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In Australia, the soil-borne disease common root rot (Bipolaris sorokiniana) (CRR) in wheat (Triticum aestivum L.) leads to substantial yield losses, yet has limited visible aboveground symptoms, making detection and identification labor intensive. Near-infrared (NIR) spectroscopy offers an early potential identification solution for CRR in wheat and has previously been reported with success for crop disease detection. This study investigated the ability of nondestructive NIR spectroscopy in combination with deep neural networks (DNN), logistic regression (LR), and principal component analysis combined with support vector machines (PCA-SVM) for early-stage CRR detection in wheat. NIR spectra of five different wheat varieties with varying resistance to CRR were collected in two seasons of glasshouse and three seasons of field trials using a portable spectrometer. Results demonstrated that DNN outperformed LR and PCA-SVM, achieving 66%–91% average classification accuracy in glasshouse trials and an average accuracy of 73% with up to 87% in field trials, effectively distinguishing inoculated and non-inoculated wheat plants from seedling to anthesis stages. Validation with a third season of field data achieved an average of 77% accuracy for the most susceptible variety during the stem elongation stage. NIR reflectance within 1600–1700 nm was identified as most important for estimating CRR presence, with initial detection occurring 35 days after sowing (DAS) in the glasshouse and 46 DAS in the field. In conclusion, a NIR spectrometer with a DNN model successfully performed disease classification, with the potential as a portable early disease detection tool to assist farm management decisions. [ABSTRACT FROM AUTHOR]

In Australia, the soil-borne disease common root rot (Bipolaris sorokiniana) (CRR) in wheat (Triticum aestivum L.) leads to substantial yield losses, yet has limited visible aboveground symptoms, making detection and identification labor intensive. Near-infrared (NIR) spectroscopy offers an early potential identification solution for CRR in wheat and has previously been reported with success for crop disease detection. This study investigated the ability of nondestructive NIR spectroscopy in combination with deep neural networks (DNN), logistic regression (LR), and principal component analysis combined with support vector machines (PCA-SVM) for early-stage CRR detection in wheat. NIR spectra of five different wheat varieties with varying resistance to CRR were collected in two seasons of glasshouse and three seasons of field trials using a portable spectrometer. Results demonstrated that DNN outperformed LR and PCA-SVM, achieving 66%–91% average classification accuracy in glasshouse trials and an average accuracy of 73% with up to 87% in field trials, effectively distinguishing inoculated and non-inoculated wheat plants from seedling to anthesis stages. Validation with a third season of field data achieved an average of 77% accuracy for the most susceptible variety during the stem elongation stage. NIR reflectance within 1600–1700 nm was identified as most important for estimating CRR presence, with initial detection occurring 35 days after sowing (DAS) in the glasshouse and 46 DAS in the field. In conclusion, a NIR spectrometer with a DNN model successfully performed disease classification, with the potential as a portable early disease detection tool to assist farm management decisions. [ABSTRACT FROM AUTHOR]

Crown rot (CR; Fusarium pseudograminearum) is a serious disease in winter cereals. Soil type, temperature, nutrients, water availability and stubble‐borne inoculum levels play major roles in determining disease severity. This paper reports the impact of two different watering regimes on the disease severity and gas exchange of F. pseudograminearum infected bread wheat for the first time. Fusarium pseudograminearum inoculated and noninoculated genotypes with different susceptibility to CR were watered to either field capacity or a reduced watering regime in three controlled environment experiments. Rate of photosynthesis, stomatal conductance, internal CO2 concentration and transpiration rate were measured using a portable photosynthesis system, together with disease severity of leaf sheaths at 28 days after planting. Significant differences in disease severity were reported between watering treatments with reduction in CR symptoms in the partially resistant genotypes in the reduced water treatment. Photosynthesis, stomatal conductance and transpiration rate were significantly decreased across most genotypes when inoculated with F. pseudograminearum. Differences in gas exchange between inoculum treatments were more evident in plants watered to field capacity. Water availability has been reported to be one of the crucial factors for initiating F. pseudograminearum infection and subsequent development of CR disease. This research demonstrates significant variation in genotype‐related responses to the complex interactions of F. pseudograminearum infection and water treatment, with a negative impact of both limited soil water availability and CR disease severity on plant gas exchange in bread wheat. [ABSTRACT FROM AUTHOR]

