Fusarium head blight (FHB) is a devastating wheat (Triticum aestivum L.) disease worldwide. Presently, there is insufficient FHB resistance in the Canadian wheat germplasm. Genome-wide association study (GWAS) and genomic selection (GS) can be utilized to identify sources of resistance that could benefit wheat breeding. To define the genetic architecture of FHB resistance, association panels from a spring and a winter collection were evaluated using the Wheat Illumina Infinium 90K array. A total of 206 accessions from the spring panel and 73 from the winter panel were evaluated in field trials for 3-4 years at two locations, namely Morden (Manitoba) and Ottawa (Ontario). These accessions were phenotyped for FHB incidence (INC), severity (SEV), visual rating index (VRI), and deoxynivalenol (DON) content. Significant (p < 0.05) differences among genotypes for all traits were found. Genetic characterization using the wheat 90K array identified a set of 20,501 single nucleotide polymorphisms (SNPs). The probe sequences (~100 bp) of these SNPs were mapped to the Chinese Spring reference genome v2.0 to identify 13,760 SNPs in the spring panel, and 10,421 SNPs in the winter panel covering all 21 wheat chromosomes. GWAS was performed to identify novel FHB resistance loci for INC, SEV, VRI and DON content for the spring and the combined panels separately using these 13,760 SNPs and for the winter panel using 10,421 SNPs. A total of 107, 157, 174 unique quantitative trait loci (QTNs) were identified for the four traits using two single-locus and seven multi-locus GWAS models for the spring, winter, and combined panels, respectively. These QTNs represent a valuable genetic resource for the improvement of FHB resistance in commercially grown wheat cultivars. In addition, these GWAS-defined QTNs were further used for GS to determine the breeding value (BV) of individuals as outlined below. In order to understand the role of the model and that of the marker type and density in trait prediction modelling, a GS study was conducted. GS is considered as an important tool for increasing genetic gain for economically important traits such as FHB resistance. GS uses genome-wide molecular markers to develop statistical models that predict genomic estimated breeding values (GEBVs) of an individual. Our results support genomic prediction (GP) as an alternative to phenotypic selection to predict the BVs of individuals for this trait. GS accounts for minor effect QTNs, which is beneficial when breeding for quantitative traits. Moderate to high GP accuracies can be achieved for FHB resistance-related traits when implemented in a breeding program. The correlation between the estimate of the missing phenotypic value and the observed phenotype is known as predictive ability (r). Overall, the predictive ability increased significantly using a QTN-based GP approach for FHB traits in wheat and its wild relatives. DON content had the highest predictive ability among all FHB traits, and that was in the winter panel, highlighting the importance of objectively measured traits in breeding for disease resistant genotypes. Interestingly, the winter panel contained several wild relative species that may harbor genes of interest to prevent the accumulation of mycotoxins in the grain. This study showed the usability of genomic prediction by improving the predictive ability of the FHB traits, which can be applied in early generation selection to accelerate the improvement of FHB resistance in wheat. The results show that GS can be successfully implemented in wheat breeding programs over multiple breeding cycles and can be effective for economically important traits. It is anticipated that GS will play a substantial role in the future of wheat breeding.

No description available.

The future resilience of Pinus radiata D. Don (Monterey pine) is dependent upon the development of a silviculture program inclusive of either preventative or management techniques for the potentially fatal pitch canker disease (Fusarium circinatum Nirenberg and O’Donnell [=F.subglutinans (Wollenw. & Reinking) Nelson et al. f. sp. Pini). As an ecologically and commercially valued species, a myriad of factors threaten the genetic resources of the geographically limited natural range. This study evaluated the effectiveness of uneven-aged forest management for regeneration success in the native, pitch canker infected Año Nuevo stand at Swanton Pacific Ranch in Davenport, California. Seedling survival and growth averages were used to evaluate the impact of the variables of gap size (0.20-hectare, 0.10-hectare, and 0.05-hectare), site-preparation treatment (pile and burn, lop and scatter), and parent tree (13 local seed sources). Pitch canker symptoms were quantified to conclude if there is indeed a range of expressed resistance according to parent tree. Statistical models (i.e. ‘mixed effect’) yielded moderately significant differences in odds of survival between site treatments, with pile and burn plots producing higher survival rates (p=0.066). No significant difference in survival was detected between gap-sizes (p=0.936 and 0.803, 0.05- and 0.10-hectare gaps respectively to 0.20-hectare reference). Significant variation was expressed (estimate=0.1219, SE=0.057) between the 13 parent trees, implicating usefulness in predicting seedling survival. ‘Mixed effect’ models only detected a significant effect from gap-size on growth measures: 0.20-hectare gaps yielded height and diameter measures significantly larger than 0.05-hectare gaps (p=0.027 and 0.0081 respectively). Contingency tables detected significant association between gap-size and number of pitch canker branch symptoms. The range of infection rates produced by the 13 parent trees did not prove significant by analysis. Pile and burn site preparation treatment increases the probability of survival for artificially regenerated seedlings and 0.20-hectare gaps yield significantly higher growth averages over 0.05-hectare gaps.

