Molecular characterization of Macrophomina phaseolina and Fusarium species by a single primer RAPD technique

Charcoal root rot and wilt, are two economically important diseases of many crop plants in North and South America, Asia and Africa and some parts of Europe. Genetic variation in 43 isolates of Macrophomina phaseolina and 22 isolates of Fusarium species, collected from geographically distinct regions over a range of hosts, was studied using random amplified polymorphic DNA (RAPD) markers. Initially, 210 arbitrary nucleotide (10-mer) primers were tested for amplification of genomic DNA of one M. phaseolina isolate, 70 primers amplified the genomic DNA of M. phaseolina. One primer OPA-13 (5'-CAGCACCCAC-3') produced fingerprint profiles, which clearly distinguished between the different isolates of M. phaseolina. UPGMA analysis classified these isolates into five major groups. By primer OPA-13, 22 isolates of pathogenic and non-pathogenic Fusarium species of different formae-speciales and races, were also distinguished from M. phaseolina. This marker is useful for distinguishing between these two important plant pathogens irrespective of hosts, virulence spectrum and races. This is the first report of reliable diagnosis of two soilborne pathogens (root/collar rot and wilt causing pathogens) at the level of isolates, formae-speciales and races by a single primer RAPD procedure with uniform PCR conditions.     

Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean and sorghum

Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina , a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58% among isolates in the tallgrass prairie, 71% in the maize fields, 75% in the sorghum fields and 80% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate 'hybrids' with novel genetic profiles and pathogenic capabilities.     

Biocontrol potential and polyphasic characterization of novel native <Emphasis Type="Italic">Trichoderma</Emphasis> strains against <Emphasis Type="Italic">Macrophomina phaseolina</Emphasis> isolated from sorghum and common bean

Native strains of Trichoderma isolated from sorghum and common bean crop soils were investigated to assess their biocontrol potential over the phytopathogenic fungus Macrophomina phaseolina, isolated from diseased plants. The Trichoderma strains were characterized with a polyphasic approach, which combined the analysis of their morphological characteristics, enzymatic activity, macro- and microculture test results, rDNA restriction patterns (AFLP), ITS1-5.8S-ITS2 rDNA sequences, and protein profiles. The integration of these data sets can be used to select new isolates as biological control agents against native fungal phytopathogens. In general, we observed a positive correlation between the secretion of beta-1,3-glucanase and N-acetylhexosaminidase, and the biocontrol capacities of all the Trichoderma isolates. Strains with the best hyperparasitic behavior against M. phaseolina isolated from diseased bean and sorghum were Trichoderma sp. (TCBG-2) and Trichoderma koningiopsis (TCBG-8), respectively.     

Effect of moisture stress, plant population density and pathogen inoculation on charcoal stalk rot of sorghum

The effects of moisture deficit stress, plant population density and pathogen inoculation technique on charcoal stalk rot in the sorghum hybrid CSH 6 were studied in the 1980–81 and 1981–82 post-rainy seasons at three locations in India. Incidence and severity of charcoal rot caused by Macrophomina phaseolina were compared in three plant population densities, subjected to different moisture stress regimes created by withholding irrigation at various plant growth stages. Natural infections were compared to artificial inoculation with M. phaseolina. Combinations of moisture stress, plant population and inoculation treatments were compared to identify the combination most likely to develop maximum disease. Lodging, the first external symptom of charcoal rot, was significantly correlated with other disease symptoms used to measure charcoal rot, such as soft stalk, number of nodes crossed by M. phaseolina infection, root damage and plant senescence. In both seasons the highest incidence of lodging occurred when moisture stress was induced at the 'flag leaf visible in the whorl' growth stage. The greatest incidence of the disease was recorded in the highest plant population (266 700 plant ha^-) at all three locations. No significant differences were found between artificially and naturally inoculated treatments. The maximum number of lodged plants was found at a density of 266 700 plants ha^-1 when moisture stress was induced at the 'flag leaf visible in the whorl' growth stage.     

Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, into specific groups using URP-PCR

Forty isolates of Macrophomina phaseolina, a pathogen causing charcoal dry root rot of soybean, cotton, and chickpea, were genetically characterized with universal rice primers (URP; primers derived from DNA repeat sequences in the rice genome) using polymerase chain reaction (URP-PCR). Out of 12 URPs used in this study, 5 primers were effective in producing polymorphic fingerprint patterns from the DNA of M. phaseolina isolates. Three primers (URP-2F, URP-6R, and URP-30F) were quite informative and produced high levels of polymorphism among the isolates of M. phaseolina. Analysis of the entire fingerprint profiles using unweighted pair-group method with arithmetic averages (UPGMA) clearly differentiated M. phaseolina isolates obtained from soybean, cotton, and chickpea hosts into specific groups. In this study, we found for the first time transferability and use of PCR primers derived from plant genomes to generate host-specific fingerprint profiles of M. phaseolina, a broad host range plant pathogenic fungus. These results demonstrate that URPs are sensitive and technically simple to use for assaying genetic variability in M. phaseolina populations.     

Stalk Rot of Maize: Host-pathogen Interaction

Four maize cultivars were each separately inoculated with 10 different isolates of Diplodia zeae, Fusarium moniliforme, F. graminearum and Macrophomina phaseolina. D. zeae consistently caused most stalk rot, followed in decreasing order by M. phaseolina, F. graminearum and F. moniliforme. Significant intraspecific differences in stalk rot were recorded. No significant stalk rot x cultivar interaction occurred. Stalk rot correlated non-significantly with yield loss but significantly with cellulase production in vitro.     

Molecular diversity of Fusarium oxysporum causing rot diseases of vanilla in south India

Incidence of root, stem and beans rot of vanilla (Vanilla planifolia Andrews) caused by Fusarium oxysporum Schlecht was surveyed in vanilla growing areas of south India during December 2008. The incidence of the disease varied from 1 to 100% in different locations. A total of 60 isolates of F. oxysporum were obtained from diseased samples, and nine morphologically different isolates were taken for molecular characterization using Randomly Amplified Polymorphic DNA (RAPD) markers to study the genetic variability if any, among them. PCR amplification of total genomic DNA with random oligonucleotide primers generated unique banding patterns depending upon primers and isolates. Nine oligonucleotide primers were selected for the RAPD assays, which resulted in 384 bands for nine isolates of F. oxysporum. The number of bands obtained was entered into a NTSYS and the results showed that the variability among the pathogen isolates was moderate. The nine isolates studied were grouped into single major cluster at 0.66 similarity index. Hence, it is inferred that F. oxysporum infecting vanilla in south India consists of a single clonal lineage with a moderate level of genetic diversification.     

Legume Hosts of Macrophomina phaseolina in Kenya and Effect of Crop Species on Soil Inoculum Levels

Studies were conducted in eastern Kenya to determine the common legume crop and weed hosts of Macrophomina phaseolina (Tassi) Goid., the inciter of charcoal rot disease. The effect of maize, sorghum, bean, and cowpea on the soil inoculum level was also investigated after field inoculation. All the legume crops and weeds tested were found to be infected by the pathogen after artificial inoculation. Common bean, soybean, cowpea were the most susceptible while pigeonpea, green gram, and hyacinth bean were moderately susceptible. Groundnut, chickpea. Cassia spp. and Crotalaria spp. were least susceptible after artificial inoculation, Monocropping of sorghum, maize, cowpea and common bean for three consecutive crop seasons increased M. Phaseolina soil inoculum in ascending order.     

Screening of sorghum genotypes and biochemical changes for resistance to damage caused by Macrophomina phaseolina

Charcoal rot, caused by Macrophomina phaseolina, is the most common yield reducing constraint in sorghum. In the present study, eight cultivars of Sorghum bicolor were screened against M. phaseolina to determine its effects on several growth parameters as well as the content of phenols, salicylic acid (SA), total protein and peroxidase activity and were examined for their relationship, with disease resistance. Out of the eight cultivars tested, PJ-1430 was the most resistant and SU-1080, the most susceptible. The roots of plants were more affected by the pathogen than the shoots. The cultivar PJ-1430 produced a higher plant root and shoot dry mass and was associated with higher polyphenols, SA, peroxidases and thus sustained less oxidative damage whereas SU-1080 experienced maximum oxidative damage, so was considered susceptible to charcoal rot. A positive relationship was observed among various biochemical parameters and disease resistance of cultivars PJ-1430 and SU-1080.     

