Impact of kiwifruit bacterial canker on productivity of cv. Hayward kiwifruit using observational data and multivariable analysis

A virulent strain of Pseudomonas syringae pv. actinidiae biovar 3 (Psa), which causes bacterial canker in kiwifruit, was first recorded in New Zealand in November 2010. This strain has severely affected Actinidia chinensis var. chinensis ‘Hort16A’ kiwifruit productivity but its effect on green Actinidia chinensis var. deliciosa ‘Hayward’ kiwifruit productivity has been variable. An observational study design was used to develop explanatory models to quantify the impacts of Psa infection on productivity (tray equivalents per hectare) of Hayward kiwifruit harvested in 2012, using data captured by industry from 2599 orchards. A total of 934 orchards were Psa positive at the end of the study period. Multivariable linear regression was used to model 2012 productivity in the presence of Psa, while controlling for regional differences, elevation, 2011 productivity, harvest dates and application of agrichemicals. The model showed productivity was initially higher in the presence of Psa, and was not reduced until after 1 year of infection. The relationship between protective spray use and productivity was also quantified. It is likely that improved disease management has offset the impact of the disease and future research should consider a reassessment of the effects of disease after longer term exposure to Psa in New Zealand. The use of an observational cohort study to assess disease impacts using multivariable analysis could have wider application in the field of plant epidemiology.     

Pseudomonas syringae pv. actinidiae: chemical control,resistance mechanisms and possible alternatives

Pseudomonas syringae pv. actinidiae (Psa) is a Gram‐negative bacterium that causes the bacterial canker of both green (Actinidia deliciosa) and yellow (Actinidia chinensis) fleshed kiwifruit. Since the emergence of an economically devastating Psa outbreak in Japan in the 1980s, the disease took a contagious turn causing severe economic loss to kiwifruit industries in Italy, South Korea, Spain, New Zealand and other countries. Research shows that the pathogenic strains isolated from different infected orchards vary in their virulence characteristics and have distinct genes coding for the production of different toxins. The global Psa outbreak has activated research around the world on developing efficient strategies to contain the pandemic and minimize loss to the kiwifruit industry. Chemical and biological control options, orchard management and breeding programmes are being employed in this global effort. Synergy between different disease control strategies has been recognized as important. Phytotoxicity, resistance development and regulatory measures in certain countries restrict the use of copper compounds and antibiotics, which are otherwise the mainstay chemicals against bacterial plant diseases. Therefore, because of the limitations of existing chemicals, it is important to develop novel chemical controls against Psa. Antimicrobial peptides, which are attractive alternatives to conventional antibiotics, have found promising applications in plant disease control and could contribute to expanding the chemical control tool box against Psa. This review summarizes all chemical compounds trialled so far against Psa and provides thoughts on the development of antimicrobial peptides as potential solutions for the future.     

Real‐time and qualitative PCR for detecting Pseudomonas syringae pv. actinidiae isolates causing recent outbreaks of kiwifruit bacterial canker

Since 2008, Pseudomonas syringae pv. actinidiae virulent strains (Psa‐V) have quickly spread across the main areas of kiwifruit (Actinidia deliciosa and A. chinensis) cultivation causing sudden and re‐emerging outbreaks of bacterial canker to both species. The disease caused by Psa‐V strains is considered worldwide as pandemic. Recently, P. syringae strains (ex Psa‐LV, now called PsD) phylogenetically related to Psa‐V have been isolated from kiwifruit, but cause only minor damage (i.e. leaf spot) to the host. The different biological significance of these bacterial populations affecting kiwifruit highlights the importance of having a diagnostic method able to detect Psa‐V, which is currently solely responsible for the severe damage to the kiwifruit industry. In order to improve the specific molecular detection of Psa‐V, a real‐time PCR assay has been developed based on EvaGreen chemistry, together with a novel qualitative PCR (PCR‐C). Both methods are based on specific primer sets for the hrpW gene of Psa. The real‐time PCR and PCR‐C were highly specific, detecting down to 50 and 200 fg, respectively, and were applied to a range of organs/tissues of kiwifruit with and without symptoms. These methods are important tools for both sanitary and certification programmes, and will help to avoid the spread of Psa‐V and to check possible inoculum sources. In addition to being used as routine tests, they will also enable the study of the biology of Psa‐V and the disease that it causes, whilst avoiding the detection of other populations of related P. syringae present in kiwifruit.     

