Academic literature on the topic 'Fusarium crown rot'

Fusarium crown rot of winter wheat is an economically important disease in most regions where winter wheat is grown. Fusarium crown rot is caused by Fusarium culmorum and F. pseudograminearum. This diagnostic guide details information to aid in field, molecular, and morphological diagnosis of Fusarium crown rot.

Fusarium crown rot of wheat has become more prevalent in China. To investigate the phylogenetic structure of Fusarium causing wheat crown rot in China, wheat basal stems with symptoms of the disease were collected from 2009 to 2013 in Jiangsu, Anhui, Henan, Hebei, and Shandong provinces. In total, 175 Fusarium isolates were collected and their mycotoxin chemotypes and distribution were identified. Among the 175 isolates, 123 were Fusarium asiaticum; 95 of these were the chemotype 3-acetyl-deoxynivalenol (3-AcDON) and 28 were nivalenol (NIV). Thirty-seven isolates belonged to F. graminearum, which were all 15-AcDON. Smaller numbers of isolates consisted of F. acuminatum, F. pseudograminearum, and F. avenaceum. The virulence of F. asiaticum and F. graminearum isolates on wheat crowns and heads was comparable. The virulence of isolates of the DON and NIV chemotype were statistically similar, but DON tended to be more aggressive. The DON concentrations in grains from wheat heads inoculated with isolates causing either Fusarium head blight or crown rot were similar. In the five provinces, F. asiaticum of the 3-AcDON chemotype was the predominant pathogen causing crown rot, followed by F. graminearum. Recent changes in causal Fusarium species, chemotypes, and distribution in China are discussed.

In Australia, Fusarium pseudograminearum and F. culmorum are the two main fungi causing crown rot, while Bipolaris sorokiniana is the causal agent of common root rot. Fusarium graminearum is typically linked with Fusarium head blight; however, it has been associated with crown rot in Australia and other parts of the world. This study investigated the reactions of single cultivars of barley, bread wheat, durum wheat, oat, and triticale to inoculation with strains of F. pseudograminearum, F. culmorum, F. graminearum and B. sorokiniana in field trials across two seasons. Fusarium pseudograminearum and F. culmorum caused greater visual discolouration than F. graminearum and B. sorokiniana on both stems and sub crown internodes of all hosts. Fusarum pseudograminearum caused the greatest reduction in plant dry weight across hosts in both years. Durum wheat (cv. Hyperno) barley (cv. Grimmett), bread wheat (cv. Livingston) and triticale (cv. Endeavour) observed significantly high levels of visual discolouration on stems when inoculated with F. pseudograminearum, while oat (cv. Genie) exhibited the least visual discolouration. Despite variation in the visual discolouration, the DNA of all pathogens were detected in all cultivars. This research further highlights the complicated nature of the pathogen × strain × cultivar × environment interaction, which remains a challenge in breeding for genetic resistance. The specific infection of each fungus and the host responses in these field trials improves our understanding of disease development and its importance in cropping systems.

In Australia, crown rot of cereals is predominantly caused by Fusarium pseudograminearum and Fusarium culmorum, and common root rot by Bipolaris sorokiniana. Fusarium graminearum is an important pathogen causing Fusarium head blight worldwide and has also been reported to cause crown rot of wheat. The comparative ability of F. pseudograminearum, F. culmorum, F. graminearum and B. sorokiniana to cause crown rot and common root rot across a range of winter cereal species requires investigation. In glasshouse trials, we inoculated one cultivar each of barley, bread wheat, durum wheat, oat and triticale with two strains of each of the four pathogens. At 21 days after inoculation, the sub-crown internode and leaf sheaths of each plant were visually rated for brown discoloration. Shoot length and dry weight of inoculated plants were compared with those of non-inoculated controls. Barley and bread wheat had the highest disease severity ratings on leaf sheaths and sub-crown internode (64.7–99.6%), whereas oat had the lowest disease severity ratings across all pathogens (<5%). The shoot length of all cultivars was significantly reduced (by 12.2–55%, P < 0.05) when exposed to F. pseudograminearum. This study provides a comparison of pathogenicity of crown rot and common root rot pathogens and demonstrates significant variation in visual discoloration and host response across a range of winter cereals.

