Disease development and genotypic diversity of Puccinia graminis f. sp. avenae in Swedish oat fields

The disease development and population structure of Puccinia graminis f. sp. avenae, which causes stem rust on oats, were studied to investigate if sexual reproduction plays an important role in the epidemiology of the disease. The genetic population structure of P. graminis f. sp. avenae in Sweden was investigated by sampling 10 oat fields in July and August 2008 and seven fields during the same period in 2009. Nine single‐pustule isolates were first used to test simple sequence repeat (SSR) markers developed for P. graminis f. sp. tritici. Eleven of the 68 tested SSR markers were useful for genotyping P. graminis f. sp. avenae. For the main study, DNA from single uredinia was extracted and the SSR markers were used to genotype 472 samples. Both allelic and genotypic diversity were high in all fields, indicating that P. graminis f. sp. avenae undergoes regular sexual reproduction in Sweden. No significant relationship between genetic and geographic distances was found. Disease development was studied on two farms during 2008 and 2009. The apparent infection rates ranged between 0·17 and 0·55, indicating the potential for rapid disease development within fields. The incidence of oat stem rust has increased recently in Sweden. One possible explanation is a resurgence of its alternate host, barberry (Berberis spp.), after the repeal of the barberry eradication law in 1994. Barberry is present in several grain‐producing areas in Sweden, which supports the conclusion that P. graminis f. sp. avenae undergoes regular sexual reproduction there.     

Development of genetic SSR markers in Blumeria graminis f. sp. hordei and application to isolates from Australia

The barley powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh), exists in numerous haplotypes and displays significant differences in fungicide sensitivity. It causes considerable yield losses throughout the world. Microsatellite SSRs are useful tools to study the population level and biogeographic aspects of intraspecific diversity, but so far none have been defined for Bgh. Here, eight polymorphic microsatellite loci were identified and characterized. Primer pairs amplifying the loci were then applied to 111 isolates of Bgh from Australia. The number of alleles per locus ranged from 4 to 13, and Nei's genetic diversity ranged from 0·25 to 0·76. The microsatellite primers detected several clones among the isolates and defined 97 unique haplotypes. There was little evidence for regional genotypic subdivision, suggesting that gene flow may not be restricted among geographic regions. All data was consistent with high levels of genetic diversity, potentially resulting from random mating and spread within each region.     

Resistance to powdery mildew (Blumeria graminis f.sp. avenae) in oat seedlings and adult plants

In this work, 165 Avena sativa and Avena byzantina accessions were screened for resistance to powdery mildew caused by Blumeria graminis f.sp. avenae and the defence mechanisms of resistant plants were further characterized. Ten resistant and moderately resistant accessions were selected according to macroscopic assessment. A detailed histological study of selected genotypes showed a range of defence mechanisms, acting alone or in combination, that impeded fungal development at different stages. Since the resistance observed in the collection was scarce, a study of adult plant resistance was carried out in 45 genotypes selected from field trials. Nine oat landraces and two commercial varieties showed very high levels of adult plant resistance. A detailed study of the components of the adult plant resistance revealed a high increase of penetration and post‐haustorial resistance in the fifth compared to the first leaves. Identification of the resistance sources and characterization of underlying defence mechanisms will be useful for future breeding programmes and for further cellular and molecular studies to unravel the genetic basis of resistance, in this species in particular and in cereal–powdery mildew interactions in general.     

Local dispersal of Puccinia striiformis f. sp. tritici from isolated source lesions

