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.     

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     

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.     

Genetic diversity and population structure of Lasiodiplodia theobromae from different hosts in northeastern Brazil and Mexico

Lasiodiplodia theobromae is one of the most frequent fungal pathogens associated with dieback, gummosis, leaf spot, stem-end rot and fruit rot symptoms in cashew, mango, papaya and grapevine. In this study, the variation in the genetic diversity of 117 L. theobromae isolates from northeastern Brazil (n = 100) and Mexico (n = 17), which were collected from these four crops, was analysed using microsatellite markers. The results revealed low genetic diversity among L. theobromae populations and the existence of two genetic groups. All Mexican isolates were grouped with Brazilian isolates, suggesting a low level of differentiation between these populations. Furthermore, no evident host or climate-based population differentiation was observed for L. theobromae in Brazil. The populations studied were mostly clonal, but additional studies are needed to better understand the mode of reproduction of the pathogen. The low genetic diversity of L. theobromae populations in northeastern Brazil suggests that resistant cultivars could be used as a durable management strategy to reduce the impact of the diseases caused by this pathogen.     

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.     

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.     

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.     

Genetic diversity and population structure of Striga hermonthica populations from Kenya and Nigeria

Striga hermonthica is a parasitic weed that poses a serious threat to the production of economically important cereals in sub‐Saharan Africa. The existence of genetic diversity within and between S. hermonthica populations presents a challenge to the successful development and deployment of effective control technologies against this parasitic weed. Understanding the extent of diversity between S. hermonthica populations will facilitate the design and deployment of effective control technologies against the parasite. In the present study, S. hermonthica plants collected from different locations and host crops in Kenya and Nigeria were genotyped using single nucleotide polymorphisms. Statistically significant genetic differentiation (F_ST = 0.15, P = 0.001) was uncovered between populations collected from the two countries. Also, the populations collected in Nigeria formed three distinct subgroups. Unique loci undergoing selection were observed between the Kenyan and Nigerian populations and among the three subgroups found in Nigeria. Striga hermonthica populations parasitising rice in Kenya appeared to be genetically distinct from those parasitising maize and sorghum. The presence of distinct populations in East and West Africa and in different regions in Nigeria highlights the importance of developing and testing Striga control technologies in multiple locations, including locations representing the geographic regions in Nigeria where genetically distinct subpopulations of the parasite were found. Efforts should also be made to develop relevant control technologies for areas infested with ‘rice‐specific’ Striga spp. populations in Kenya.     

甘肃中部及周边地区小麦条锈菌种群的遗传结构分析

为明确甘肃中部与周边地区小麦条锈菌种群的遗传结构及关系,利用SSR分子标记技术对采自甘肃、陕南、青海及新疆等7个地区共369份小麦条锈病菌标样的群体遗传结构进行了分析。结果表明,小麦条锈菌群体Nei’s基因多样性指数为0.39、Shannon信息指数为0.57,各地区条锈菌群体遗传多样性较为丰富,且在不同地区之间存在明显差异,7个条锈菌群体中以天水种群的遗传多样性相对较高,其Nei’s基因多样性指数为0.42、Shannon信息指数为0.61。该地区小麦条锈菌群体间和群体内都存在着一定的遗传分化,群体间遗传变异占总变异的2.24%,群体内遗传变异占总变异的97.76%。表明甘肃中部及周边地区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;甘肃中部、陇南及陕南3地的小麦条锈菌种群遗传相似度较高,菌源交流密切。     

小麦抗条锈品种遗传多样性的SSR分析

［目的］ 利用SSR标记分析我国几大小麦产区主栽品种中抗锈品种的遗传多样性,为小麦抗条锈育种亲本材料的选择提供参考。［方法］ 以当前条锈菌优势小种接种成株期小麦,从几大小麦产区主栽品种中筛选出抗条锈品种。然后利用SSR标记对筛选出的抗锈品种的遗传多样性进行分析。［结果］ 27对SSR引物在上述抗锈品种中共检测到104个等位变异,平均为3.85个;引物的多态信息含量（PIC）在0.210~0.712之间,平均为0.455;抗锈品种间遗传相似系数平均为0.723,表明筛选出的抗锈品种遗传多样性较低,亲缘较近。［结论］ 聚类分析的结果将抗锈品种分为了4个类群,类群的分布与亲缘的远近和品种的地域有一定的相关性。     