Detection,identification and morphological characteristic of Macrophomina phaseolina: the charcoal rot disease pathogens isolated from infected plants in Northern Jordan

This is the first report about charcoal rot disease in Jordan. Twenty-five Macrophomina phaseolina isolates were collected from infected plants showing typical symptoms of charcoal rot disease. All of the 25 M. phaseolina isolates were pathogenic to cucumber plants under green house effect. The amplification of the isolated DNA from the 25 pathogenic fungal cultures using ITS specific primers (ITS 1?+?ITS 4) showed a single band of 580?bp. There was a significant variation of their mycelial linear growth rate on PDA medium. The 25 M. phaseolina isolates showed a wide heterogeneity in their mycelium colour, microsclerotia distribution, pycnidia formation and chlorate phenotypes. Based on the morphological characterisation, the 25 isolates were grouped into seven different groups as indicated in a dendrogram of their morphological variation. The overall means similarity matrix of the 25 M. phaseolina recovered isolates were 0.58. The means of similarity matrix of the 25 M. phaseolina was in between 0.83 and 0.14. The similarity coefficient between the 25 isolates varies between 0.27 and 1.0.     

Genetic relatedness of Brazilian Colletotrichum truncatum isolates assessed by vegetative compatibility groups and RAPD analysis

The genetic variation among nine soybean-originating isolates of Colletotrichum truncatum from different Brazilian states was studied. Nitrate non-utilizing (nit) mutants were obtained with potassium chlorate and used to characterize vegetative compatibility reactions, heterokaryosis and RAPD profile. Based on pairings of nit mutants from the different isolates, five vegetative complementation groups (VCG) were identified, and barriers to the formation of heterokaryons were observed among isolates derived from the same geographic area. No complementation was observed among any of the nit mutants recovered from the isolate A, which was designed heterokaryon-self-incompatible. Based on RAPD analysis, a polymorphism was detected among the wild isolate C and their nit1 and NitM mutants. RAPD amplification, with five different primers, also showed polymorphic profiles among Brazilian C. truncatum isolates. Dendrogram analysis resulted in a similarity degree ranging between 0.331 and 0.882 among isolates and identified three RAPD groups. Despite the lack of a correlation between the RAPD analysis and the vegetative compatibility grouping, results demonstrated the potential of VCG analysis to differentiate C. truncatum isolates genotypically similar when compared by RAPD.     

Genetic and morphological comparisons ofGlomerella (Colletotrichum) isolates from maize and from sorghum

Various morphological and genetic characteristics were compared among six isolates ofColletotrichum from maize and six from sorghum. For the first time, a teleomorph was induced in sorghum isolates by pairing them on autoclaved sorghum leaves in a humidity chamber. The sorghum teleomorph was morphologically similar toGlomerella graminicola andGlomerella tucumanensis, the teleomorphs ofColletotrichum isolates from maize and from sugarcane, respectively. Mating tests demonstrated thatGlomerella isolates from maize and sorghum were not interfertile. Several small but consistent differences in the morphologies of the isolates from maize and from sorghum were observed which agreed with earlier reports. DNA fingerprints detected as restriction fragment length polymorphisms of mitochondrial DNA and random polymorphic DNA (RAPD) produced from nuclear DNA by the polymerase chain reaction could be used to reliably and unambiguously distinguish members of the two groups of isolates. Results of a statistical analysis of similarity of the RAPD fingerprints suggested that maize and sorghum isolates ofColletotrichum are only about 45% similar (±10%) and represent two distinct and separate genetic lineages. We conclude that isolates ofColletotrichum from maize and sorghum are sibling species since they are morphologically very similar but reproductively completely isolated.     

Microsatellites from the charcoal rot fungus (Macrophomina phaseolina)

Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were polymorphic and the number of alleles per locus ranged from 6 to 22. These microsatellites will be useful in population and pathogenicity studies to correspond with development of potential disease-resistant soybean and other susceptible crops.     

Biological and molecular variability of Sarocladium oryzae, the sheath rot pathogen of rice (Oryza sativa L.)