Understanding how disease foci arise from single source lesions has not been well studied. Here, single wheat leaves were inoculated with Puccinia striiformis f. sp. tritici urediniospores, and all wheat leaves within two intersecting 0.3 × 3.0 m transects were sampled in eight replicates over 3 years. The lesions observed on each of the top three leaves on plants within 1.5 m from the source lesion were three‐dimensionally mapped. The total number of lesions within a 1.5 m radius was estimated by dividing the number of lesions observed within each 0.025 m‐wide annulus by the fraction of the annulus sampled. The estimated total number of lesions produced within 1.5 m of a single source lesion ranged from 27 to 776, with a mean of 288 lesions. Eighty percent of the lesions were recorded within 0.69 m of the source infection. The proportion of total lesions observed at a given distance from the source was fitted well by the Lomax and Weibull distributions, reflecting the large proportion of lesions arising close to the source, and when fitted by an inverse power distribution had a slope (b) of 2.5. There were more lesions produced on leaves higher in the canopy than on lower leaves, with more lesions being detected above than below the point of inoculation. Simultaneous measurement of lesion gradients and spore dispersal in the final year of the study suggests that this pattern is due to greater susceptibility of upper leaves, rather than increased dispersal to upper leaves.     

Comparison of Puccinia graminis f.sp. tritici from South America and Europe

Twenty isolates of Puccinia graminis f.sp. tritici from South America were compared with 19 from Europe using virulence, isozymes and random amplified polymorphic DNA (RAPD) markers. The isozyme and virulence patterns for these isolates were also compared with those of 11 isolates representative of the common race clusters in North America. All three types of marker showed a level of similarity between the South American and European isolates comparable with that between isolates from the same continent. The average similarity coefficients between the South American and European isolates were 0.65 for virulence, 0.67 for isozymes, and 0.70 for RAPD markers. Among South American isolates the values were 0.63 for virulence, 0.64 for isozymes and 0.72 for RAPDs. For the South American and European isolates, correlation between the similarity matrices based on RAPDs and on isozyme markers, respectively ( r  = 0.52), was higher than that between the RAPD and virulence matrices ( r  = 0.32) or between isozyme and virulence matrices ( r  = 0.16). The North American isolates had a comparable level of similarity for virulence and isozymes to both the South American and European populations. There was no clear distinction between the South American, North American and European isolates, which is consistent with the hypothesis that these populations may have had a common origin.     

Colonization of lettuce cultivars and rotation crops by Fusarium oxysporum f. sp. lactucae,the cause of fusarium wilt of lettuce

The severity of fusarium wilt is affected by inoculum density in soil, which is expected to decline during intervals when a non‐susceptible crop is grown. However, the anticipated benefits of crop rotation may not be realized if the pathogen can colonize and produce inoculum on a resistant cultivar or rotation crop. The present study documented colonization of roots of broccoli, cauliflower and spinach by Fusarium oxysporum f. sp. lactucae, the cause of fusarium wilt of lettuce. The frequency of infection was significantly lower on all three rotation crops than on a susceptible lettuce cultivar, and the pathogen was restricted to the cortex of roots of broccoli. However, F. oxysporum f. sp. lactucae was isolated from the root vascular stele of 7·4% of cauliflower plants and 50% of spinach plants that were sampled, indicating a greater potential for colonization and production of inoculum on these crops. The pathogen was also recovered from the root vascular stele of five fusarium wilt‐resistant lettuce cultivars. Thus, disease‐resistant plants may support growth of the pathogen and thereby contribute to an increase in soil inoculum density. Cultivars that were indistinguishable based on above‐ground symptoms, differed significantly in the extent to which they were colonized by F. oxysporum f. sp. lactucae. Less extensively colonized cultivars may prove to be superior sources of resistance to fusarium wilt for use in breeding programmes.     

禾谷丝核菌基因组SSR标记的开发及评价

群体遗传学研究对于了解病原菌的流行、变异及进化规律具有重要意义。但是到目前为止,对小麦纹枯病菌禾谷丝核菌群体遗传结构的了解并不深入,缺乏有效的SSR标记是主要原因。本研究根据禾谷丝核菌全基因组序列进行了微卫星位点搜索并设计SSR引物,通过电泳筛选和测序验证,最终筛选出12个多态性较好且稳定可靠的SSR标记。利用这些标记对收集自我国安徽、江苏、河南三省的23个禾谷丝核菌菌株进行了多态性分析,结果发现禾谷丝核菌基因组中长片段微卫星位点较少。12对引物扩增出的等位基因数平均为6.1个,期望杂合度平均为0.651,观测杂合度平均为0.508,表明这些标记具有较高的多态性,能够满足禾谷丝核菌群体遗传学研究需要。本研究为进一步进行禾谷丝核菌的多样性、群体遗传结构分析及进化学研究提供了有效工具。     

