotic isolate of cowpea mild mottle virus (CPMMV) and a susceptible soybean genotype submitted to serial inoculations. We show that the virus lost the capacity to cause necrosis after six passages through the host plant. When a severe bottleneck was imposed, virulence reduction occurred in the second passage. The change to milder symptoms had fitness benefits for the virus (higher RNA accumulation) and for its vector, the whitefly Bemisia tabaci. Genetic polymorphisms were highest in ORF1 (viral replicase) and were independent of the symptom pattern. Recombination was a major contributor to this diversity - even with the strong genetic bottleneck, recombination events and hot spots were detected within ORF1. Virulence reduction was associated with different sites in ORF1 associated to recombination events in both experiments. Overall, the results demonstrate that the reduction in virulence was a consequence of the emergence of new variants, driven by recombination. Besides providing details of the evolutionary mechanisms behind a reduction in virulence and its effect under viral and vector fitness, we propose that this recombination-driven switch in virulence allows the pathogen to rapidly adapt to a new host and, potentially, switch back.

Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches.

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

Effects of Temperature on Events in the Infection Cycle of Two Clonal Lineages of Phytophthora infestans Causing Late Blight on Tomato and Potato in Brazil.

In Brazil, US-1 and BR-1 clonal lineages of Phytophthora infestans are widely distributed throughout the major growing areas of tomato and potato, respectively. Quantitative information regarding the effects of temperature (10, 15, 22, and 27°C) on direct and indirect sporangia germination, incubation period (IP), latent period (LP), lesion area (LA), and sporulation (SP), as well as combined temperature and leaf wetness duration periods (6, 12, 18, and 24 h) on the number of lesions (NL) was obtained under controlled conditions on either detached leaflets or whole plants. The percentage of indirect germination was higher for BR-1 isolates than for US-1. The percentage of direct germination was higher for US-1 than for BR-1. The shortest IP and LP were recorded at 22°C for both lineages: 69.3 h and 93.3 h for US-1 isolates on detached tomato leaflets, and 44.0 h and 68 h for BR-1 isolates on detached potato leaflets, respectively. US-1 isolates did not sporulate at 10°C, and BR-1 isolates did not sporulate at 27°C. Isolates of both lineages induced the largest LA at 22°C. The NL was highest at 15°C for US-1 isolates on whole tomato plants, and at 10°C for BR-1 isolates on whole potato plants. The differential effects of temperature on US-1 and BR-1 suggest that current decision support systems initially developed for controlling US-1 in Brazil may now be inaccurate for controlling BR-1, and management strategies should be properly validated before being used.

Fusarium Wilt of Banana: Current Knowledge on Epidemiology and Research Needs Toward Sustainable Disease Management.

Banana production is seriously threatened by Fusarium wilt (FW), a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). In the mid-twentieth century FW, also known as "Panama disease", wiped out the Gros Michel banana industry in Central America. The devastation caused by Foc race 1 was mitigated by a shift to resistant Cavendish cultivars, which are currently the source of 99% of banana exports. However, a new strain of Foc, the tropical race 4 (TR4), attacks Cavendish clones and a diverse range of other banana varieties. Foc TR4 has been restricted to East and parts of Southeast Asia for more than 20 years, but since 2010 the disease has spread westward into five additional countries in Southeast and South Asia (Vietnam, Laos, Myanmar, India, and Pakistan) and at the transcontinental level into the Middle East (Oman, Jordan, Lebanon, and Israel) and Africa (Mozambique). The spread of Foc TR4 is of great concern due to the limited knowledge about key aspects of disease epidemiology and the lack of effective management models, including resistant varieties and soil management approaches. In this review we summarize the current knowledge on the epidemiology of FW of banana, highlighting knowledge gaps in pathogen survival and dispersal, factors driving disease intensity, soil and plant microbiome and the dynamics of the disease. Comparisons with FW in other crops were also made to indicate possible differences and commonalities. Our current understanding of the role of main biotic and abiotic factors on disease intensity is reviewed, highlighting research needs and futures directions. Finally, a set of practices and their impact on disease intensity are discussed and proposed as an integrative management approach that could eventually be used by a range of users, including plant protection organizations, researchers, extension workers and growers.

Independently founded populations of Sclerotinia sclerotiorum from a tropical and a temperate region have similar genetic structure.

Sclerotinia sclerotiorum populations from tropical agricultural zones have been suggested to be more variable compared to those from temperate zones. However, no data were available comparing populations from both zones using the same set of markers. In this study, we compared S. sclerotiorum populations from the United States of America (USA, temperate) and southeast Brazil (tropical) using the frequency of mycelial compatibility groups (MCGs) and 13 microsatellite (SSR) markers. Populations were sourced from diseased plants within leguminous crops in New York, USA (NY; n = 78 isolates), and Minas Gerais State, Brazil (MG; n = 109). Twenty MCGs were identified in NY and 14 were previously reported in MG. The effective number of genotypes based on Hill's number of order 0, which corresponded to the number of multilocus genotypes (MLGs) were 22 (95% CI = 15.6-28.4) and 24 (95% CI = 18.9-29.1) in NY and MG, respectively. Clonal fractions of MLGs were 71.8% (NY) and 78.0% (MG). The effective number of genotypes based on Hill's number of orders 1 and 2 in NY were 8.9 (95% CI = 5.2-12.6) and 4.4 (95% CI = 2.6-6.1), respectively. For MG these indices were 11.4 (95% CI = 8.7-14.1) and 7.1 (95% CI = 5.1-9.0), respectively. There were no significant differences of allelic richness, private allelic richness, gene diversity, effective number of alleles and genotype evenness between the NY and MG populations. The populations were differentiated, with 29% of total variance attributed to differences between them and G''ST and Jost's D indices higher than 0.50. Cluster analysis revealed dissimilarity higher than 80% among most MLGs from both populations. Different alleles segregated in the populations but both had similar levels of genotypic variability.