Diversity and distribution of pathotypes of the soybean rust fungus Phakopsora pachyrhizi in East Africa

Phakopsora pachyrhizi is a biotrophic fungus that causes rust on soybean, leading to devastating yield losses. Development of resistant cultivars for deployment in different geographic regions requires a comprehensive understanding of the prevalent P. pachyrhizi pathotypes. To determine the pathotypes existing in four East African countries, 65 isolates were tested on 11 soybean host differentials. In addition, the virulence spectrum of isolates collected from the same region over multiple years was compared. The majority of the isolates (54%) belonged to pathotype 1000, which was found in all countries. The pathotypes with the most complex virulence spectrum, which comprised isolates from Kenya and Malawi, were virulent on four differentials. All pathotypes were virulent on soybean genotypes carrying the Rpp1 resistance gene to P. pachyrhizi, but they were avirulent on cultivars carrying the Rpp1b, Rpp2, or Rpp3 gene, as well as on cultivar No6-12-1 that carries Rpp2, Rpp4, and Rpp5. Two of the pathotypes were virulent on cultivar UG 5 that carries Rpp1 and Rpp3 and on Hyuuga that carries Rpp3 and Rpp5. The isolates collected from different countries differed in their virulence spectrum across the years. Shannon's index (H) and Simpson's index (S) of diversity indicated that the isolates from Malawi were more diverse (H = 1.55, S = 0.90) while those from Uganda had lower diversity (H = 0.78, S = 0.46 ). The Rpp genes that were found to provide resistance to all pathotypes of P. pachyrhizi can be employed for soybean breeding aimed at durable rust resistance.     

Systemic properties of myclobutanil in soybean plants, affecting control of Asian soybean rust (Phakopsora pachyrhizi)

BACKGROUND: The demethylation inhibitor (DMI) fungicide myclobutanil can be an effective component of spray programmes designed to control the highly destructive plant pathogen Phakopsora pachyrhizi Syd. & P. Syd., causal agent of Asian soybean rust. Myclobutanil is known from previous studies in grapevines to be xylem mobile. This study investigates the mobility profile of myclobutanil in soybean as an important component of its effective field performance. RESULTS: Over a 12 day period under greenhouse conditions, a constant uptake of myclobutanil from leaflet surfaces into the leaflet tissue was observed. Once in the leaflet, myclobutanil was seen to redistribute throughout the tissue, although no movement out of leaflets occurred owing to a lack of phloem mobility. The ability of myclobutanil to redistribute over distance within the soybean plant was revealed when visualizing movement of the compound to foliage above the point of application on the plant stem. An efficacy bioassay demonstrated that the systemic properties of myclobutanil allow control of disease at a point remote from the initial site of compound application. CONCLUSION: It is suggested that the high degree of xylem systemicity displayed by myclobutanil in soybean foliage is a contributory factor towards its commercial effectiveness for control of Asian soybean rust. Copyright © 2008 Society of Chemical Industry     

A major variation in the virulence of the Asian soybean rust pathogen (Phakopsora pachyrhizi) in Bangladesh

Asian soybean rust (ASR) caused by Phakopsora pachyrhizi is a major threat to soybean production in Bangladesh. Understanding the yearly changes and the current status of pathogenic structures is essential for developing appropriate breeding strategies for obtaining ASR-resistant soybean lines. Thirty-four P. pachyrhizi samples were collected from ASR hotspot areas (Chandpur, Lakshmipur, Noakhali, Barisal and Bhola districts) of Bangladesh in 2018 and 2019 and evaluated for pathogenicity on 12 soybean differential lines. The tested samples showed similar and dissimilar pathogenicity patterns on the differentials, yielding 21 distinct pathotypes. The cluster analysis, principal coordinate analysis and principal component analysis of the disease phenotypes of 47 samples collected in 2016, 2018 and 2019 indicated a higher pathogenic diversity and virulence variation in the P. pachyrhizi samples of 2018 and 2019 compared to that of 2016. The pathogenicity profiles of the Bangladeshi P. pachyrhizi samples appeared distinct from those of Argentinian and Brazilian samples, but showed slight similarities with Japanese, Mexican and Paraguayan samples. Furthermore, none of the resistance genes for P. pachyrhizi (Rpp genes) was solely effective against all the tested samples from 2018 and 2019, while samples (BdRP-48, BdRP-56 and BdRP-58) virulent to all Rpp1–Rpp6 genes were detected. The Rpp-pyramided line No6–12–1, carrying Rpp2, Rpp4 and Rpp5, was capable of conferring robust resistance to these virulent samples. Altogether, these results indicate an increase in the virulence of the current ASR pathogen in Bangladesh, which can be resolved by pyramiding different resistance genes in soybean cultivars.     