Frost promotes the pathogenicity of Pseudomonas syringae pv. actinidiae in Actinidia chinensis and A. deliciosa plants

Frost occurs in all major areas of cultivation, presenting a threat for the production of kiwifruit crops worldwide. A series of experiments were performed on 1‐year‐old, potted plants or excised twigs of Actinidia chinensis and A. deliciosa to verify whether strict relationships exist between bacterial canker outbreaks from Pseudomonas syringae pv. actinidiae (Psa) attacks and the occurrence of autumn and winter frost events. The association between the occurrence of autumn frost and the sudden outbreak of bacterial canker in A. chinensis in central Italy has been confirmed. Both autumn and winter frosts promote Psa multiplication in the inoculated twigs of both species. The day after the frost, reddish exudates oozing from the inoculation sites were consistently observed in both species, and Psa was re‐isolated in some cases. During the thawing of both A. deliciosa and A. chinensis twigs, the 2‐cm upward and downward migration of Psa from the inoculation site was observed within 3 min, and the leaves were consistently colonized with the pathogen. A consistent brown discoloration, accompanied with a sour‐sap odour, was observed throughout the length of the excised twigs of both Actinidia species after Psa inoculation and winter frost. Psa inoculation induced a remarkably higher necrosis in excised twigs that were not frozen compared with P. s. pv. syringae inoculation. Antifreeze protection using irrigation sprinklers did not influence the short‐term period of Psa and P. s. pv. syringae multiplication in both A. deliciosa and A. chinensis twigs. Thus, the damage from frost, freeze thawing and the accumulation of Psa in Actinidia twigs promotes the migration of the pathogen within and between the orchards. Taken together, the results obtained in this study confirmed that A. deliciosa is more frost tolerant than A. chinensis, autumn frosts are more dangerous to these crops than winter frosts, and in the absence of Psa, young kiwifruit plants remain sensitive to frost.     

Molecular and phenotypic features of Pseudomonas syringae pv. actinidiae isolated during recent epidemics of bacterial canker on yellow kiwifruit (Actinidia chinensis) in central Italy

Pseudomonas syringae pv. actinidiae (Psa) was identified as the causal agent of severe epidemics of bacterial canker on Actinidia chinensis (yellow kiwifruit) in central Italy occurring during 2008–9. A total of 101 strains were obtained from infected leaves, twigs, branches and trunks of cvs Hort16A, Jin Tao and CK3. Outbreaks were also found on A. deliciosa cv. Hayward. A representative set of 21 strains were compared with other Psa strains isolated from previous outbreaks in Japan and Italy as well as with P. s. pv. syringae strains obtained from A. chinensis and with strains of genomospecies 8. Repetitive‐sequence PCR (rep‐PCR) typing using BOX and ERIC primer sets revealed that all Psa strains obtained during 2008–9 showed the same fingerprinting profile. This profile, however, was different from those of strains previously isolated in Japan and Italy. Multilocus sequence typing (MLST) of gapA, gltA, gyrB and rpoD revealed a higher genetic variability among the strains than rep‐PCR, with some of them showing the same sequence pattern although isolated from different areas, cultivars and years. None of the recently obtained strains possessed genes coding for phaseolotoxin or coronatine, and all had an effector protein, namely hopA1, differentiating them from the strains causing past outbreaks in Japan and Italy. All isolates were inhibited in vitro by copper‐based compounds, antibiotics, geraniol, citronellol and by a chitin‐based organic compound. The recent epidemics found in central Italy on yellow kiwifruit appear to have been caused by a different Psa population than those previously recorded in Japan, South Korea and Italy.     

Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov.