Temperature adaptation in Australasian populations of Puccinia striiformis f. sp. tritici

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the major fungal pathogens of wheat. A new pathotype was introduced to Australia in 2002 and several derivative pathotypes were detected in subsequent seasons. It has been suggested that the severity of stripe rust outbreaks in Australia since 2002 could be as a result of traits other than virulence in the pathogen population. This study was conducted to investigate the hypothesis that the stripe rust pathogen population dominant in Australia since 2002 was better adapted to warm temperature conditions compared to previous pathogen populations. Sixteen pathotypes were selected to examine the influence of two contrasting temperature regimes during the 24 h incubation (10°C and 15°C) and the subsequent post‐inoculation (17°C and 23°C) periods on latent period and infection efficiency on four susceptible wheat cultivars. In addition, the effect of two contrasting incubation temperatures on urediniospore germination was examined. The results indicated that pathotypes of P. striiformis f. sp. tritici detected after 2002 did not show evidence of adaptation to high temperatures, which suggests that other factors contributed to the observed increased aggressiveness.     

Microsatellite and mating type markers reveal unexpected patterns of genetic diversity in the pine root‐infecting fungus Grosmannia alacris

Grosmannia alacris is a fungus commonly associated with root‐infesting bark beetles occurring on Pinus spp. The fungus has been recorded in South Africa, the USA, France, Portugal and Spain and importantly, has been associated with pine root diseases in South Africa and the USA. Nothing is known regarding the population genetics or origin of G. alacris, although its association with root‐infesting beetles native to Europe suggests that it is an invasive alien in South Africa. In this study, microsatellite markers together with newly developed mating type markers were used to characterize a total of 170 isolates of G. alacris from South Africa and the USA. The results showed that the genotypic diversity of the South African population of G. alacris was very high when compared to the USA populations. Two mating types were also present in South African isolates and the MAT1‐1/MAT1‐2 ratio did not differ from 1:1 (χ² = 1·39, P = 0·24). This suggests that sexual reproduction most probably occurs in the fungus in South Africa, although a sexual state has never been seen in nature. In contrast, the large collection of USA isolates harboured only a single mating type. The results suggest that multiple introductions, followed by random mating, have influenced the population structure in South Africa. In contrast, limited introductions of probably a single mating type (MAT1‐2) may best explain the clonality of USA populations.     

Characterization of Puccinia graminis f. sp. tritici isolates derived from an unusual wheat stem rust outbreak in Germany in 2013

An unusual stem rust infestation occurred in German wheat fields in summer 2013. This study analysed 48 isolates derived from 17 Puccinia graminis f. sp. tritici (Pgt) samples and six races were identified: TKTTF, TKKTF, TKPTF, TKKTP, PKPTF and MMMTF. Infection type and genotypic data confirmed that none of these races belonged to the TTKS (Ug99) race group. German isolates of race TKTTF are phenotypically different to the ones responsible for the stem rust epidemic in Ethiopia in 2013–2014. Forty isolates were genotyped using a custom SNP array. Phylogenetic analysis showed that these 40 isolates represented two distinct lineages (clade IV and clade V). Thirty‐eight isolates clustered into clade IV, which previously was defined by Ethiopian isolates of race TKTTF. Race TKKTP is of special concern due to its combined virulence to stem rust resistance genes Sr24, SrTmp and Sr1RS^Amigo. The vulnerability to race TKKTP in US and international winter wheat was confirmed as 55% of North American and international cultivars and breeding lines resistant to race TTKSK (Ug99) became susceptible to TKKTP. Races identified in Germany in 2013 confirmed the presence of virulence to important resistance genes that are effective against race TTKSK. This information should be useful for breeders to select diverse and effective resistance genes in order to provide more durable stem rust resistance and reduce the use of fungicides.     