Genetic diversity and population structure of Acidovorax avenae subsp. avenae isolated from sugarcane in Argentina

A significant increase in the occurrence of red stripe (caused by Acidovorax avenae subsp. avenae) has been observed in the last decade in Argentina. Considering that no extensive sampling of the main sugarcane-producing area in the country has been conducted to characterize the diversity and population structure of A. avenae subsp. avenae, molecular markers were employed to analyse 112 isolates from Tucumán. By using repetitive element polymorphism-based polymerase chain reaction (rep-PCR) almost all isolates were differentiated and grouped into 10 clusters, revealing a high genetic diversity. Using the amplified fragment length polymorphism (AFLP) technique, five pairs of isolates were discriminated that could not be distinguished with rep-PCR. Cluster analysis showed no clear association between isolate clustering, sugarcane host genotype, crop age, type of tissue sampled, fertilization, or year of sampling. Linkage equilibrium analysis by using rep-PCR data indicated that the population has some degree of clonality. Three housekeeping genes were also sequenced: ugpB and pilT sequences were highly similar to A. avenae subsp. avenae sequences from other Argentinian isolates, whereas the lepA sequence did not reveal significant similarity. An additional four housekeeping genes could not be amplified, suggesting the existence of differences in those regions. Subsequently, virulence of 14 A. avenae subsp. avenae isolates was evaluated under controlled conditions. Results showed a differential level of aggressiveness among the isolates on a resistant sugarcane variety. This study confirmed that rep-PCR is an adequate tool for genetic analysis and population structure characterization in bacteria, and revealed both high genetic diversity and clonal population structure of A. avenae subsp. avenae in Tucumán, Argentina.     

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near‐Himalayan region

Isolates of recently spreading races of yellow rust from wheat and triticale in Europe were analysed using virulence phenotypic data of 2605 isolates sampled in 12 countries between 2000 and 2014. A subset of 239 isolates was investigated by microsatellite markers. At least three races of non‐European origin, termed ‘Warrior’, ‘Kranich’ and ‘Triticale aggressive’, were identified in the post‐2011 population. The Warrior race was already present in high frequencies in the first year of detection in most European countries and to a large extent it replaced the pre‐2011 European population. In contrast, the two other exotic races were localized to certain regions and/or crop type. The presence already of at least six multilocus genotypes of the Warrior race and five genotypes of the Kranich race in the first year of detection and across large areas is consistent with a hypothesis of aerial spread from genetically diverse source populations. A comparison with reference isolates sampled from six continents suggested that the Warrior and Kranich races originated from sexually recombining populations in the centre of diversity of the yellow rust fungus in the near‐Himalayan region of Asia. However, the Triticale aggressive race was most similar to populations in the Middle East/Central Asia. The study illustrated the potential role of sexual Puccinia striiformis populations as a reservoir for new races replacing distant clonal populations.     

Low diversity and fast evolution in the population of Puccinia triticina causing durum wheat leaf rust in France from 1999 to 2009, as revealed by an adapted differential set

No internationally agreed differential set is available for characterization of virulences in populations of Puccinia triticina causing wheat leaf rust on durum wheat. In a first step, 73 potentially differential host genotypes were tested with 96 durum leaf rust isolates collected in France. A differential set, adapted to the local epidemiological context and useful for comparison with international studies was selected, including French commercial cultivars, Thatcher lines with Lr genes, and international cultivars. In the second step, a sample of 310 isolates collected in France from 1999 to 2009 was characterized on this set. Diversity was very low, as only five pathotypes were distinguished. Genotyping of a subset of 76 isolates according to 20 SSR markers confirmed this low diversity, with 73 isolates belonging to a single dominant genotype. Population was strongly shaped by cultivars, and the findings explain the successive breakdown of resistance sources deployed in French durum wheat cultivars. The gene Lr14a, suggested to be an efficient source of resistance in several European and American countries, was overcome by pathotypes frequent in France since 2000. Postulation of resistance genes in the commercial cultivars led to a proposed simplified version of the differential set. This study, providing new information about leaf rust resistance genes present in the French durum wheat germplasm, highlights the need to diversify sources of resistance to P. triticina in this germplasm. The results are also discussed in terms of relatedness and intercontinental migration of P. triticina on durum wheat.     