Since 2008, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis) caused by Pseudomonas syringae pv. actinidiae (Psa) has resulted in severe economic losses worldwide. Four biovars of Psa can be distinguished based on their biochemical, pathogenicity and molecular characteristics. Using a range of biochemical, molecular and pathogenicity assays, strains collected in France since the beginning of the outbreak in 2010 were found to be genotypically and phenotypically diverse, and to belong to biovar 3 or biovar 4. This is the first time that strains of biovar 4 have been isolated outside New Zealand or Australia. A multilocus sequence analysis based on four housekeeping genes (gapA, gltA, gyrB and rpoD) was performed on 72 strains representative of the French outbreak. All the strains fell into two phylogenetic groups: one clonal corresponding to biovar 3, and the other corresponding to biovar 4. This second phylogenetic group was polymorphic and could be divided into four lineages. A clonal genealogy performed with a coalescent approach did not reveal any common ancestor for the 72 Psa strains. Strains of biovar 4 are substantially different from those of the other biovars: they are less aggressive and cause only leaf spots whereas Psa biovars 1, 2 and 3 also cause canker and shoot die‐back. Because of these pathogenic differences, which were supported by phenotypic, genetic and phylogenetic differences, it is proposed that Psa biovar 4 be renamed Pseudomonas syringae pv. actinidifoliorum pv. nov. Strain CFBP 8039 is designated as the pathotype strain.     

Sooty spot of kiwifruit caused by Pseudocercospora actinidiae Deighton

Leaf spots on the lower leaf surface and sunken spots on the fruit of kiwifruit (Actinidia deliciosa and A. chinensis) were found in Fukuoka Prefecture, Japan. The observed fungus was identified as Pseudocercospora actinidiae Deighton. We propose the name sooty spot of kiwifruit (“susuhan-byo” in Japanese) as a new disease fullfilling Koch’s postulates.     

Highly specific assays to detect isolates of Pseudomonas syringae pv. actinidiae biovar 3 and Pseudomonas syringae pv. actinidifoliorum directly from plant material

Pseudomonas syringae pv. actinidiae (Psa) is responsible for bacterial canker of kiwifruit. Biovar 3 of Psa (Psa3) has been causing widespread damage to yellow‐ and green‐fleshed kiwifruit (Actinidia spp.) cultivars in all the major kiwifruit‐producing countries in the world. In some areas, including New Zealand, P. syringae pv. actinidifoliorum (Pfm), another bacterial pathogen of kiwifruit, was initially classified as a low virulence biovar of Psa. Ability to rapidly distinguish between these pathovars is vital to the management of bacterial canker. Whole genome sequencing (WGS) data were used to develop PCR assays to specifically detect Psa3 and Pfm from field‐collected material without the need to culture bacteria. Genomic data from 36 strains of Psa, Pfm or related isolates enabled identification of areas of genomic variation suitable for primer design. The developed assays were tested on 147 non‐target bacterial species including strains likely to be found in kiwifruit orchards. A number of assays did not proceed because although they were able to discriminate between the different Psa biovars and Pfm, they also produced amplicons from other unrelated bacteria. This could have resulted in false positives from environmental samples, and demonstrates the care that is required when applying assays devised for pure cultures to field‐collected samples. The strategy described here for developing assays for distinguishing strains of closely related pathogens could be applied to other diseases with characteristics similar to Psa.     

Occurrence and molecular characterization of Actinidia virus C (AcVC), a novel vitivirus infecting kiwifruit (Actinidia spp.) in China

Kiwifruit (Actinidia spp.) is an economically important fruit crop in the world. China is the largest producer of kiwifruit in terms of both acreage and yield. In this study, a novel virus, tentatively named Actinidia virus C (AcVC), was discovered in Actinidia deliciosa ‘Xuxiang’ grown in commercial kiwifruit fields in the Shaanxi province, a major kiwifruit-growing region in China. Sequencing of the complete genome showed that AcVC has 7,668 nucleotides (not including the poly-(A) sequence). Complete genome comparison and phylogenetic analysis showed that AcVC is most closely related to AcVA and then to AcVB. AcVC shares 69.2% nucleotide identity with AcVA (GenBank accession number JN427014 ). Based on these data, Actinidia virus C is assigned as a new tentative member of the genus Vitivirus in the family Betaflexiviridae. AcVC was found to infect A. deliciosa and A. chinesis, the two major cultivated kiwifruits. Infection frequency of AcVC varied with the kiwifruit-growing regions and cultivars in the Shaanxi province of China.     