Alfalfa Medicago sativa L. (‘Fla. 77’) was inoculated with three different isolates of Fusarium and defoliated to varying levels with yellowstriped armyworms, Spodoptera ornithogalli (Guenée), to determine the effect of insect defoliation on the development of crown-rot under greenhouse conditions. There were no significant interactions between short-term insect defoliation and Fusarium crown-rot on forage quality, yield, or root carbohydrate reserves. Although insect defoliation alone did reduce plant height, yield, and maturity (18, 33, and 30% respectively) at the first harvest, no significant effects were observed at two subsequent harvests. Of the three isolates tested, Fusarium oxysporum Schlecht was the most virulent. Short-term defoliation did not increase the severity of Fusarium crown-rot in alfalfa.

The efficacy of benomyl, prochloraz, flusilazole and other fungicides in controlling crown rot, a postharvest disease of bananas, was studied. In experiments with harvested fruit, prochloraz and flusilazole were the most effective fungicides. Benomyl was less effective than prochloraz. In 1 experiment, Fusarium pallidoroseum and a Verticillium sp. were frequently isolated from diseased crowns of untreated fruit. Both fungi were pathogenic and sensitive to prochloraz in vitro, but only F. pallidoroseum was sensitive to benomyl. The Verticillium sp. was consistently isolated from diseased crowns of benomyl-treated fruit. The failure of benomyl to control crown rot adequately in Queensland may be related to the presence of benomyl-tolerant crown rot fungi in the flora of banana plantations. In 2 experiments, prochloraz gave good control of crown rot in fruit stored for extended periods before ripening; however, it failed to give adequate control in a third.

Fusarium root and crown rot of hosta plants grown in containers is caused primarily by Fusarium hostae. In an effort to develop an integrated strategy for managing this disease at nurseries, the effects of wounding, container mix content, watering schedule, and temperature on disease development were investigated. Plants were not wounded or were wounded by severing the roots, severing the roots and making incisions in the crown, or severing the roots and removing a small piece of the crown. Plants were inoculated by dipping roots and crowns into a suspension of conidia from one of two isolates of F. hostae. In addition, some plants were inoculated by wounding crowns with a scalpel dipped in a conidium suspension. Disease development was examined on plants grown at different temperatures (18, 25, or 32°C), grown in different container mixes (100% Canadian sphagnum peat, 100% aged and processed pine bark, or a mixture of 50% peat and 50% bark), and watered on different schedules (which kept the container mix wet, moist, or dry). Significant levels of disease occurred only on plants that were wounded when inoculated. Fusarium root and crown rot was more severe when both the roots and crowns were wounded than when only the roots were wounded. Disease symptoms developed when crowns of plants were wounded with a scalpel infested with conidia, suggesting that contaminated tools used for vegetative propagation may transfer F. hostae. Disease development also was affected significantly by container mix content, watering schedule, and temperature. In separate experiments, disease was most severe on plants grown in 100% aged pine bark, in dry container mix, or at 18 to 25°C. Disease development was significantly less when plants were grown in 100% peat, in wet container mix, or at 32°C. These results suggest that altering or manipulating cultural practices used to produce hostas in containers at nurseries can reduce the impact from Fusarium root and crown rot.

In southeastern Australia, Fusarium crown rot, caused by Fusarium culmorum or F. pseudograminearum, is an increasingly important disease of cereals. Because in-crop control options are limited, it is important for growers to know prior to planting which fields are at risk of yield loss from crown rot. Understanding the relationships between crown rot inoculum and yield loss would assist in assessing the risk of yield loss from crown rot in fields prior to planting. Thirty-five data sets from crown rot management experiments conducted in the states of South Australia and Victoria during the years 2005 to 2010 were examined. Relationships between Fusarium spp. DNA concentrations (inoculum) in soil samples taken prior to planting and disease development and grain yield were evaluated in seasons with contrasting seasonal rainfall. F. culmorum and F. pseudograminearum DNA concentrations in soil prior to planting were found to be positively related to crown rot expression (stem browning and whiteheads) and negatively related to grain yield of durum wheat, bread wheat, and barley. Losses from crown rot were greatest when rainfall during September and October (crop maturation) was below the long-term average. Losses from crown rot were greater in durum wheat than bread wheat and least in barley. Yield losses from F. pseudograminearum were similar to yield losses from F. culmorum. Yield loss patterns were consistent across experiments and between states; therefore, it is reasonable to expect that similar relationships will occur over broad geographic areas. This suggests that quantitative polymerase chain reaction technology and soil sampling could be powerful tools for assessing crown rot inoculum concentrations prior to planting and predicting the risk of yield loss from crown rot wherever this disease is an issue.

