Molecular characterization of Fusarium oxysporum f. melongenae by ISSR and RAPD markers on eggplant

Identity, Pathogenicity, and Genetic Diversity of Lasiodiplodia Species Associated with Stem-End Rot of Avocado in China

Stem-end rot (SER) causes brown necrotic lesions in the pulp near the base of the fruit pedicel and is one of the most devastating postharvest diseases of avocados in all avocado-growing regions of the world. China's avocado industry is growing very rapidly, and the planting area is expanding, but little is known about the pathogens and genetic diversity of avocado SER. To determine the causal agents of SER, avocado fruits were sampled from the main avocado-producing areas in China during 2020 and 2021. Fungal isolates were obtained from SER symptomatic avocado fruits and identified by morphology combined with phylogenetic analysis of internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), and β-tubulin (TUB2) gene sequences. All 101 isolates belonged to Lasiodiplodia spp.; four Lasiodiplodia species were identified, namely, L. pseudotheobromae (59.41%), L. theobromae (24.75%), L. mahajangana (7.92%), and L. euphorbiaceicola (1.98%); and six others are classified as Lasiodiplodia sp. (5.94%). There were only slight morphological differences in colonies and conidia of these four species of Lasiodiplodia. The pathogenicity tests showed symptoms of SER, and 92.08% of the isolates exhibited a high level of virulence on avocado (disease index >70), related to the disease severity on avocado fruits. All tested isolates grew well under the temperature ranging from 23 to 33°C. There was a significant difference in mycelial growth between the four species of Lasiodiplodia after treatment with high or low temperatures. The growth of L. pseudotheobromae was the fastest at 13 to 18°C but was the lowest at 38°C (P < 0.05). The red pigment could be produced by all tested isolates after culturing for 7 days at 38°C. The mycelial growth rate was the fastest on PDA medium, and the slowest on the OMA medium but promoted spore formation (P < 0.05). In addition, the genetic diversity of pathogenic Lasiodiplodia species associated with SER collected from avocado, mango, guava, and soursop fruits was determined. A total of 74 isolates were clustered into four main ISSR groups by the unweighted pair-group method with arithmetic mean analysis, and the classification of this group was related to the host. Extensive diversity was detected in the Lasiodiplodia populations. The diverse geographical origins and host species significantly influenced the population differentiation, and most of the genetic variation occurred within populations (P < 0.001). This is the first study to identify the major pathogens of avocado SER in China, survey their occurrence and pathogenicity, and include a comparative analysis of genetic diversity with Lasiodiplodia spp. causing SER on other fruit hosts. Collectively, the Lasiodiplodia species complex affecting avocado showed high pathogenicity and diversity, while L. pseudotheobromae was the most frequently isolated species in China. The results of this study provide insights into the aspects of the epidemic of SER disease caused by Lasiodiplodia species, which will help in developing strategies for the management and control of SER in avocado.

Biochemical, pathological and molecular characterisation of Phomopsis vexans: A causative of leaf blight and fruit rot in brinjal

The pathogen Phomopsis vexans causes leaf blight, fruit rot, and damping off in brinjal plants, all of which are extremely detrimental. The pathogen affects host plant photosynthetic efficiency and fruit quantity and quality. An appreciation of the pathogenicity of P. vexans is essential for the effective control of infections in the field. Consequently, the goal of this study was to characterise P. vexans in terms of their biochemistry, molecular diversity, and pathogenicity. In terms of cellulase (97.7 U), catalase (12.2 U), and ascorbate peroxidase (147.3 U) activity, isolate PV1 performed best, followed by PV5 (CL-97.0 U, CAT-11.1 U and APX-144.4 U), and PV8 (CL-88.8 U, CAT-9.8 U and APX-141.9 U). In a greenhouse pathogenicity test, isolate PV1 had the highest incidence (97%) and severity (88.6%) of disease, whereas isolate PV6 showed the lowest incidence (57.2%) and severity (70%) of disease. The biochemical enzyme activity of P. vexans corresponds well with its greenhouse pathogenicity results, and its combination can be exploited to identify pathogenic P. vexans isolates. Using RAPD and ISSR primers, molecular characterisation indicated genetic diversity but could not distinguish isolates by geographical origin or pathogenicity. The pathogen P. vexans was verified by ITS1 and ITS4 molecular analysis, and the sequences were subsequently deposited in the NCBI database. In conclusion, the enzyme activity relevant to pathogenicity (CL, CAT and APX) in conjunction with the in-vivo pathogenicity assay might be utilised to differentiate between pathogenic (virulent) and non-pathogenic (avirulent) P. vexans isolates and develop suitable disease management strategies.