Redefining the global populations of Pseudomonas syringae pv. actinidiae based on pathogenic,molecular and phenotypic characteristics

Knowing the population structure of a pathogen is fundamental for developing reliable phytosanitary legislation, detection techniques, and control strategies based on the actual aggressiveness and distribution of the pathogen. Currently, four populations of Pseudomonas syringae pv. actinidiae (Psa) have been described: Psa 1, Psa 2, Psa 3 and Psa 4. However, diagnostic assays specific for Psa populations do not detect Psa 4, the less virulent (LV) strains isolated in New Zealand. Similarly, multilocus sequence typing (MLST) of housekeeping genes, or broad Psa strain genome comparisons, revealed that Psa 4‐LV strains clustered separately from other Psa populations. In order to examine whether the placement of Psa 4 in the pathovar actinidiae was appropriate, various tests were carried out. It was shown that the Psa 4‐LV strains induced leaf and shoot wilting in Prunus cerasus, extensive necrotic lesions in Capsicum annuum fruits, and no significant symptoms in Actinidia deliciosa. Moreover, repetitive‐sequence PCR fingerprinting, type III secretion system effector protein genes detection and colony morphology clearly indicated the distinctiveness of Psa 4‐LV strains from the other three Psa populations. Rep‐PCR molecular typing revealed a high similarity of the Psa 4‐LV strains with members of Pseudomonas avellanae species. The Psa 4‐LV strains, most probably, belong to a new, still unnamed pathovar. It was concluded that the Psa 4‐LV strains isolated in New Zealand do not belong to the pathovar actinidiae, and, consequently, three Psa populations pathogenic to Actinidia spp. should currently include Psa 1, Psa 2 and Psa 3.     

Evaluation of the wild Actinidia germplasm for resistance to Pseudomonas syringae pv. actinidiae

Bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae (Psa) is a catastrophic disease that threatens the global kiwifruit industry. As yet, no cure has been developed. Planting resistant cultivars is considered as one of the most effective ways to control Psa. However, most existing cultivars lack Psa-resistance genes. Wild Actinidia resources contain rich genetic diversity and may have powerful disease-resistance genes under long-term natural selection, but lack of knowledge about the resistance to Psa for most Actinidia species results in some excellent wild resistant genotypes being underutilized. In this study, the response to Psa of 104 wild genotypes of 30 Actinidia species (including 37 taxa) was tested with an in vitro bioassay, and a considerable number of individuals from different species with tolerance or high resistance to Psa were identified. The results showed high consistency between years. This is the first large-scale evaluation of diverse Actinidia species with resistance to Psa through an in vitro bioassay. The resistant genotypes of A. chinensis identified could be used in future kiwifruit improvement programmes. The findings should help provide an understanding of the resistance to Psa.     

猕猴桃溃疡病菌不致病菌株G230的鉴定及形成原因分析

为探索田间猕猴桃溃疡病菌Pseudomonas syringae pv. actinidiae(Psa)致病力丧失的分子机制,针对从猕猴桃果园中分离获得的1株不致病菌株G230,通过特异性引物检测和多基因序列分析明确其分类地位,并设计引物检测其是否由已知遗传变异引起,通过比较基因组学、基因表达、超敏反应和荧光素酶报告菌株检测确定引起菌株G230致病力丧失的原因。结果表明,不致病菌株G230为Psa生物型3(Psa3),其致病缺陷不是由已报道的遗传变异引起;基于基因组比较分析发现菌株G230中的hrpS基因被转座子ISPsy36插入破坏,导致Ⅲ型分泌系统（type Ⅲ secretion system,T3SS）不能正常表达;而在不致病菌株G230中表达hrpS基因后能恢复其T3SS功能,使其具备致病能力及激发非寄主超敏反应的能力。表明转座子ISPsy36插入hrpS基因内部可以破坏Psa的T3SS功能进而使其丧失致病力,这是自然条件下Psa3丧失致病力的一种新型机制。     