La fusariose des épis, causée majoritairement par le champignon pathogène Fusarium graminearum (Fg), est une des principales maladies du blé tendre (Triticum aestivum). Pendant son cycle infectieux, l’agent pathogène produit des mycotoxines appartenant principalement aux trichothécènes de type B, tel que le déoxynivalénol (DON), qui sont toxiques pour l’homme et l’animal. Plusieurs loci à caractère quantitatif (QTLs) impliqués dans la résistance à la fusariose des épis ont été identifiés. Certains ont été corrélés avec une détoxication de la mycotoxine, principalement par conjugaison du DON en DON-3-O-glucose (D3G), une réaction enzymatique catalysée par des UDP-glucosyltransferases (UGT). Néanmoins, peu d’études ont conduit des analyses fonctionnelles dans des plantes hôtes de la maladie afin de relier directement la glucosylation de la mycotoxine avec la résistance à la maladie in planta, et aucune d’entre elles n'a été effectuée sur des gènes de détoxication du blé tendre. Notre équipe, à l'aide de la céréale modèle Brachypodium distachyon, a démontré que l'UGT Bradi5g03300 est capable de conférer une tolérance au DON par glucosylation en DON 3-O-glucose et qu’elle est impliquée dans l'établissement précoce d'une résistance quantitative à la fusariose des épis. Le présent travail avait pour objectif de transférer les analyses fonctionnelles menées sur la céréale modèle Brachypodium distachyon au blé tendre. Dans une première approche, le gène Bradi5g03300 a été introduit dans la variété de blé Apogée, sensible à la fusariose. Les analyses phénotypiques effectuées sur les lignées de blé transgéniques exprimant constitutivement le gène Bradi5g03300, montrent une résistance plus élevée à la maladie ainsi qu'une tolérance à la mycotoxine par rapport à la lignée contrôle. Parallèlement, en utilisant une approche de synténie entre les génomes de B. distachyon et du blé tendre, nous avons identifié un gène de blé, orthologue au gène Bradi5g03300.La transformation de l’écotype de B. distachyon sensible à la fusariosepar ce gène candidat a été effectuée pour déterminer rapidement sa capacité à conjuguer le DON in planta et son implication dans la résistance à la fusariose. En conclusion, ce projet contribue à accroître les connaissances concernant la relation fonctionnelle entre la glucosylation DON et la résistance à la fusariose dans le blé tendre et à fournir des gènes candidats à inclure dans les processus de sélection. / Fusarium head blight (FHB) caused by fungi of the Fusarium genus is a widespread disease of wheat (Triticum aestivum) and other small-grain cereal crops. The main causal agent of FHB, Fusarium graminearum, can produce mycotoxins mainly belonging to type B trichothecenes, such as deoxynivalenol (DON) that can negatively affect humans, animals and plants. Several quantitative trait loci (QTLs) for resistance to FHB have been identified some of which have been correlated with efficient DON detoxification, mainly through the conjugation of DON into DON-3-O-glucose (D3G), a reaction catalyzedby UDP-glucosyltransferases (UGTs). Nevertheless, only few studies have conducted functional analyses to directly correlate DON glucosylation and resistance in planta and none were performed on wheat UGT gene(s). Our team, using the model cereal species Brachypodium distachyon, has recently demonstrated that the Bradi5g03300 UGT is able to confer tolerance to DON following glucosylation of DON into DON 3-O-glucose and is involved in the early establishment of quantitative resistance to FHB. In the present work, we transferred the functional analyses conducted on the model species Brachypodium distachyon to bread wheat. In a first approach the B. distachyon Bradi5g03300 gene has been introduced through biolistic-mediated transformation in the wheat variety Apogee, susceptible to FHB. The phenotypic analyses conducted on homozygous transgenic wheat constitutively expressing the Bradi5g03300 gene showed that they exhibit higher resistance to FHB as well as increased root tolerance to DON compared to the control line. In parallel, using a synteny approach between B. distachyon and bread wheat genomes we identified a wheat candidate gene orthologous to the B. distachyon Bradi5g03300 gene. This wheat gene after validation through gene expression pattern during wheat infection, was introduced by transformation into B. distachyon to rapidly determine its ability to conjugate DON into D3G in planta and its involvement in FHB resistance. In conclusion, this project contributes to increase the knowledge concerning the functional relationship between DON glucosylation and FHB resistance in wheat and provide candidate genes to include in selection processes.