Identification of genes expressed by Phakopsora pachyrhizi,the pathogen causing soybean rust,at a late stage of infection of susceptible soybean leaves

Soybean is one of the top five agricultural products in the United States and is highly susceptible to Phakopsora pachyrhizi, an exotic obligate biotrophic fungus. The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.     

Pathogenic Races of Phakopsora pachyrhizi on Soybean and Wild Host Plants Collected in Japan

A total of 45 single uredinial isolates of Phakopsora pachyrhizi were collected from rust-infected soybean and wild host plants (Pueraria lobata and G. soja ) at different localities in central and southwestern Japan. Eighteen pathogenic races were identified using a set of differential varieties composed of nine cultivars of soybean and two accession lines of G. soja. Nine and 11 races were found on soybean and wild host plants, respectively. Two races were common to soybean and wild host plants. Received 27 April 2001/ Accepted in revised form 22 August 2001     

Nickel potentiates soybean resistance against infection by Phakopsora pachyrhizi

Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, causes significant yield losses worldwide. Nickel (Ni) plays a key role in the metabolism of some profitable crops, such as soybeans, because it is a constituent of several biomolecules and is required for the catalytic process of several enzymes. This study investigated the effect of foliar Ni treatment on the potentiation of soybean cultivar TMG 135 resistance to P. pachyrhizi infection at the microscopic, biochemical, and molecular levels. The severity of ASR decreased by 35% in plants treated with Ni. The malondialdehyde concentration, an indicator of cellular oxidative damage, was high in the leaves of plants that were not treated with Ni and was linked to ASR severity and the extensive colonization of the palisade and spongy parenchyma cells by fungal hyphae. The lignin concentration, β-1,3-glucanase activity, and expression of the URE gene and the defence-related genes PAL1.1, PAL2.1, CHI1B1, and PR-1A were up-regulated in Ni-treated plants infected with P. pachyrhizi. The information provided by this study shows the great potential of Ni to increase the basal level of soybean resistance to ASR and to complement other control methods within the context of sustainable agriculture.     

Potentiation of soybean resistance against Phakopsora pachyrhizi infection using phosphite combined with free amino acids

Considering the importance of Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, in the decrease in soybean yield, this study investigated the potential of using phosphite combined with l -α-free amino acids (referred to as induced resistance [IR] stimulus hereafter) to boost defence responses of soybean plants against P. pachyrhizi infection. Plants were sprayed with water (control), acibenzolar-S-methyl (ASM) or IR stimulus and noninoculated or inoculated with P. pachyrhizi. Urediniospore germination was not affected by the IR stimulus in vitro. Reduced ASR severity, lower malondialdehyde concentration and less colonization of leaf tissues by P. pachyrhizi (lower TEF-1α expression from 1 to 15 days after inoculation [dai]) occurred for IR stimulus-sprayed plants. The pattern of gene expression for IR stimulus-sprayed and infected plants was strikingly similar but sometimes more remarkable than that in ASM-sprayed and infected plants. Higher production of phenolics and lignin along with stronger up-regulation of PAL1.3 (5 and 10 dai), PAL2.2 (3 dai), PAL3.1 (1, 3 and 5 dai), ICS1 (5 dai), CHIA1 (1, 5 and 10 dai), CHI1B1 (5 dai), PR-1A (5 and 10 dai), NR1-2 (5 and 10 dai) and INR-2 (5 and 10 dai) for IR stimulus-sprayed plants increased their resistance against ASR. In addition, IR stimulus-sprayed and infected plants showed less impairment of the photosynthetic apparatus and maintained high concentrations of chlorophyll a + b and carotenoids. These findings highlight the potential of using this IR stimulus for developing a well-tuned and effective defensive strategy in soybean plants against P. pachyrhizi infection.     

Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi

Soybean is a major source of oil and proteins worldwide. The demand for soybean has increased in Africa, driven by the growing feed industry for poultry, aquaculture and home consumption in the form of processed milk, baked beans and for blending with maize and wheat flour. Soybean, in addition to being a major source of cooking oil, is also used in other industrial processes such as in the production of paints and candle wax. The demand for soybean in Africa so far outweighs the supply, hence the deficit is mainly covered through imports of soybean products such as soybean meal. The area under soybean production has increased in response to the growing demand, a trend that is expected to continue in the coming years. As the production area increases, diseases and insect pests, declining soil fertility and other abiotic factors pose a major challenge. Soybean rust disease, caused by the fungus Phakopsora pachyrhizi, presents one of the major threats to soybean production in Africa due to its rapid spread as a result of the ease by which its spores are dispersed by the wind. Disease control by introducing resistant soybean varieties has been difficult due to the presence of different populations of the fungus that vary in pathogenicity, virulence and genetic composition. Improved understanding of the dynamics of rust ecology, epidemiology and population genetics will enhance the effectiveness of targeted interventions that, in turn, will safeguard soybean productivity.     

Performance of dual and triple fungicide premixes for managing soybean rust across years and regions in Brazil: A meta-analysis

Soybean rust in Brazil is currently controlled with several commercial fungicide premixes composed of demethylation inhibitors (EPOXiconazole, CYPRoconazole, PROThioconazole, TEBUconazole), quinone-outside inhibitors (AZOXystrobin, TriFLoXystrobin, PYRAclostrobin, PICOxystrobin), and succinate demethylation inhibitors (BENZovindiflupyr, BIXaFen, FLUXapyroxad). Here, we summarize the performance of eight premixes evaluated in 177 cooperative trials conducted in 46 locations across 10 states from 2015 to 2020. All fungicide treatments were sprayed three times starting at R1/R2. Percentage control (, %), from back-transforming meta-analytic estimates of the log of the ratio, ranged from 56.2% (PICO + CYPR) to 76.8% (BIXF + TFLX + PROT). Estimates of mean yield difference (, kg/ha) between fungicide-treated and untreated plots were greatest for BIXF + TFLX + PROT (1,080) followed by PICO + BENZ (1,010), PYRA + EPOX + FLUX (981.5), AZOX + BENZ (910), TFLX + PROT (891), PICO +TEBU (682), TFLX + CYPR (646), and PICO + CYPR (600). Significant declines in both and in as little as 4 years were detected for AZOX + BENZ (35.3%; 550 kg/ha) and PICO + BENZ (15.5%; 359.8 kg/ha). Variance in was reduced by the inclusion of baseline severity as covariate. In trials where baseline disease was ≥70%, yield was 250 kg/ha greater compared to areas with low baseline disease. Disease control and yield response were generally greater in the south-east, where the frequency of profitable scenarios was 30% higher on average than in the north-west. Results of this meta-analysis are critical for supporting decisions during planning of fungicide programmes.     

The origin and genetic diversity of the causal agent of Asian soybean rust,Phakopsora pachyrhizi,in South America

A sequence‐based approach was used to investigate molecular genetic variations in Phakopsora pachyrhizi, an obligate biotrophic pathogen that causes Asian soybean rust. In Argentina, the samples came from uredinium‐bearing leaves taken from 11 soybean fields; in Brazil, the samples comprised urediniospores from leaves of 10 soybean genotypes that had been grown in three experimental stations during two growing seasons. PCR‐based cloning techniques were used to generate DNA sequences for two gene regions and alignments were supplemented with data from GenBank. A total of 575 sequences for the internal transcribed spacer region (18 ribotypes) and 160 partial sequences for a housekeeping gene encoding ADP‐ribosylation factor (10 haplotypes) were obtained. Ribotype accumulation curves predicted that about 20 bacterial clones would recover 5–6 ribotypes (c. 70–80% of the total molecular variation) per locality. The samples from the three experimental stations in Brazil displayed most (14 out of 16) ribotypes found worldwide; the lack of genetic structure and differentiation at a diverse geographic scale suggests that both local and distant sources provide airborne inoculum during disease establishment. Soybean genotypes with resistance genes for the Asian soybean rust did not decrease the molecular genetic variation of fungal populations.     