Fungus under a Changing Climate: Modeling the Current and Future Global Distribution of Fusarium oxysporum Using Geographical Information System Data

The impact of climate change on biodiversity has been the subject of numerous research in recent years. The multiple elements of climate change are expected to affect all levels of biodiversity, including microorganisms. The common worldwide fungus Fusarium oxysporum colonizes plant roots as well as soil and several other substrates. It causes predominant vascular wilt disease in different strategic crops such as banana, tomato, palm, and even cotton, thereby leading to severe losses. So, a robust maximum entropy algorithm was implemented in the well-known modeling program Maxent to forecast the current and future global distribution of F. oxysporum under two representative concentration pathways (RCPs 2.6 and 8.5) for 2050 and 2070. The Maxent model was calibrated using 1885 occurrence points. The resulting models were fit with AUC and TSS values equal to 0.9 (±0.001) and 0.7, respectively. Increasing temperatures due to global warming caused differences in habitat suitability between the current and future distributions of F. oxysporum, especially in Europe. The most effective parameter of this fungus distribution was the annual mean temperature (Bio 1); the two-dimensional niche analysis indicated that the fungus has a wide precipitation range because it can live in both dry and rainy habitats as well as a range of temperatures in which it can live to certain limits. The predicted shifts should act as an alarm sign for decision makers, particularly in countries that depend on such staple crops harmed by the fungus.

Phenotypic variability, race profiling and molecular diversity analysis of Indian populations of Fusarium oxysporum f. sp. lentis causing lentil wilt

Wilt (Fusarium oxysporum f. sp. lentis; Fol) is one of the major diseases of lentil worldwide. Two hundred and thirty-five isolates of the pathogen collected from 8 states of India showed substantial variations in morphological characters such as colony texture and pattern, pigmentation and growth rate. The isolates were grouped as slow (47 isolates), medium (118 isolates) and fast (70 isolates) growing. The macroconidia and microconidia (3.0-77.5 × 1.3-8.8 µm for macroconidia and 1.8-22.5 × 0.8-8.0 µm for microconidia for length × width) were variable in size and considering the morphological features, the populations were grouped into 12 categories. Seventy representative isolates based on their morphological variability and place of origin were selected for further study. A set of 10 differential genotypes was identified for virulence analysis and based on virulence patterns on these 10 genotypes, 70 Fol isolates were grouped into 7 races. Random amplified polymorphic DNA (RAPD), universal rice primers (URPs), inter simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) were used for genetic diversity analysis. URPs, ISSR and SRAP markers gave 100% polymorphism while RAPD gave 98.9% polymorphism. The isolates were grouped into seven clusters at genetic similarities ranging from 21 to 80% using unweighted paired group method with arithmetic average analysis. The major clusters include the populations from northern and central regions of India in distinct groups. All these three markers proved suitable for diversity analysis, but their combined use was better to resolve the area specific grouping of the isolates. The sequences of rDNA ITS and TEF-1α genes of the representative isolates were analysed. Phylogenetic analysis of ITS region grouped the isolates into two major clades representing various races. In TEF-1α analysis, the isolates were grouped into two major clades with 28 isolates into one clade and 4 remaining isolates in another clade. The molecular groups partially correspond to the lentil growing regions of the isolates and races of the pathogen.

Elucidating genetic diversity and population structure of Pyricularia oryzae isolates causing wheat blast in Bangladesh