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.     

玉米抗南方锈病种质标记基因型鉴定与遗传多样性分析

为阐明玉米抗南方锈病种质的标记基因型和遗传背景,利用7个与玉米抗南方锈病3个基因连锁的SSR标记鉴定了38份抗病玉米种质的标记基因型,并采用40个多态性SSR标记对39份抗南方锈病的玉米自交系和6个标准测验种进行了遗传多样性研究。结果表明,7个与抗病基因连锁的SSR标记将38份抗病种质鉴定为17种标记基因型,表明可能存在多样的抗性基因组合方式;辽2204等9份种质仅扩增出齐319的标记基因型,沈136和W456仅扩增出W2D的标记基因型;种质LO932未扩增出与齐319、P25和W2D相同的标记,可能携带新的抗南方锈病基因;相近遗传背景的抗性种质分属不同的标记基因型,表明抗病种质可能携带的抗南方锈病基因在育种选择中发生了分离。40对多态性SSR引物在45份自交系中共检测出115个等位基因变异,平均每对引物检测到2.88个等位基因,变异范围为2~4;平均多态性信息含量为0.4649,变化范围为0.1258~0.6951;通过UPGMA聚类分析,39份抗病材料被划分到以标准测验种为代表的6个杂种优势亚群中,与系谱分析基本一致,这为在育种中合理利用抗源提供了信息。     

Pathotypes of Melampsora rust on Salix in short-rotation forestry plantations

Melampsora epitea , the causal agent of leaf rust on willow ( Salix spp.) in short-rotation forestry, was sampled over four consecutive years (1993–96) in Sweden. The pathotype patterns of 332 single-spore isolates were examined for virulence characteristics using a defined set of willow hosts. Thirty-seven pathotypes of M. epitea were identified and grouped into three formae speciales . No race or morph subdivision was observed among the isolates, other than the three formae speciales . For monitoring and studying the ecological and evolutionary dynamics of virulence for M. epitea , an internationally useful naming system for pathotypes is proposed, with a three-digit code referring to virulence on a specified set of standard test clones.     

Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = ?0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.     

Genetic structure of Fusarium oxysporum f. sp. cubense in different regions from Brazil

Panama disease, caused by Fusarium oxysporum f. sp. cubense (Foc), is ranked among the most destructive diseases of banana. The use of resistant varieties is the most desirable and effective control measure. Information on the pathogen population structure is essential, as durability of the resistance and effective cultivar deployment are strongly linked to this structure. In this study, 214 Foc isolates from different banana producing states in three regions of Brazil (northeastern, southeastern and southern) were analysed. Initially, nine microsatellite markers (SSR) were tested, which revealed 52 distinct haplotypes distributed in the different geographical regions and cultivars. While amova analysis showed that 68·01% of the total variation occurred within states, correlation between genetic and geographical distances was only found in the southern region. Results indicated that isolates from different states comprise a single population, which is predominantly clonal. When isolates representing different haplotypes were inoculated in four banana cultivars, differences in severity were found, with the high severity values being caused by isolates from haplotypes H7, H31 and H41. The diversity found here points to the need for additional studies, as this characteristic may be related to Foc's evolutionary potential and possibly to its ability to overcome the resistance from breeding programme‐generated cultivars. This is the most comprehensive study on population biology of Foc in Brazil.     

Genetic diversity and population structure analysis of isolates of the rice false smut pathogen Ustilaginoidea virens in India

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.