Fusarium virguliforme (Aoki, O’Donnell, Homma & Lattanzi), the causal agent of sudden death syndrome (SDS) of soybean (Glycine max [L.] Merrill), is responsible for major soybean yield losses in North America and South America. Despite the importance of SDS, few agronomic practices have been used to manage SDS successfully. Understanding the pathogen and the mechanisms it uses to cause disease is vital to devise effective disease control strategies. However, our knowledge of the pathogenicity mechanisms used by F. virguliforme is limited. The identification of pathogenic genes will shed light on the molecular basis of the interaction between F.virguliforme and soybean, which may ultimately lead to better management of SDS. Therefore, the studies presented in this thesis were aimed at identifying and characterizing candidate pathogenicity genes in F. virguliforme.To fulfill this objective, 40 candidate pathogenicity genes of F. virguliforme were identified based on a combined approach, which included hands-on literature and database mining, functional genomics as well as transcriptome analyses. From these genes, the FvSNF1gene (a sucrose non-fermenting protein kinase 1 ortholog), the Fvstr1 gene (a striatin protein ortholog) were functionally characterized through a gene knock-out strategy. Targeted disruption of the FvSNF1 locus in wild type F. virguliforme strain reduced virulence significantly on soybean and abolished galactose utilization. In addition, the FvΔSNF1 mutant displayed significant reduction in expression of several CWDEs genes and was defective in colonizing the vascular system of the roots. To identify putative target genes regulated by FvSNF1, transcriptome analyses were performed in the FvSNF1 deletion mutant and in the wild-type. Disruption of FvSNF1 affected the level of transcription of 393 genes and a majority of the genes were involved in carbohydrate metabolism, lignin degradation, and cellular signaling pathway. The disruption of Fvstr1, a striatin ortholog in F. virguliforme, resulted in a complete loss of virulence as well as impaired conidiation, conidiophore development and pigmentation in the fungus. The FvΔstr1 mutant also failed to colonize the vascular tissues of roots of inoculated soybean plants. The results suggest that FvSNF1and Fvstr1 have critical roles in pathogenicity. Another part of the study was to investigate the efficacy of ILeVO®, a succinate dehydrogenase inhibitor fungicide from Bayer CropScience, against F. virguliforme. Our results showed that ILeVO® was very active against F. virguliforme in vitro and was very effective in minimizing F. virguliforme infection thus providing yet another tool to combat SDS.

Soybean crops are vulnerable to a wide range of pathogens that reduce yield and cause extensive losses worldwide. In the United States, the soilborne pathogens Pythium spp., causing soybean damping-off, and Fusarium virguliforme, causing sudden death syndrome (SDS) of soybean, have been among the top diseases that most reduced soybean yields. This study demonstrated that biological control using native fungal antagonists could be a powerful tool to integrate with current management strategies for more efficient control of Pythium damping-off and SDS in soybean. Trichoderma spp. and Clonostachys rosea demonstrated the ability to mycoparasitize and antagonize the pathogens using different mechanisms and exhibited a protective effect on soybean in field conditions. The development of an efficient biological control program for disease management relies on a deep understanding of the BCA-pathogen interaction’s biology. This research also uncovered the molecular mechanisms involved in the F. virguliforme-T. afroharzianum interaction by using a dual RNAseq approach. Significant changes in both fungal organisms’ transcriptomes were discovered at different stages in their interaction. The results provided here can contribute to the future implementation of effective biological control programs for soybean. The benefits may also extend to other crops.

No description available.

No description available.

The Spok genes are a group of selfish genetic elements in the fungus Podespora anserina which kills spores lacking them. These Spoks function through a toxin and resistance domain. Homologues of these have been found across other species such as in the Fusarium genus. Nechadraft_82228 is a Spok homologue present in the species Fusarium vanettenii, with uncertain killer action. In this study the killer action is examined through site directed mutagenesis (SDM) of the resistance domain in Nechadraft_82228. The site directed mutagenesis was performed successfully and showed negative results regarding whether the Nechadraft_82228 had functioning killer action and resistance. Growth pattern for spot assays hinted at the existence of a different underlying reason for the lack of growth, opposed to a functional toxin/killer action. Namely respiratory dysfunction in the transformed Saccharomyces. Cerevisiae, potentially due to unfit heat shock temperature.

Observations of Bromus tectorum L. (cheatgrass or downy brome) monocultures have shown that populations are susceptible to stand die-off or replacement failures. Die-offs, where the seed bank from the previous year fails to emerge, occurs in cheatgrass stands and it is unclear the trigger or cause. The fungus Fusarium has been identified in plant and seed samples from die-offs and may drive die-off activity through pathogenicity. Die-off recovery may take several years but cheatgrass populations eventually reestablish. The purpose of our study was to determine whether Fusarium is a potential player in a die-off, and understand how die-offs recover after multiple years of stand failure. Our objectives were to determine: 1- litter and water effects on die-off activity; 2- if fungal pathogens, such as Fusarium, decrease the proportion of cheatgrass emergence in a die-off; and 3- whether direct or broadcast seeding, water, and litter treatments increase establishment in recovering die-offs. Litter absent plots had significantly (P < 0.0001 and P < 0.001) more emergence at 49.2% and 41% compared to litter present plots 21.3% and 23.7%. The litter absent plots significantly (P = 0.0003 and P = 0.001) increased survival (82% and 52%) compared to litter present plots (70% and 41%). Direct planted versus broadcast seeding had significantly (P < 0.0001) more emergence, 36% to 11.9%. The addition of Fusarium inoculum to field plots did not effectively replicate anticipated disease levels. The fungicide treatment did not have a significant influence at either site. The results from the study indicate that nothing inhibits cheatgrass from establishing following a persistent die-off disturbance. A unique window may be available for land managers to revegetate natives in invasive populations as large quantities of cheatgrass seeds fail to emerge during die-off events.