Phoma leaf spot of wasabi (Wasabia japonica) caused by Leptosphaeria biglobosa

A leaf spot disease on wasabi plants grown in commercial greenhouses in the Fraser Valley of British Columbia was characterized. Mycelial growth and pycnidial formation were observed within lesions when leaves were incubated under conditions of high humidity. Isolation from diseased tissues consistently yielded colonies of a Phoma species. Sequence analysis of the rDNA internal transcribed spacer (ITS1‐5.8S‐ITS2) region of eight isolates showed 100% nucleotide sequence identity with Phoma wasabiae and Leptosphaeria biglobosa subspecies ‘occiaustralensis’ and 99.2% identity with L. biglobosa ‘canadensis’. Pathogenicity studies on wasabi leaves showed that wounding greatly facilitated infection and enhanced lesion development for most isolates but was not required for all isolates. Chlorotic areas appeared around the inoculation sites within 4 days, followed by necrosis. Isolates displayed a range of virulence, from weakly to highly virulent, on wasabi leaves. Similar results were observed on leaves of canola cultivar Westar, i.e. wounding significantly increased lesion size and isolates displayed a range of virulence. An isolate of Leptosphaeria maculans ‘brassicae’ from canola was highly virulent on wasabi and canola leaves, causing lesions similar to those of L. biglobosa ‘occiaustralensis’ while an isolate of L. biglobosa ‘canadensis’ from canola was weakly virulent on both hosts and required wounds to infect. These results demonstrate that isolates of L. biglobosa ‘occiaustralensis’ from wasabi are as virulent as L. biglobosa ‘canadensis’ on wasabi and canola leaves but in some cases were comparable in virulence to L. maculans ‘brassicae’.     

Phylogenetic Relationships Among Global Populations of Pseudomonas syringae pv. actinidiae

ABSTRACT Pseudomonas syringae pv. actinidiae, the causal agent of canker in kiwifruit (Actinidia spp.) vines, was first detected in Japan in 1984, followed by detections in Korea and Italy in the early 1990s. Isolates causing more severe disease symptoms have recently been detected in several countries with a wide global distribution, including Italy, New Zealand, and China. In order to characterize P. syringae pv. actinidiae populations globally, a representative set of 40 isolates from New Zealand, Italy, Japan, South Korea, Australia, and Chile were selected for extensive genetic analysis. Multilocus sequence analysis (MLSA) of housekeeping, type III effector and phytotoxin genes was used to elucidate the phylogenetic relationships between P. syringae pv. actinidiae isolates worldwide. Four additional isolates, including one from China, for which shotgun sequence of the whole genome was available, were included in phylogenetic analyses. It is shown that at least four P. syringae pv. actinidiae MLSA groups are present globally, and that marker sets with differing evolutionary trajectories (conserved housekeeping and rapidly evolving effector genes) readily differentiate all four groups. The MLSA group designated here as Psa3 is the strain causing secondary symptoms such as formation of cankers, production of exudates, and cane and shoot dieback on some kiwifruit orchards in Italy and New Zealand. It is shown that isolates from Chile also belong to this MLSA group. MLSA group Psa4, detected in isolates collected in New Zealand and Australia, has not been previously described. P. syringae pv. actinidiae has an extensive global distribution yet the isolates causing widespread losses to the kiwifruit industry can all be traced to a single MLSA group, Psa3.     