Sheath rot disease of rice caused by Sarocladium oryzae (Sawada) (=Acrocylindrium oryzae, Sawada) has become an important production constraint in all rice-growing countries. Pathogenicity, phytotoxic metabolites, and random amplified polymorphic DNA (RAPD) markers were used to assess the level of genetic variability of S. oryzae derived from rice cultivars, CR1018, IR36, and IR50, of different locations in North East and South India. Variability in pathogenicity, phytotoxic metabolite production, and DNA polymorphisms was detected among S. oryzae isolates. Results indicated that S. oryzae isolates produced both cerulenin and helvolic acid at concentrations 0.3–0.62 and 0.9–4.8 μg mL⁻¹ of culture filtrate, respectively. Isolates that produce higher concentration of helvolic acid induced a high percent incidence of sheath rot disease. Oligonucleotide primers, GF and MR, generated either a simple (up to 2 bands) or complex (up to 6 bands) RAPD pattern. According to their level of similarity, S. oryzae isolates from North East and South India were grouped separately into two major clusters and 13 genotypes. Molecular- and pathogenicity-based classifications were not correlated, but a high level of genetic variability within S. oryzae isolates was identified. The molecular variability of S. oryzae isolates will be an important consideration in breeding programs to develop durable resistance for sheath rot disease.     

Molecular characterisation of Fusarium oxysporum causing rot diseases in small cardamom (Elettaria cardamomum Maton)

Incidence of root rot and foliar yellowing, rhizome rot, panicle wilt and stem rot diseases of small cardamom (Elettaria cardamomum Maton) are caused by Fusarium oxysporum Schlecht., and were surveyed in the high ranges of Idukki district, Kerala during 2010–2011. The diseases were noticed in different areas to varying degrees. Root rot was found to be most severe, followed by pseudostem rot, rhizome rot and panicle wilt. The Fusarium infections were prevalent throughout the year (January–December) and varied from 1.5 to 10.6%. Even though the pathogen was isolated from different plant parts, during pathogenicity studies, all the isolates could cross-infect other plant parts too. Twenty different isolates of F. oxysporum were obtained from diseased samples, and five morphologically distinct isolates were analysed with Randomly Amplified Polymorphic DNA (RAPD) markers to study the genetic variability, if any, among them. PCR amplification of total genomic DNA with random oligonucleotide primers generated unique banding patterns, depending upon primers and isolates. Nine oligunucleotide primers were selected for the RAPD assays, which resulted in 221 bands for the five isolates of F. oxysporum. The number of bands obtained was entered into an NTSYS, and the results showed moderate genetic variability among F. oxysporum isolates causing root rot, rhizome rot, panicle wilt and pseudostem rot, collected from different locations. The dendrogram of different isolates into groups resulted in one major cluster at 0.61 similarity index comprising of four isolates (CRT 3, CRR 3, CPW 2 and CSR 1) and one isolate (CRT 5) formed in a separate cluster. Among the five isolates of F. oxysporum, CRT 5 was entirely different from the other four isolates. The isolates also differ according to the geographical area, as revealed from the genetic variability observed in different root rot isolates (CRT 3 and CRT 5). It is inferred that despite moderate variability, F. oxysporum, infecting small cardamom in Idukki district of Kerala, consists of a single clonal lineage.     

Determination of genetic diversity among Indian isolates of Rhizoctonia bataticola causing dry root rot of chickpea

Genetic diversity among 27 isolates (23 from chickpea and 4 from other host crops) of Rhizoctonia bataticola representing 11 different states of India was determined by random amplified polymorphic DNA (RAPD), internal transcribed spacer restriction fragment length polymorphism (ITS-RFLP) and ITS sequencing. The isolates showed variability in virulence test. Unweighted paired group method with arithmetic average cluster analysis was used to group the isolates into distinct clusters. The clusters generated by RAPD grouped all the isolates into six categories at 40% genetic similarity. High level of diversity was observed among the isolates of different as well as same state. Some of the RAPD (OPN 4, OPN 12, and OPN 20) markers clearly distinguished majority of the isolates into the area specific groups. The ITS I, 5.8rDNA and ITS II regions of 11 isolates representing different RAPD groups were amplified with primers ITS 1 and ITS 4 and digested with seven restriction enzymes. The restriction enzymes DraI, MboI, RsaI, and AluI were found to be suitable for differentiating the isolates into five categories by showing isolate specific ITS-RFLP patterns. The isolates were variable in their nucleotide sequences of the ITS regions. This is the first study on genetic diversity among chickpea isolates of R. bataticola.     