Host suitability and response of different vegetable genotypes to Meloidogyne incognita race 2 and Meloidogyne javanica in South Africa

The host suitability of 20 locally available genotypes of Capsicum, 10 of Daucus carota, 7 of Beta vulgaris- and 3 of Spinacea oleracea were assessed in separate greenhouse studies for resistance to Meloidogyne incognita race 2 and M. javanica, respectively. Substantial variation existed amongst the vegetable genotypes in the greenhouse screenings with regard to their host status to the respective root-knot nematode species. None of the genotypes of D. carota, B. vulgaris and S. oleracea showed resistance to the nematode species tested. However, resistance to M. incognita race 2 was identified in Capsicum genotype “Tobasco”, which was subsequently verified in a follow-up microplot trial using a range of initial population densities together with a susceptible Capsicum genotype “Paprika”. Reproduction factors of the nematodes were used as the main criterion to evaluate resistance. In the microplot trial, genotype “Tobasco” showed resistance at the lower inoculum levels but not at the higher nematode population levels. The need exists for more frequent and extensive screenings of the various vegetable genotypes in order to provide small-scale farmers with better options for improved and sustainable yields.     

Profitability of fungicide applications for managing soybean rust in scenarios of variable efficacy and costs: A stochastic simulation

Soybean rust (SBR) in Brazil is controlled with fungicides, which have shown variable, sometimes declining, efficacy over time. A Monte Carlo simulation framework was implemented as a decision tool and to estimate the probability for a fungicide programme being profitable depending on efficacy and total cost defined by the user. Probability distributions were fitted to slopes and intercepts of the disease–yield relationship and severity in the untreated plots reported in the literature, as well as historical records of soybean price. Simulations of disease reduction conditioned to predefined control efficacy and total application costs were split into scenarios that combined two categories of severity (high and low) and two attainable yield classes (high and low). These categories were defined based on the median of severity (57.8%) and median of the intercept (yield when severity is zero, 2995.1 kg/ha). Probability matrices were constructed relating fungicide efficacy and costs. A higher frequency of break-even events occurred in scenarios of high disease pressure and higher yield. Yearly simulations, starting with 79.4% efficacy, assuming two rates of decline previously determined for tebuconazole (high decline rate), showed that the programme may remain profitable during the first 5 to 7 years of use, in contrast to cyproconazole (low decline rate), a fungicide that would be profitable during the entire decade. This approach was shown to be useful and can be adapted to other diseases of soybean and other crops, as long as damage functions are available. An interactive web app was developed to perform the simulations accessible at alvesks.shinyapps.io/rusty-profits/.     

黄淮海大豆新品种（系）的抗病性评价

大豆花叶病毒（SMV）、大豆孢囊线虫（SCN）和大豆根腐病（SRR）是危害中国乃至世界大豆生产的3种主要病害。为了评价黄淮海选育的大豆新品种（系）对这3种病害的抗性水平, 采用温网室接种鉴定及田间调查自然发病的方法, 对72份大豆新品种（系）进行了抗病性鉴定。结果表明, ‘中作J8012’、‘蒙01-38’、‘汾豆86’、‘中作X96328’、‘阜08-190’等9个品系对SMV流行株系SC3和SC7表现高抗或抗病, 占参试品种总数的12.5%; ‘周01015-1’、‘远育8号’和‘冀豆17’ 3个品系对SCN 1号生理小种表现中抗; 自然条件下, 抗SRR病情指数在15以下的大豆材料有31份, 占鉴定总数的43.06%; 对SMV和SRR的抗性水平均在中抗及以上的有‘阜08-325’、‘HD0113’、‘太丰6号’等8个品系, 占参试品种数的11. 11%, 而对3种病害的抗性水平均在中抗以上的材料仅有‘冀豆17’1份。本研究的结果可为大豆抗病育种选择亲本和培育多抗性的大豆新品种提供参考。     

Fungicide sensitivity and monocyclic parameters related to the Phakopsora pachyrhizi–soybean pathosystem from organic and conventional soybean production systems

The failure of chemical control of soybean rust has been related to the selection of less sensitive isolates, and the infection capacity of such isolates could have implications for the management of the disease. The aims of the present study were to compare the sensitivity to tebuconazole and azoxystrobin and the monocycle of soybean rust using isolates of Phakopsora pachyrhizi from two soybean fields with different production systems (organic and conventional) in 2012/13 and 2013/14 seasons, and to monitor mutations in the CYP51 gene. To assess the sensitivity to tebuconazole and azoxystrobin, detached leaf tests and in vitro germination, respectively, were used. To evaluate the monocycle, detached leaves were inoculated with a urediniospore suspension and evaluated daily by counting the number of uredia. The occurrence of the mutations in CYP51 was investigated by a pyrosequencing assay. In both 2012/13 and 2013/14 seasons, the EC₅₀ to tebuconazole was lower for the population from the organic system (0.41 and 0.10 μg mL^?1, respectively) compared to the conventional system (1.60 and 4.44 μg mL^?1, respectively), while the EC₅₀ to azoxystrobin was similar for both populations. The lower sensitivity to tebuconazole and azoxystrobin was associated with F120L + Y131H mutations in CYP51, and the F129L mutation in CYTB, respectively. The monomolecular model fitted to monocycle data and parameters related to the maximum asymptote and the AUDPC were superior for organic than the conventional system.     