Fusarium crown rot becomes most severe when wheat is stressed for water near the time of anthesis. This research examined the potential to study crown rot in the gradient of resource competition near a tree windbreak. Winter wheat was planted for 2 years into a field infested by Fusarium pseudograminearum and bordered by 17-m-high Austrian pines. Crown rot, plant growth and yield, and soil water content were evaluated at six distances (5 to 46 m) perpendicular to the tree line in strip plots inoculated or not inoculated with the pathogen. Crown rot was minor (<5% whiteheads) in noninoculated strips and greater in inoculated strips (26 to 35%) in a 21-m zone from 9 to 30 m from the tree line (0.5–1.8 times the tree height; 0.5–1.8H). At 46 m (2.7H), crown rot was similar in noninoculated and inoculated strips (2 to 5% whiteheads). Whiteheads and culm browning were roughly the reverse of soil water depletion by tree roots. Grain yield at 23 m compared with 46 m was reduced by 33 to 35% in noninoculated plots and by 43 to 49% in inoculated plots. It is possible to study associations between water stress and Fusarium crown rot in the zone of resource competition near windbreaks.

Fusarium root and crown rot in alfalfa subjected to an autumn harvest was studied in plots established in the spring of 1996 or 1997, at three sites in Quebec. Autumn harvest treatments were started the year following establishment at each site. They were made at either 400, 500 or 600 growing degree-days (GDD; 5°C) after the last summer harvest. Samples were assessed for fusarium root and crown rot severity in autumn 1998 and spring 1999. Disease severity over all sites, cultivars, and sampling periods was ranked in the following order: 400 GDD > 500 GDD > 600 GDD > control (no fall harvest). Key words: Fusarium, root and crown rot, alfalfa, harvest management

This thesis had three objectives: i) Determining distribution of FCR and common root rot (CRR) of wheat in Montana; ii) Determining population dynamics between F. pseudograminearum and Bipolaris sorokiniana at different wheat development stages, and iii) Development of an integrated disease management program for Fusarium crown rot (FCR) using biological and fungicide seed treatments, cultivar resistance, and induced systemic resistance (SAR). Surveys of 91 fields over two years using qPCR identified FCR in 57% and CRR in 93% of the fields surveyed. Bipolaris sorokiniana, F. culmorum and F. pseudograminearum were isolated from 15, 13 and 8% of tillers respectively. FCR distribution was highly clustered while CRR was uniformly distributed with soil type, elevation and growing degree days influencing distribution. Data from intensively sampled fields estimated yield losses caused by FCR and CRR at 3.2 to 34.9% with losses influenced by pathogen population. This study is the first time qPCR was used to survey the distribution of FCR and CRR and to study the interaction of the respective pathogens. The effect of F. pseudograminearum and B. sorokiniana inoculum applied singly or in combination at three rates showed high and low rates of F. pseudograminearum inoculum reduced Bipolaris populations, while B. sorokiniana inoculations did not affect Fusarium populations in stems. Populations of both pathogens increased from heading until harvest with Fusarium colonizing stems earlier than Bipolaris. Mixed inoculations increased incidence of infection and co-infection relative to that observed in production fields. Both fungi alone or combined reduced the seedling counts. Grain yield was inversely correlated with Fusarium populations. Difenoconazole-mefenoxam seed treatment reduced FCR severity between 29.3-50% and fungal and bacterial seed treatments were ineffective. The cv. Volt was identified as partially resistant and had the highest levels of chitinase and beta-1, 3-glucanase activity of cultivars evaluated. Induction of SAR by Bacillus mycoides isolate BmJ or acibenzolar Smethyl significantly reduced the severity of FCR compared to water controls. Integration of cultivar resistance plus fungicide seed treatment or SAR induction provided equal control in greenhouse and irrigated trials. In a dryland field trial, integration of all management tools reduced FCR more than individual tools.