Adaptation of the New Zealand Psa risk model for forecasting kiwifruit bacterial canker in Korea

Bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), is a severe threat to kiwifruit production in Korea. An existing infection risk model from New Zealand was adopted to respond to this epidemic. Disease incidence (proportion of diseased leaves on each vine) and weather (hourly temperature, rainfall and relative humidity) data required to develop the model were collected and analysed in the study. Disease incidence data were used to modify and validate the existing model. Because the Psa risk model was originally developed in a region where the characteristic climatic conditions are completely different from those in Korea, the temperature and rainfall functions of the existing model were modified. Analyses using statistical correlation and prediction–realization tables revealed that the modified model is valid with high agreement (a correlation coefficient of 0.85 and an accuracy of 85.7%, respectively) between the observed disease incidence and simulated disease risk from the model. The model was also found to be more highly sensitive to the presence or absence of rainfall than any other weather variable inputs. Uncertainty in simulated disease risk was measured based on the level of uncertainty in temperature input from weather forecasts. Overall, these results indicate that the modified Psa risk model can be used to provide practical and applicable information for timely disease control to the kiwifruit growers in Korea.     

猕猴桃褪绿环斑相关病毒在陕西省的分布、分子变异及其2个分离物的基因组序列

为明确我国陕西省猕猴桃主产区的徐香、海沃德、华优和秦美4个猕猴桃品种上的猕猴桃褪绿环斑相关病毒(Actinidia chlorotic ringspot-associated virus,AcCRaV)的分布情况,对采集自该省4个地区的493份样品进行AcCRaV检测,基于cp基因序列对获得的AcCRaV分离物进行分子变异分析,并采用高通量测序技术对其中2份样品进行转录组测序。结果显示:AcCRaV在陕西省猕猴桃上分布广泛,且检出率较高,其中周至县秦美猕猴桃上AcCRaV的检出率最高,为45.0%,在杨凌区秦美猕猴桃上AcCRaV的检出率最低,为10.0%。测定的23个AcCRaV分离物cp基因序列全长均为945 nt。系统发育树显示AcCRaV分离物共分成2个组,存在较大的分子变异。AcCRaV的cp基因分子变异与猕猴桃品种有一定关系,而与地理位置相关性不明显。获得了2个AcCRaV分离物ZZ1和ZZ2的基因组序列,RNA1长度分别为7 049 nt和7 274 nt,RNA2长度均为2 266 nt,RNA3长度分别为1 691 nt和1 696 nt,RNA4长度分别为1 736 nt和1 683 nt,RNA5长度分别为1 460 nt和1 497 nt。分离物ZZ1和ZZ2的基因组序列与GenBank中唯一报道的我国湖北省AcCRaV分离物HN-6基因组序列比对中,分离物ZZ2与HN-6的RNA4同源率最高,为96.0%,分离物ZZ2与HN-6的RNA1同源率最低,为87.8%。表明AcCRaV在我国陕西省猕猴桃主产区分布较广泛,且其分子变异与猕猴桃品种有一定关系。     

Comparative genomics‐informed design of two LAMP assays for detection of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae and discrimination of isolates belonging to the pandemic biovar 3

The aim of this study was to develop a rapid, sensitive and reliable field‐based assay for detection of the quarantine pathogen Pseudomonas syringae pv. actinidiae (Psa), the causal agent of the most destructive and economically important bacterial disease of kiwifruit. A comparative genomic approach was used on the publicly available Psa genomic data to select unique target regions for the development of two loop‐mediated isothermal amplification (LAMP) assays able to detect Psa and to discriminate strains belonging to the highly virulent and globally spreading Psa biovar 3. Both LAMP assays showed specificity in accordance with their target and were able to detect reliably 125 CFU per reaction in less than 30 min. The developed assays were able to detect the presence of Psa in naturally infected kiwifruit material with and without symptoms, thus increasing the potential of the LAMP assays for phytosanitary use.     