A new race of Fusarium oxysporum f. sp. lactucae of lettuce

Fusarium oxysporum f. sp. lactucae, the causal agent of fusarium wilt of lettuce (Lactuca sativa), occurs in most countries in which lettuce is grown and causes serious economic losses. Three races (1, 2 and 3) of the pathogen have previously been identified on the basis of their ability to cause disease on differential lettuce cultivars, as well as by means of molecular tools developed to characterize different races of this pathogen. Only race 1 has been detected in Europe so far. In this study, two isolates of F. oxysporum, obtained from lettuce plants grown in the Netherlands showing symptoms of wilt, have been characterized by combining the study of pathogenicity with differential cultivars of lettuce and molecular assays to determine whether the isolates are different from the known races of F. oxysporum f. sp. lactucae. This study reports the presence of F. oxysporum f. sp. lactucae for the first time in the Netherlands. The causal pathogen has been identified, using the IRAP‐SCAR technique, as a new race of F. oxysporum f. sp. lactucae. Specific primers have been designed to identify this new race.     

陕西省小麦条锈菌群体遗传结构分析

 利用TP-M13-SSR自动荧光检测技术,对陕西省小麦条锈菌群体遗传结构进行了分析。研究结果显示,在物种水平上,陕西省小麦条锈菌群体Nei’s基因多样性指数（H）为0.18、Shannon 信息指数（I）为0.29,表明该省条锈菌群体遗传多样性较为丰富。同时,条锈菌群体遗传多样性在地区之间也存在明显的差异,在7个条锈菌群体中,宁强种群遗传多样性相对较高（H为0.18,I为0.28）。AMOVA分析显示,陕西省小麦条锈菌在地区间、种群间和群体内的遗传分化分别为：12.26%、10.88%和76.86%,表明陕西省小麦条锈菌群体存在一定的遗传分化,但遗传变异主要发生在群体内部。     

Overwintering and epidemiology of Puccinia dracunculina,the causal agent of rust in open tarragon fields

Rust, caused by Puccinia dracunculina, is the main foliar disease of open‐field tarragon (Artemisia dracunculus) crops in Israel. As not much is known about the biology or epidemiology of this pathogen, the long‐term objective of the current study was to accumulate the knowledge needed to develop an effective, environmentally friendly means of adequately managing the disease. Puccinia dracunculina is an autoecious brachy‐form pathogen, but it is not known whether the life cycle is completed under field conditions in Israel. Field observations and greenhouse studies revealed that although the telial stage is produced, the pathogen overwinters in the uredinial stage. In vitro experiments were used to quantify the temperature and wetness requirements for urediniospore germination and to calculate the daily duration of conducive weather (DDCW); DDCW was defined as the number of hours during which temperature ranged between 15 and 25°C and RH was >90%. Cumulative DDCW values (CDDCW) were a good predictor of disease under natural conditions in two growing seasons. Disease onset occurred when CDDCW values reached a level of 10 and the relationship between log CDDCW values and season‐long severity values (in logit) was highly significant, explaining 90·6% of the variation.     

SSR assessment of Phytophthora infestans populations on tomato and potato in British gardens demonstrates high diversity but no evidence for host specialization

Phytophthora infestans populations can differ in composition as a result of host specialization on tomato and potato hosts. In Great Britain many amateur gardeners grow outdoor tomatoes but there is little or no commercial tomato production outdoors. This study analysed isolates of P. infestans from British gardens with 12 multiplexed simple sequence repeat markers that are used to monitor the disease on commercial potato crops. Samples of P. infestans from tomato hosts were collected in 3 years and from potato in 1 year from across Great Britain. Seven previously unreported clonal lineages were detected in garden populations and higher frequencies of unique clonal lineages (28–40%) were present compared with populations from British commercial potato crops reported elsewhere. Garden populations had a lower proportion (11–48% less) of the most common lineages (13_A2 and 6_A1) that together made up at least 86% of the commercial potato populations during the sampling period. Host species accounted for only 2·0% of molecular variance detected between garden potato‐ and tomato‐hosted samples. No significant difference in clonal lineage composition was found between host species in Great Britain and this could be due to the whole P. infestans population overwintering on potato. British garden populations on both hosts were much more diverse than those on commercial potato crops; this finding may be influenced by less frequent fungicide use by gardeners and a higher diversity of unsprayed susceptible potato cultivars, enabling metalaxyl‐sensitive and less aggressive genotypes to survive in gardens.     