La fusariosi della spiga e il marciume al colletto in frumento sono malattie causate da Fusarium graminearum, F. culmorum e F. pseudograminearum. Essi determinano ingenti perdite di raccolto oltre a contaminare il prodotto con micotossine appartenenti alla famiglia dei tricoteceni. I batteri Gram-positivi appartenenti al genere Streptomyces sono ubiquitari nel suolo ed endofiti dei tessuti interni delle radici. Essi producono una vasta gamma di metaboliti secondari con proprietà antimicrobiche e possono essere utilizzati come agenti promotori della crescita delle piante, limitando lo sviluppo dei patogeni. L’obiettivo del presente dottorato di ricerca è stato quello di selezionare ceppi di streptomiceti attivi contro Fusarium spp. in grano. La prima fase dello studio ha permesso di conoscere lo stato dell’arte sull’utilizzo di streptomiceti contro specie micotossigene appartenenti al genere Fusarium (Chapter 1). Successivamente sono state sviluppate strategie innovative per la selezione degli stessi (Chapter 2) e l’efficacia dei ceppi più promettenti è stata poi saggiata in diverse condizioni (Chapter 3). Inoltre, i metaboliti secondari responsabili dell’attività antifungina sono stati caratterizzati (Chapter 4). L’influenza della variabilità dei ceppi di Fusarium spp. e dei substrati colturali sull’attività di biocontrollo è stata valutata tramite saggi di antibiosi. Questi fattori hanno avuto un’influenza significativa nel determinare il livello di attività in vitro. I mezzi standard utilizzati in laboratorio hanno diminuito infatti tale parametro. Inoltre è stata riscontrata un’assenza di correlazione con il livello di biocontrollo ottenuto in pianta. Unica eccezione è per i risultati ottenuti utilizzando un terreno a base di frumento, che ha permesso di osservare un valore di correlazione più elevato con il livello di biocontrollo riscontrato contro marciume radicale in frumento (r = 0.5). Successivamente, al fine di saggiare metaboliti limitanti la produzione di tricoteceni, è stato sviluppato un sistema in micropiastra che misura la fluorescenza emessa da un ceppo di F. graminearum trasformato con il costrutto TRI5::GFP. TRI5 è il primo gene essenziale coinvolto nella via metabolica di produzione di tricoteceni. Da questa prova si è potuto selezionare il ceppo di streptomicete DEF39 che riduce significativamente la produzione di DON. Le potenziali attività di promozione della crescita e di biocontrollo di una selezione dei ceppi più promettenti (N = 21) sono state saggiate in pianta. Gli streptomiceti testati non hanno esibito la capacità di aumentare i parametri di sviluppo dei germinelli di frumento, ma il ceppo DEF09 ha ridotto significativamente il marciume al colletto e la fusariosi della spiga ottenendo livelli di protezioni sopra al 40% e del 60% rispettivamente. Basandosi sui risultati ottenuti, quattro ceppi (DEF09, DEF20, DEF39, DEF48) sono stati applicati su grano sterilizzato testando due tempistiche di trattamento per osservarne la capacità di riduzione della biomassa fungina e della produzione di DON. Inoltre tramite qPCR si è osservata la fitness degli agenti di biocontrollo nelle condizioni testate. Gli streptomiceti, abili colonizzatori del substrato testato, sono stati efficaci nel ridurre la produzione di micotossine, limitando -quando co-inoculati con il patogeno- lo sviluppo dello stesso. I ceppi selezionati agiscono perciò sia contro lo sviluppo fugino e/o contro la produzione di DON. Ulteriori studi saranno necessari per confermarne l’attività in pianta, così come per permettere lo sviluppo di formulati efficaci per limitare la contaminazione da tricoteceni.
Fusarium head blight (FHB), root rot (FRR) and foot rot (FFR) cause important yield losses in wheat. The harvested product is often contaminated with mycotoxins, belonging to the group of trichothecenes. The main causal agents are Fusarium graminearum, F. culmorum and F. pseudograminearum. The biocontrol approach is a feasible option in order to reduce disease severity, as well as trichothecene contamination in grains. Streptomyces spp. are Gram-positive bacteria, ubiquitous in soil and endophytes of inner tissues of plant roots. They produce a wide range of secondary metabolites able to limit pathogen development and disease severity in planta, as well as to enhance plant growth. This PhD project aimed to select Streptomyces strains active within the wheat-Fusarium spp. pathosystem. To achieve this, a detailed literature and patents analysis focused on biocontrol of toxigenic Fusarium spp. was carried out (Chapter 1) and new methodological approaches for antagonist screening have been developed (Chapter 2). Furthermore, the biocontrol efficacy of a selected subset of strains obtained from the culture collection maintained at the Plant Pathology laboratory (DeFENS, University of Milan, Italy) was evaluated in different conditions (Chapter 3) and bioactive metabolites were isolated (Chapter 4). The influence of growth media and Fusarium strain diversity on streptomycete antifungal activity was assessed in dual culture assays. All the factors influenced the level of antifungal activity. The media commonly used for in vitro screening reduced the inhibitory activity of streptomycetes. Overall, results from dual culture assays and level of disease protection observed in planta did not correlate, except for those recorded on a medium based on wheat grains. Indeed, it was the most effective in eliciting antifungal activity and showed the highest correlation (r = 0.5) with FRR inhibition. Subsequently, being TRI5 the first and essential gene involved in trichothecene biosynthetic pathway in Fusarium spp., a microplate bioassay using a TRI5::GFP transformed F. graminearum strain was developed and validated in order to screen the effect of natural products on GFP fluorescence and consequently on trichothecene production. Surprisingly, culture filtrate from DEF39 strain completely suppressed deoxynivalenol (DON) production without affecting fungal growth. The most promising isolates (N = 21) were further characterized for their potential plant growth promotion ability, as well as for their activity against FRR and FFR in wheat seedlings. None of them was able to increase plant growth. However, DEF09 strain exhibited consistent efficacy to limit FRR-FFR symptom severity (protection level > 40%) in soil and soilless conditions. Therefore, a field trial was performed to test its ability to reduce FHB severity, obtaining up to 60% protection. Based on the activity observed from the previous screenings, four promising streptomycetes (DEF09, DEF20, DEF39, DEF48) were applied on sterilized wheat grains (microsilage) at two timepoints of application, in order to evaluate their ability to suppress fungal growth and DON production. Moreover, the fitness of streptomycetes in microsilage conditions was assessed by qPCR analysis. Streptomycetes were able to efficiently colonize the substrate, which resulted in reducing fungal biomass and DON accumulation only when co-inoculated with the pathogen. A pool of promising biocontrol agents has been selected against fungal development and/or DON production. This research highlighted the complexity of finding an efficient screening procedure due to multiple interactions occurring in wheat-Fusarium spp. pathosystem. Further studies will be needed to confirm the activity of the strains in planta. The identification of the mechanisms of action and the molecules involved in the bioactivity of the strains will possibly allow to develop effective treatments limiting trichothecene accumulation in wheat.