Partial characterisation of a novel <Emphasis Type="Italic">Tobamovirus</Emphasis> infecting <Emphasis Type="Italic">Actinidia chinensis</Emphasis> and <Emphasis Type="Italic">A. deliciosa</Emphasis> (Actinidiaceae) from China

Actinidia chinensis and A. deliciosa plants from China, showing a range of symptoms, including vein clearing, interveinal mottling, mosaics and chlorotic ring spots, were found to contain ~300 nm rod-shaped virus particles. The virus was mechanically transmitted to several herbaceous indicators causing systemic infections in Nicotiana benthamiana, N. clevelandii, and N. occidentalis, and local lesions in Chenopodium quinoa. Systemically- infected leaves reacted with a Tobacco mosaic virus polyclonal antibody in indirect ELISA. PCR using generic and specific Tobamovirus primers produced a 1,526 bp sequence spanning the coat protein (CP), movement protein (MP), and partial RNA replicase genes which showed a maximum nucleotide identity (88%) with Turnip vein clearing virus and Penstemon ringspot virus. However, when the CP sequence alone was considered the highest CP sequence identity (96% nt and 98% aa) was to Ribgrass mosaic virus strain Kons 1105. The morphological, transmission, serological and molecular properties indicate that the virus is a member of subgroup 3 of the genus Tobamovirus.     

Predicting the potential distribution of Pseudomonas syringae pv. actinidiae in China using ensemble models

Pseudomonas syringae pv. actinidiae (Psa) is a causal agent of kiwifruit bacterial canker worldwide, which has affected kiwifruit vines in China since 1996 and has subsequently spread to the main cultivation areas. Based on occurrence of Psa and pseudo-absences randomly generated in China, the consensus-based modelling technique was used to estimate the spatial spread of Psa epidemics within China. Environmental variables that related to Psa development were identified, and their contributions to Psa development were evaluated. Three modelling algorithms, namely generalized boosting models (GBM), random forests (RF) and classification tree analysis (CTA) within the BIOMOD2 framework, were employed to construct the model. The ensemble models weighted by the true skill statistic (TSS) value were used to predict the current habitat suitability of Psa, and were projected using the four general circulation models (GCMs) to assess range shifts under two types of representative concentration pathways (RCP 4.5 and RCP 8.5) by 2050. The results indicated that precipitation in March and mean temperature of warmest quarter were the most important limiting factors for distribution of Psa. The predictive accuracy of the ensemble model showed acceptable predictive powers (TSS = 0.852). Under future climate conditions, substantial net loss of suitability for Psa was estimated to be 3.03–12.5% under RCP 4.5 (except one GCM), and 2.46–9.89% under RCP 8.5. Shrinkage of suitable habitats was detected mainly in the areas currently infected by Psa. Special attention should be given to recent infectious regions in south and southwest China, considering the locally expanding kiwifruit commercial plantations.     

Phytophthora infestans populations in central,eastern and southern African countries consist of two major clonal lineages

Limited knowledge is available on Phytophthora infestans populations in Sub‐Saharan Africa (SSA). Therefore, and in response to recent severe late blight epidemics, P. infestans isolates from potato, tomato and Petunia × hybrida from eight SSA countries were characterized. Isolates were characterized with ‘old’ markers, including mating type (176 isolates), mitochondrial DNA haplotype (mtDNA) (281 isolates), glucose‐6‐phosphate isomerase (Gpi) (70 isolates), restriction fragment length polymorphism analysis with probe RG‐57 (49 isolates), and by metalaxyl sensitivity (64 isolates). Most isolates belonged to the US‐1 genotype or its variants (US‐1.10 and US‐1.11). The exceptions were genotype KE‐1 isolates (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and unique RG‐57 genotype), identified in two fields in Kenya, which are related to genotypes previously identified in Rwanda (RW‐1 and RW‐2), Ecuador and Europe. Metalaxyl‐resistant P. infestans isolates from potato were present in all the countries except Malawi, whereas all the isolates from tomato were sensitive. Genotyping of 176 isolates with seven simple sequence repeat (SSR) markers, including locus D13 that was difficult to score, revealed 79 multilocus genotypes (MLGs) in SSA. When this locus was excluded, 35 MLGs were identified. Genetic differentiation estimates between regional populations from SAA were significant when locus D13 was either excluded (P = 0·05) or included (P = 0·007), but population differentiation was only low to moderate (F_ST = 0·044 and 0·053, respectively).