Development and validation of a quantitative PCR assay method of assessing relative resistance of oat (Avena sativa) to crown rust (Puccinia coronata f. sp. avenae)

Evaluation of oat crown rust resistance is usually based on visual assessment of disease severity or infection types. Visual assessment is subjective, prone to rater bias and requires expert knowledge. PCR-based quantitative assays can overcome challenges associated with visual assessment. New TaqMan primers and probes were designed from Puccinia coronata f. sp. avenae (Pca) sequences. The primer–probe sets were specific to Pca, amplified using as little as 0.5 pg fungal DNA (fDNA) and allowed for scaling to variation in sample total DNA quantity. The quantitative PCR (qPCR) assay was validated using oat recombinant inbred lines (RILs) from the Provena × 94197A1-9-2-2-2-5 cross evaluated under a controlled environment. For comparison with fDNA load, inoculation with the Pca race LCBB provided segregation data on the hypersensitive response, while Pca race LSLG provided data on segregation for reduced pustule number. fDNA content was positively correlated with both pustule number and infection type (IT). Composite interval mapping identified two quantitative trait loci (QTLs) on oat linkage groups Mrg12 and Mrg20 using visual and qPCR assessments (pustule number, IT and fDNA). In this study a qPCR assay method that can be used to assess the relative resistance of oat to crown rust was refined and validated, and single nucleotide polymorphisms (SNPs) closely linked with two QTLs derived from the crown rust resistant line 94197A1-9-2-2-2-5 were identified.     

Host switching between native and non‐native trees in a population of the canker pathogen Chrysoporthe cubensis from Colombia

The purpose of this study was to test the hypothesis that Chrysoporthe cubensis on native trees in South America could be the source of the pathogen that causes severe stem cankers and often mortality in commercially propagated Eucalyptus trees. This was done by investigating populations originating from two adjacent Eucalyptus (Myrtaceae) plantations in Colombia, and wild Miconia rubiginosa trees (Melastomataceae) growing alongside these stands. Polymorphic microsatellite markers were used to quantify allele sizes in 20 and 39 isolates from the two Eucalyptus stands and 32 isolates from adjacent M. rubiginosa trees. Gene and genotypic diversities were calculated from these data, and population differentiation and assignment tests were performed to ascertain whether the populations were genetically different. Results showed that there were no differences between any of the populations using these techniques, and that they can be treated as a single population. Therefore, the results support the hypothesis that host switching has occurred in C. cubensis in Colombia.     

Evidence for selection pressure from resistant potato genotypes but not from fungicide application within a clonal Phytophthora infestans population

Insight into pathogen population dynamics provides a key input for effective disease management of the potato late blight pathogen Phytophthora infestans. Phytophthora infestans populations vary from genetically complex to more simple with a few clonal lineages. The presence or absence of certain strains of P. infestans may impact the efficacy of fungicides or host resistance. Current evidence indicates that genetically, the Irish populations of P. infestans are relatively simple with a few clonal lineages. In this study, P. infestans populations were genetically characterized based on samples collected at the national centre for potato breeding during the period 2012–16. The dominance of clonal lineages within this P. infestans population was confirmed and the potential selection pressure of fungicide treatment (2013–15) and host resistance (2016) on this clonal P. infestans population was then investigated. It was found that fungicide products did not notably affect the genetic structure of sampled populations relative to samples from untreated control plants. In contrast, samples taken from several resistant potato genotypes were found to be more often of the EU_13_A2 lineage than those taken from control King Edward plants or potato genotypes with low resistance ratings. Resistant potato varieties Sarpo Mira and Bionica, containing characterized R genes, were found to strongly select for EU_13_A2 strains.