Crown rot is one of the most important postharvest diseases with a great negative impact on banana fruit quality. Bananas are harvested green and many packaging processes are carried out before coming on the market. The infections occur at harvest, but the symptoms appear after overseas transportation. Different pathogens are involved in crown rot, varying according to farming area. Little is known about its etiology and causal agents in organic farming. Dominican Republic is one of the leading exporters of organic bananas, and therefore, in this PhD thesis, five organic farms and their corresponding packing stations located in Valverde were investigated. To the best of our knowledge this is the first study covering Dominican Republic and it focused in particular on: the disease etiology, conditions, infection time and mechanisms that determine its development. Over a period of three years, 558 banana hands were collected and a total of 5000 fungal colonies were obtained from the crown tissues and 1750 representative colonies were purified. The identification of mycoflora associated with crown tissues was carried out with the final aim to search for disease management strategies compatible with organic production. Fungi were found in all the analyzed samples collected from various processing stages: from field to packing houses, and obtained in high rate starting from field from flowers as well as crown parts. The diffusion of the pathogen inoculum occurs principally during the banana processing, especially during the dehanding and in washing tanks. The final crown trimming followed by washing and quality of water used in the application of protective products were the critical points of crown infections. Five hundred and eighteen representative colonies were characterized and identified using morphological and molecular methods. The fungal community was dominated by Fusarium, the most frequent genus (55%) found in more than 80% of all analyzed samples. It was represented by nine species; F. incarnatum 53%, F. verticillioides 12%, F. sacchari 12%, F. proliferatum 7%, and F. solani 6%. Strains belonging to eight less frequent genera were represented by Colletotrichum musae 7% and found in 13% of all samples; Lasiodiplodia theobromae 4% and L. pseudotheobromae 1%, both found in 7% of all samples; Nigrospora sp. 11%, Alternaria spp. 6%, Phoma spp. 2%, Pestalotiopsis sp. 2%, Curvularia spp. 1% and Microdochium sp. 1%. Considering the main genera, the results based on morphological and molecular aspects showed a high variability among strains. By conducting the experimental inoculation trials, C. musae strains resulted from the most virulent among different species, followed by F. sacchari, L. theobromae, L. pseudotheobromae and F. verticillioides. The remaining strains had low pathogenicity, and their role could be ancillary in the crown rot development, or could be considered saprophytic. Summarizing the isolation frequency and pathogenicity tests, F. incarnatum strains played the main role in crown rot disease of organic bananas in the investigated areas.

