Identification of quantitative trait loci (QTL) for resistance to Fusarium crown rot (Fusarium pseudograminearum) in multiple assay environments in the Pacific Northwestern US

Fusarium crown rot (FCR), caused by and , reduces wheat ( L.) yields in the Pacific Northwest (PNW) of the US by as much as 35%. Resistance to FCR has not yet been discovered in currently grown PNW wheat cultivars. Several significant quantitative trait loci (QTL) for FCR resistance have been documented on chromosomes 1A, 1D, 2B, 3B, and 4B in resistant Australian cultivars. Our objective was to identify QTL and tightly linked SSR markers for FCR resistance in the partially resistant Australian spring wheat cultivar Sunco using PNW isolates of in greenhouse and field based screening nurseries. A second objective was to compare heritabilities of FCR resistance in multiple types of disease assaying environments (seedling, terrace, and field) using multiple disease rating methods. Two recombinant inbred line (RIL) mapping populations were derived from crosses between Sunco and PNW spring wheat cultivars Macon and Otis. The Sunco/Macon population comprised 219 F₆:F₇ lines and the Sunco/Otis population comprised 151 F₅:F₆ lines. Plants were inoculated with a single PNW isolate (006-13) in growth room (seedling), outdoor terrace (adult) and field (adult) assays conducted from 2008 through 2010. Crown and lower stem tissues of seedling and adult plants were rated for disease severity on several different scales, but mainly on a numeric scale from 0 to 10 where 0 = no discoloration and 10 = severe disease. Significant QTL were identified on chromosomes 2B, 3B, 4B, 4D, and 7A with LOD scores ranging from 3 to 22. The most significant and consistent QTL across screening environments was located on chromosome 3BL, inherited from the PNW cultivars Macon and Otis, with maximum LOD scores of 22 and 9 explaining 36 and 23% of the variation, respectively for the Sunco/Macon and Sunco/Otis populations. The SSR markers and flank these QTL and are being validated for use in marker-assisted selection for FCR resistance. This is the first report of QTL associated with FCR resistance in the US.Keywords: Root, Winter wheat, Management, Barley, Markers, Map, Seedling resistance, Triticum aestivum L, Graminearum group-1, Foot ro

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA.We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens

Biocontrol Potential of Forest Tree Endophytes

Peer reviewe

Chapitre 14: Phytopathogènes et stratégies de contrôle en aquaponie

peer reviewedAmong the diversity of plant diseases occurring in aquaponics, soil-borne pathogens, such as Fusarium spp., Phytophthora spp. and Pythium spp., are the most problematic due to their preference for humid/aquatic environment conditions. Phytophthora spp. and Pythium spp. which belong to the Oomycetes pseudo-fungi require special attention because of their mobile form of dispersion, the so-called zoospores that can move freely and actively in liquid water. In coupled aquaponics, curative methods are still limited because of the possible toxicity of pesticides and chemical agents for fish and beneficial bacteria (e.g. nitrifying bacteria of the biofilter). Furthermore, the development of biocontrol agents for aquaponic use is still at its beginning. Consequently, ways to control the initial infection and the progression of a disease are mainly based on preventive actions and water physical treatments. However, suppressive action (suppression) could happen in aquaponic environment considering recent papers and the suppressive activity already highlighted in hydroponics. In addition, aquaponic water contains organic matter that could promote establishment and growth of heterotrophic bacteria in the system or even improve plant growth and viability directly. With regards to organic hydroponics (i.e. use of organic fertilisation and organic plant media), these bacteria could act as antagonist agents or as plant defence elicitors to protect plants from diseases. In the future, research on the disease suppressive ability of the aquaponic biotope must be increased, as well as isolation, characterisation and formulation of microbial plant pathogen antagonists. Finally, a good knowledge in the rapid identification of pathogens, combined with control methods and diseases monitoring, as recommended in integrated plant pest management, is the key to an efficient control of plant diseases in aquaponics.Cos