Wheat blast, caused by Pyricularia oryzae pathotype Triticum, is one of the most notorious diseases of wheat. In this study, a total of twenty-four monoconidial isolates representing four major wheat blast affected districts, namely Chuadanga, Meherpur, Kustia and Jhenaidah of Bangladesh were analyzed. Eight RAPD and four ISSR primers being used for genetic diversity assay produced a total of 94 bands of which 85% were polymorphic. UPGMA dendrogram based on combined dataset (RAPD and ISSR) separated all the isolates into two main clusters having similarity ranged from 64 to 93%. Principal coordinate analysis showed congruent result with cluster analysis. However, clustering of the isolates according to their origin and plant part sampled was not apparent in the dendrogram. The genetic diversity indices unveiled that genetic diversity in P. oryzae populations is low. Average Nei's gene diversity (h) and Shannon's Information Index (I) calculated for isolates from each district were found 0.16 and 0.24, respectively. The population structure analysis of the isolates revealed the presence of two sub-populations with admixture of alleles. Analysis of molecular variance indicated that significantly higher level of variation (96%) in the population was present within districts while a relatively low proportion (4%) of the variation was detected among districts. Knowledge generated in this study will give a pace in the development of appropriate wheat blast management strategies to control this disease in Bangladesh.

Pathological, biochemical and molecular variability of Colletotrichum truncatum incitant of anthracnose disease in chilli (Capsicum annuum L.)

The present study aims to establish pathogenic variability among Colletotrichum truncatum, an incitant of anthracnose disease across different chilli growing regions of Karnataka. Thirty suspected C. truncatum isolates were identified based on their morphological and conidial characteristics and further confirmed by Internal Transcribed Spacer DNA sequence analysis. Pathogenicity test was carried out by in vitro detached leaf and fruit assay, and also under greenhouse conditions using 20 different chilli cultivars grown across Karnataka. Colletotrichum truncatum isolates recorded the varied degree of pathogenicity index (PI) on different chilli cultivars. Isolate UOM-02 was found highly virulent (PI > 80 against 12 tested cultivars) and cultivar cv. 4 was found highly resistant to C. truncatum infection (Average PI, 48.21). Further, the involvement of enzymes such as cellulase, pectin methylesterase and ascorbate peroxidase in determining the virulence of the pathogen was established. The highest activity of catalase (UOM-24; 7.38 units), ascorbate peroxidase (UOM-02; 2.9 units), cellulase (UOM-02; 0.58 units), and pectin methylesterase (UOM-02; 6.7 units), was recorded by different C. truncatum isolates. Cellulase and pectin methylesterase activities were positively correlated with their pathogenicity, while catalase activity was found least correlated. Results of RAPD and ISSR analysis recorded higher polymorphism among the isolates. Interestingly these isolates were not clustered based on their geographical origin, Pathogenicity index and biochemical characters. From this study, the existence of highly virulent C. truncatum isolate (UOM-02), which can cause severe loss under favourable conditions, was revealed. Further, possible use of specific enzymes as an indicator of virulence of the pathogen is discussed.

Epitypification of Fusarium oxysporum - clearing the taxonomic chaos

Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.

Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum (Fo). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. "Super Marmande," while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. "Rio Grande." Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on "SM" tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively.

Genetic diversity analyses of Lasiodiplodia theobromae on Morus alba and Agave sisalana based on RAPD and ISSR molecular markers

Genetic diversity of 23 Lasiodiplodia theobromae isolates on Morus alba and 6 isolates on Agave sisalana in Guangxi province, China, was studied by using random amplified polymorphic DNA and inter-simple sequence repeat molecular markers. Results of two molecular markers showed that the average percentage of polymorphic loci of all isolates was more than 93%. Both dendrograms of two molecular markers showed obvious relationship between groups and the geographical locations where those strains were collected, among which, the 23 isolates on M. alba were divided into 4 populations and the 6 isolates on A. sisalana were separated as a independent population. The average genetic identity and genetic distance of 5 populations were 0.7215, 0.3284 and 0.7915, 0.2347, respectively, which indicated that the genetic identity was high and the genetic distance was short in the 5 populations. Average value of the gene diversity index (H) and the Shannon's information index (I) of 29 isolates were significantly higher than 5 populations which showed that genetic diversity of those isolates was richer than the populations and the degree of genetic differentiation of the isolates was higher. The Gst and Nm of 29 isolates were 0.4411, 0.6335 and 0.4756, 0.5513, respectively, which showed that the genetic diversity was rich in those isolates.

Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici

The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin.

Evaluation of two methods for direct detection of Fusarium spp. in water

Fusarium is a waterborne fungus that causes severe infections especially in patients with prolonged neutropenia. Traditionally, the detection of Fusarium in water is done by culturing which is difficult and time consuming. A faster method is necessary to prevent exposure of susceptible patients to contaminated water. The objective of this study was to develop a molecular technique for direct detection of Fusarium in water. A direct DNA extraction method from water was developed and coupled to a genus-specific PCR, to detect 3 species of Fusarium (verticillioides, oxysporum and solani). The detection limits were 10 cells/L and 1 cell/L for the molecular and culture methods, respectively. To our knowledge, this is the first method developed to detect Fusarium directly from water.