菜用大豆品种资源对大豆花叶病毒病的抗性评价

对40个供试菜用大豆品种进行了抗2个SMV流行株系的鉴定。结果表明,有4个品种抗SC-3株系,分别是‘苏鲜4号’、‘浙鲜豆5号’、‘奎丰4号’和‘KVS124’;‘浙农8号’和‘苏鲜4号’抗SC-7株系,‘苏鲜4号’兼抗SC-3和SC-7株系。这些品种可作为抗源用于抗病品种选育和与抗性遗传相关的研究。此外,还鉴定筛选出‘通豆6号’、‘青酥2号’、‘青酥4号’、‘青酥5号’和‘青酥6号’等5个品种对SMV的主要流行株系SC-3表现耐病,这些品种可直接用于菜用大豆的生产。研究还显示,来自江苏地区的育成品种抗性相对较好,而来自上海崇明的地方大豆品种资源抗性普遍较差,这可能与该地区流行的SMV株系的类型相关。     

Variation in resistance to the root-knot nematode Meloidogyne incognita in tomato genotypes bearing the Mi gene

Root-knot nematodes ( Meloidogyne spp.) are among the main pathogens of tomato ( Lycopersicon esculentum ) worldwide. Plant resistance is currently the method of choice for controlling these pests and all the commercially available resistant cultivars carry the dominant Mi gene, which confers resistance to the three main species Meloidogyne arenaria , M. incognita and M. javanica . However the emergence of virulent biotypes able to overcome the tomato resistance gene may constitute a severe limitation to such a control strategy. To date, little was known of the possible influence of the homozygous vs heterozygous allelic state of the Mi locus, or the tomato genetic background, on the expression of the resistance. In order to test both these factors, the resistance was evaluated of a large panel of L. esculentum genotypes (selected from the Vilmorin germplasm stock collection) to seven M. incognita lines avirulent or virulent against the Mi gene. Plant resistance was estimated by counting the egg masses on the root systems after inoculation with second-stage juveniles (J₂). Reproduction of the nematodes was similar or, more often, significantly higher on heterozygous tomato genotypes than on homozygous ones, suggesting a possible dosage effect of the Mi gene. Data also indicated that the tomato genetic background had a major effect on the variations observed in nematode reproduction, especially when tomato genotypes were heterozygous for the Mi gene. These results have important consequences in terms of breeding strategies and durability of the resistance conferred by the Mi gene.     

Coinfection of soybean plants with Phytophthora sojae and soybean cyst nematode does not alter the efficacy of resistance genes

The soybean cyst nematode (SCN) Heterodera glycines and the oomycete Phytophthora sojae are among the most damaging pathogens of soybean worldwide. Resistant cultivars are commonly used to manage these diseases. As it is known that the presence of SCN can facilitate the development of other pathogens, it is important to verify if there is a synergistic activity between SCN and P. sojae. The purpose of this study was to evaluate a possible interaction on susceptible and resistant soybean lines. The plants were inoculated with one or both organisms at different stages (5 or 10 days old). Two levels of SCN inoculum (2,000 and 10,000 eggs/plant) and different timing between SCN and P. sojae inoculation (2, 5, or 8 days) were compared. The results on 5-day-old plants showed that SCN did not influence P. sojae development. The resistant cultivar to P. sojae remained effective (0% mortality) and susceptible cultivars exhibited high mortality (100%) in the presence or absence of SCN. Experiments on 10-day-old plants showed that SCN resistance was not affected by the presence of P. sojae. SCN inoculum density and timing of P. sojae infection did not affect the virulence of these pathogens and the efficacy of resistance genes. However, the number of SCN cysts was decreased by more than 50% (p < .001) when P. sojae was coinfesting the susceptible cultivar. This suggests that P. sojae might indirectly influence SCN development by reducing the root mass. This study confirmed that resistant cultivars remain a valid option for the management of P. sojae and SCN.