[Abstract]Crown rot, caused by Fusarium pseudograminearum (Fpg), is an important soilborne disease of wheat and barley. The degree of crop damage depends on seasonal conditions. Typically, high moisture conditions early in the season encourage seedling infection from stubble residues. Moisture stress later in the season leads to the production of unfilled “whiteheads”. Current control relies on cultural practices and sowing of partially resistant varieties. In order to understand the nature of partial resistance, I have examined the patterns of disease symptom development and pathogen spread in susceptible and partially resistant tissues of both pot-grown wheat, barley and oat seedlings and field-grown inoculated wheat trials. Further research was conducted to determine whether differences in pathogenicity occur amongst a small subset of Australian Fpg isolates. Seedling experiments confirmed that differences in disease ratings between susceptible and partially resistant genotypes are detected in younger leaf sheaths of older seedlings. At later harvest times differences between these genotypes are not significant in older leaf sheaths. Re-isolation of Fpg from inoculated seedlings has shown that each tissue was infected later in partially resistant genotypes compared to susceptible ones with a significantly lower number of isolations recorded at each harvest time in 42 day old seedlings. Barley cultivars were rapidly infected by the pathogen and exhibited high levels of disease symptoms. By comparison levels of infection in oats were low compared to all other genotypes. No significant differences between genotypes were observed in coleoptile tissues, either in fungal colonisation or development of disease symptoms. Disease development in the subcrown internode varied between lines/cultivars but was not representative of the relative susceptibility of each genotype. The pathogen did not appear to invade plant tissue via the vascular system but rather spread directly across the stem from leaf sheath to leaf sheath. Field trials were designed to study disease symptom development and localisation of Fpg hyphae in all expanded tissues (excluding head and roots) in wheat genotypes of known susceptibility to crown rot. Plants were harvested at approximately fortnightly intervals throughout the growing season. The main effects and interactions of harvest, genotype and tiller on each plant part were examined with a detailed statistical analysis of differences seen in these factors between susceptible and partially resistant wheat genotypes, in two inoculated field trials. While differences between genotypes were mostly not significant at each harvest when disease rating or isolations from leaf sheath tissues were examined, important differences between susceptible and resistant genotypes were seen in disease developments and Fpg infections of stem tissue in field trials. Restriction of pathogen growth and symptom development was more pronounced in the tissues of 2-49 (possesses seedling resistance) than in the field resistant Sunco. At present, the mechanisms that lead to these resistance responses are unknown. The pathogenicity study aimed to determine whether 7 Fpg isolates and a mixed inoculum differed in ability to cause crown rot in 9 wheat genotypes ranging in susceptibility to this disease. Although a genotype*inoculum interaction was significant, there is no evidence of stable pathogenic races in the isolates examined in these experiments. The growth of all isolates was partially inhibited in a consistent manner on resistant genotypes when compared to very susceptible genotypes. These results confirm significant differences in the aggressiveness of Fpg isolates on wheat, evidenced by variation in mean disease severity between isolates growing on a range of host genotypes.