高粱丝黑穗病菌种内分化的RAPD分析*

应用随机引物对来自不同地理来源、不同寄主和经寄主致病力测定的高粱丝黑穗病菌2、3号生理小种的10个菌株的DNA进行分析,所产生的RAPD结果表明,丝黑穗病菌S.reilianum具有丰富的种内遗传多样性,存在明显的分化现象。经聚类分析可将供试菌株大致分成两组,辽宁清原H2和黑龙江绥化H9菌株为一组。辽宁沈阳(H3)、阜新(H1)、营口(H10),山西榆次(H4),吉林四平(H5),黑龙江哈尔滨(H6),河北张家口(H8)等高粱丝黑穗病菌株以及辽宁沈阳的玉米丝黑穗病菌株(H7)为另一组,并且同一组内的DNA多态性亦有差异。高粱丝黑穗病菌2号生理小种和3号小种间在分子水平上存在差异明显。     

高粱丝黑穗病菌种内分化的RAPD分析

应用随机引物对来自不同地理来源、不同寄主和经寄主致病力测定的高粱丝黑穗病菌2、3号生理小种的10个菌株的DNA进行分析,所产生的RAPD结果表明,丝黑穗病菌S.reilianum具有丰富的种内遗传多样性,存在明显的分化现象。经聚类分析可将供试菌株大致分成两组,辽宁清原H2和黑龙江绥化H9菌株为一组。辽宁沈阳(H3)、阜新(H1)、营口(H10),山西榆次(H4),吉林四平(H5),黑龙江哈尔滨(H6),河北张家口(H8)等高粱丝黑穗病菌株以及辽宁沈阳的玉米丝黑穗病菌株(H7)为另一组,并且同一组内的DNA多态性亦有差异。高粱丝黑穗病菌2号生理小种和3号小种间在分子水平上存在差异明显。     

Genetics of nonsenescence and charcoal rot resistance in sorghum

Summary Nonsenescence is a delayed leaf and plant death resistance mechanism in sorghum that circumvents the detrimental effects of reduced soil moisture combined with high temperatures during post-anthesis growth. This drought-tolerance mechanism is often equated with charcoal rot resistance, a widespread root and stalk disease of great destructive potential. Therefore, the inheritance of charcoal rot resistance was investigated directly, by exposure of sorghum to Macrophomina phaseolina, the causal organism, and indirectly, by determination of the inheritance of nonsenescence. Sorghum families derived from diallel crosses between two nonsenescent, resistant inbreds (B35, SC599-11E) and two senescent, susceptible inbreds (BTx378, BTx623) were evaluated in 1989 at College Station and at Lubbock, Texas, under controlled and field conditions. We determined that nonsenescence was regulated by dominant and recessive epistatic interactions between two nonsenescence-inducing loci and a third locus with modifying effects. The same conclusion was reached for charcoal rot resistance. The presence of different genetic mechanisms within SC599-11E for nonsenescence and charcoal rot resistance verifies that these two forms of resistance are not different manifestations of a single trait, i.e., they are not to be equated with each other. We conclude that nonsenescence alone cannot account for, and should not be used as the sole breeding criterion for, resistance to charcoal rot in sorghum.     

Genetic diversity of <Emphasis Type="Italic">Macrophomina phaseolina</Emphasis> isolates from certain agro-climatic regions of India by using RAPD markers

Genetic diversity analysis of Macrophomina phaseolina isolates obtained from different host range and diverse geographical locations in India was carried out using RAPD fingerprinting. Of the thirteen 10-mer random primers used, primer OPB-08 gave the maximum polymorphism and the UPGMA clustering could separate 50 isolates in to ten groups at more than 65% similarity level. The ten clusters correlated well with the geographical locations with exceptions for isolates obtained from Eastern and Western Ghats. There was a segregation of isolates from these two geographical locations in to two clusters thus, distributing 10 genotypes in to eight geographical locations. All the isolates M. phaseolina irrespective of their host and geographical origin, exhibited two representative monomorphic bands at 250 bp and 1 kb, presence of these bands suggests that isolates might have evolved from a common ancestor but due to geographical isolation fallowed by natural selection and genetic drift might have segregated in to subpopulations. Genetic similarity in the pathogenic population reflects the dispersal of single lineage in all locations in India.