Antifungal activity of Microgramma vacciniifolia rhizome lectin on genetically distinct Fusarium oxysporum f. sp. lycopersici races

Fusarium oxysporum f. sp. lycopersici races 1, 2, and 3 deteriorate tomato crops since they cause a vascular wilt. Lectins are carbohydrate-binding proteins with hemagglutinating and antifungal activities. This work reports that Microgramma vacciniifolia rhizome lectin (MvRL) inhibits F. oxysporum f. sp. lycopersici race 3 growth (61 %) more intensely than of races 1 (55 %) and 2 (45 %). The hemagglutinating activity of MvRL was inhibited by glycoprotein preparations from mycelia of races 1, 2, and 3, and these data indicate that lectin carbohydrate-binding sites recognized glycosylated molecules from races. Inter-simple sequence repeat (ISSR) marker system showed that race 3 is genetically distinct from races 1 and 2, and thus the highest sensitiveness of F. oxysporum f. sp. lycopersici race 3 to MvRL may be due to molecular characteristics of this race.

Production of interspecific hybrids between commercial cultivars of the eggplant (Solanum melongena L.) and its wild relative S. torvum

Interspecific hybrids between cultivars of eggplant (Solanum melongena L.) and its wild relative S. torvum, which has disease resistance and desirable traits for crop improvement, were obtained by cross-hybridization and embryo rescue. Twenty-one hybrid progenies were obtained and examined based on morphological traits, RAPD and ISSR markers. Five of them were confirmed to be true interspecific hybrids. Eighteen and 14 bands from 7 RAPD and 14 ISSR primers, respectively, were polymorphic and present in all five hybrid seedlings and their parents. The morphological characteristics of leaf margin, inflorescence type and spine positions of the five seedlings were intermediate to the parents. These interspecific hybrids had low pollen viability, probably due to abnormal meiosis.

A new strategy employed for identification of sweet orange cultivars with RAPD markers

We optimized RAPD techniques by increasing the length of RAPD primers and performing a strict screening of PCR annealing temperature to distinguish 60 sweet orange cultivars from the Research Institute of Pomology at the Chinese Academy of Agricultural Sciences. A new approach called cultivar identification diagram (CID) was used to improve the efficiency of RAPD markers for cultivar identification. Thirteen effective primers were first screened from 54 RAPD arbitrary 11-mer primers based on their amplification products and amplified polymorphic bands; they were then used for PCR amplification of all 60 cultivars. All cultivars were manually and completely separated by the polymorphic bands appearing in DNA fingerprints from 13 primers; a CID of the 60 sweet orange cultivars was then constructed. This CID separated all the cultivars from each other, based on the polymorphic bands; the corresponding primers were marked in the correct positions on the sweet orange CID. The CID strategy facilitates the identification of fruit cultivars with DNA markers. This CID of sweet orange cultivars will be very useful for the protection of cultivar rights and for early identification of seedlings in the nursery industry.

Development of a novel and efficient strategy for practical identification of Pyrus spp (Rosaceae) cultivars using RAPD fingerprints

Accurate and reliable cultivar identification of crop species is essential to guarantee plant material identity for purposes of registration, cultivar protection and production. To facilitate identification of plant cultivars, we developed a novel strategy for efficient recording of DNA molecular fingerprints in genotyped plant individuals. These fingerprints can be used as efficient referential information for quick plant identification. We made a random amplified polymorphic DNA (RAPD) marker analysis of 68 pear cultivars. All pear genotypes could be distinguished by a combination of eight 11-mer primers. The efficiency of the method was further verified by correct identification of four cultivars randomly chosen from the initial 68. The advantages of this identification include use of fewer primers and ease of cultivar separation by the corresponding primers marked on the cultivar identification diagram. The cultivar identification diagram can efficiently serve for pear cultivar identification by readily providing the information needed to separate cultivars. To the best of our knowledge, this is the most efficient strategy for identification of plant varieties using DNA markers; it could be employed for the development of the pear industry and for the utilization of DNA markers to identify other plant species.