Fusarium crown rot (FCR) is a severe and chronic disease of barley and wheat. The disease is predominantly found in many parts of the semiarid regions worldwide. Growing resistant cultivars is an effective way to manage crown rot. Several quantitative trait loci (QTL) conferring FCR resistance have been detected in barley. As each of these loci conferring only partial resistance, this project was to investigate the effect of gene pyramiding on overall resistance. For this purpose, we developed and assessed two barley doubled haploid populations segregating for three large-effect QTL located on the long arms of chromosomes 1H, 3H and 4H, respectively. Significant effects were detected for each of the three QTL in both populations. Lines with any combination of two resistant alleles gave, on average, significantly better resistance than those with a single resistant allele only, and lines with resistant alleles from all three QTL gave the least FCR symptom. However, wide variations in FCR severity were detected for lines belonging to each of the groups with different numbers of resistant alleles. Significant effects of plant height on FCR were detected in both populations, and a significant association between heading date and FCR severity was also detected in one of the populations. We also found that the effects of a given resistant allele decreased with the increase in the number of resistant alleles. Overall, results from this study demonstrated that gene pyramiding can be an effective approach in improving FCR resistance and those lines with all three resistant alleles could be valuable for breeding programs. Most of the works on FCR resistance stopped after mapping the QTL. However, QTL mapping provides only limited resolution for a targeted locus due to the heterogeneity in genetic backgrounds in mapping populations. Thus molecular markers obtained from such studies can often be reliably used to tag a targeted QTL. One of the approaches to obtain populations with uniform genetic backgrounds is to develop and exploit a series of near isogenic lines (NILs). As part of our long term objectives to develop diagnostic markers and investigate functions of FCR resistance genes in cereals, we have developed 10 pairs of NILs for a major QTL conferring FCR resistance in barley. The locus locates on the long arm of chromosome 4H and the presence of the resistance allele reduced FCR severity by between 32.8 and 63.4% with an average of 43.9% across these NILs. Histological and quantitative PCR analyses confirmed that the rates of Fusarium infection and disease development were much lower in the resistant isolines compared with those in the susceptible isolines. The results from this study would facilitate efforts in cloning and functional analyses of genes conferring resistance to FCR. Also the availability of these NILs offers an excellent genetic resource for transcriptional analysis. RNA sequencing (RNA-seq) has become a powerful tool for transcriptome analysis which is not only highly sensitive and efficient for identifying differentially expressed genes (DEGs) but can also be used for detecting single nucleotide polymorphisms (SNPs) in transcribed genes that co-locate with a target locus when combined with genomic and genetic analysis. We used three sets of NILs (197 Gb sequences) to examine transcriptional changes associated with FCR resistance locus located on the long arm of chromosome 4H. Owing to the lack of annotated genes in barley genome currently, we also used the expressed reads from our RNAseq data to find out the unannotated genes. When considered both annotated and unannotated genes, a total of 2,359 genes were expressed to a significantly higher level, of which 103 were expressed in NIL1, 28 were in NIL2 and 2,228 were in NIL3. Also a total of 4,074 down-regulated annotated and unannotated DEGs were identified, of which 947 were expressed in 'S‘ isolines of NIL1, 120 were in NIL2 and 3,007 in NIL3. It has been hypothesized in this experiment that the use of multiple sets of NILs would allow the identification of better defined sets of candidate genes underlying the targeted locus. When compared among the three NILs, only two DEGs commonly expressed among all NILs, whereas for down-regulated genes, 40 were commonly expressed. Also a total of 10,141 induced genes (7,650 up- and 2,491 down-regulated) were detected between the two isolines of NIL1 following Fp-infection and mock treatments. Of the 76 commonly expressed genes containing SNPs (SNP-EGs) across the NILs, 73 were mapped to the long arm of chromosome 4H where the targeted QTL resides. Functional annotation of the transcripts indicated that several of these identified DEGs and SNP-EGs were involved in host-pathogen interactions. These results showed that the multi-NIL approach is a powerful tool in transcriptomic analysis and the DEGs and SNPs identified here will improve the accuracy of fine mapping to develop markers for breeding programs.

Submitted in partial fulfillment for the Degree of Master of Technology: Biotechnology, M. L. Sultan Technikon, 2002.
Fusarium species produce toxic mycotoxins that are known to exert adverse health effects in humans and animals. No attempts have been made to establish mycotoxin-producing capabilities of isolates of Fusarium species from bananas exhibiting symptoms of crown rot. Crown rot is one of the most serious post harvest problems in banana and the disease is caused by different fungal species, principally Fusarium species. Banana, which is of great economic significance in growing countries (i.e. Costa Rica, Cameroon, Ecuador) is seriously affected by crown rot and is a major cause of fruit loss
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The biological control of crown and root rot in tomato was studied in a sterile system in which tomato seedlings were grown on water agar in petri plates or on filter wicks in test tubes containing fertilizer solution. The biological control agent, nitBl, was a nonpathogenic strain of Fusarium oxysporum which had been mutated to a nitrate non-utilizing form in order to distinguish it from the pathogen, Fusarium oxysporum f. sp.radicis-lycopersici (FORL). Four different approaches were used to deduce possible mechanisms of control. One approach was to study the effect of inoculum timing and inoculum density on biological control. Biological control was demonstrated when nit B1 was inoculated to the roots as much as 21 days before FORL, and persisted for at least 23 days after the FORL inoculation. When nit B1 was inoculated to seedling roots at least 3 days before FORL, there was good disease control even when the initial inoculum density of nit B1 was 60 times lower than that of FORL. As the lag between inoculations decreased, higher densities of nit B1 were needed to bring about control, and when the two fungi were inoculated simultaneously the inoculum density of nit B1 had to be at least 10 times that of FORL for there to be any reduction of disease symptoms. The second approach was to observe the colonization of seedling roots by the two strains. Both nit B1 and FORL colonized the outer layers of the root. However, when nit B1 was inoculated to the root 4 days before FORL, the rate of increase of nit B1 was greater than the rate of increase of FORL. The third approach was to test possible elicitors of a defence reaction in tomato for their biological control ability. Sterile filtrates from cultures of nit B1 grown in nutrient broth, sterile exudates from nit B1-infested germinating seeds and seedling roots, heat-killed nit B1 spores, and the cell wall fraction from nit B1 all failed to protect seedlings against crown and root rot induced by FORL. The fourth approach was to test nutrient competition by adding an excess of nutrients that might otherwise be limiting. Biological control by nit B1 was not affected when excess glucose or iron were added to the growth medium. In a related experiment, FORL caused severe disease symptoms (in the absence of nit B1) even when iron availability was artificially decreased by adding a strong iron chelator to the growth medium. The conclusion from all these experiments was that nit B1may elicit a defense response in tomato roots, possibly dependent on the prior colonization of the roots by this strain, which makes the roots resistant to subsequent infection by FORL.

Wilt and crown rot are two important diseases of tomato caused by different strains ("formae speciales") of the fungus, Fusarium oxysporum. While both pathogens are members of the same fungal species, each differs genetically and resistance to the diseases is controlled by different genes in the plant. Additionally, the formae speciales differ in their ecology (e.g. optimal temperature of disease development) and epidemiology. Nevertheless, the distinction between these diseases based on symptoms alone may be unclear due to overlapping symptomatology. We have found in our research that the ambiguity of the pathogens is further confounded because strains causing tomato wilt or crown rot each may belong to several genetically and phylogenetically distinct lineages of F. oxysporum. Furthermore, individual lineages of the pathogen causing wilt or crown rot may themselves be very closely related. The diseases share the characteristic that the pathogen's inoculum may be aerially dispersed. This work has revealed a complex evolutionary relationship among lineages of the pathogens that makes development of molecular diagnostic methods more difficult than originally anticipated. However, the degree of diversity found in these soil-borne pathogens has allowed study of their population genetics and patterns of dispersal in agricultural settings.