Common root rot (CRR) caused by the soilborne pathogen Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is becoming increasingly prevalent worldwide. Identification of CRR is difficult and time‐consuming for human assessors due to the non‐distinctive above‐ground symptoms, with browning of subcrown internodes and roots the most distinguishing symptom of infection. CRR disease has been recognized as a significant disease for cereal crops in many countries. In 2009, CRR in Australia was estimated to cause $30 million average annual yield loss for wheat and $13 million for barley. Recent evidence indicates CRR may be more prevalent than expected in Australian wheat cropping areas due to lack of research on this disease. Low levels of B. sorokiniana survive in the soil for up to 10 years and attack plants at early stages of growth. Therefore, mitigating CRR in wheat and barley may not be practical at the late stages of infection due to lack of effective methods; however, early detection might be viable to alleviate the impact of this disease. A comprehensive overview of CRR caused by B. sorokiniana, including disease background, worldwide economic losses, management methods, potential CRR detection using multispectral and hyperspectral sensors and the research focus over the past 50 years is provided in this article. This review paper is expected to provide thorough supplemental information for current studies about CRR and proposes recommendations for whole‐of‐field disease scouting methods to farmers, enabling reduced time and cost for CRR management and increasing wheat and barley production worldwide. [ABSTRACT FROM AUTHOR]

Yield losses of bread wheat due to crown rot can be more severe when drought conditions occur during the grain-filling period. Root architecture characteristics are important for soil exploration and belowground resource acquisition and are essential for adaptation to water-limited environments. Traits such as root angle, length and density have been strongly associated with acquisition efficiency and contribute to yield stability of the crop. The impact of crown rot pathogens on wheat root architecture is poorly understood. We examined differences in root angle, length and number, as well as dry root weight of the crown rot-susceptible bread wheat cultivar, Livingston inoculated with one of two crown rot pathogens Fusarium culmorum or Fusarium pseudograminearum in a transparent-sided root observation chamber. Significant adverse impacts on plant health and growth were revealed by visual discolouration of the leaf sheaths; fresh and dry shoot weight; leaf area of the oldest and the youngest fully expanded leaf and leaf number. Values of most recorded root system measurements were reduced when inoculated with either F. culmorum or F. pseudograminearum. In contrast, root angle was increased in the presence of F. culmorum but was not significantly changed by F. pseudograminearum. The development of whiteheads and grain losses in bread wheat caused by crown rot have previously been associated with blockages of the vascular systems. The method employed here was able to identify differences in the pathogen impacts on roots, which were not detected using previous systems. This research indicates that in the presence of F. culmorum and F. pseudograminearum infection, not only reductions in the size and biomass of the shoot system but also changes in the length, biomass and architecture of the root system could play an important role in yield loss. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. Genetic studies on FCR resistance have mainly focused on disease symptoms measured by the browning of either leaf sheaths in seedlings or stems of mature plants. Two major QTLs conferring FCR resistance in barley, Qcsr.cpi-1H and Qcrs.cpi-4H, were previously identified in the growth room. They could explain up to 33.4 and 45.3% of phenotypic variance, respectively. This is the first study where the possible effects of FCR-resistant loci identified in the previous studies based on seedling assay are tested for their abilities to reduce grain yield loss. Near isogenic lines (NILs) and backcross (BC) lines targeting these two loci were assessed in the 2017 and 2018 crop seasons. Results from the NILs showed that the presence of a resistance allele at either the 1HL or 4HL locus reduced grain yield loss by an average of 12.0% and 10.7%, respectively. Grain yields of the top BC lines containing resistance alleles at both loci were 34.4% higher than the average of the commercial varieties under FCR inoculation. These lines will be highly valuable in breeding barley varieties with enhanced resistance to FCR. [ABSTRACT FROM AUTHOR]

Achieving genetic gain when selecting for genotypes with favourable grain production traits in the presence of the fungal pathogen Fusarium pseudograminearum can involve potentially competitive objectives of breeding for tolerance and breeding for resistance. A method for the selection of genotypes for both tolerance and resistance to crown rot in wheat, caused by this fungal pathogen, is presented through a combined analysis of grain yield and symptoms of disease severity across inoculated and uninoculated treatments. The symptoms of disease severity are measured as basal stem browning in the plant, and this trait provides a measure of resistance in this study. The measurement of grain yield in uninoculated and inoculated treatments provides a measure of yield potential and yield in the presence of disease, respectively. Interpretation of analysis results through the regression inherent in the statistical model allows us to derive and select for three traits of interest. Firstly, yield retention can be derived from a random regression of yield of genotypes in inoculated versus uninoculated treatments, independently of yield potential in that environment. Secondly, severity of disease symptoms in inoculated treatments can be used to select genotypes with superior resistance. Finally, a tolerance measure can be derived from the yield retention, when it is assessed independently of the disease severity measured as stem browning. In theory, this method is superior to traditional approaches of forming a yield difference or a percentage yield loss calculation. In practice, genetic gain can be made for tolerance through accurate phenotyping of the trait, independently of resistance in that environment. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Summary: An emerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a 'cry for help' strategy is limited.We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture‐based methods to systematically investigate a three‐way interaction between the wheat plant, wheat‐associated microbiomes and Fusarium pseudograminearum (Fp).A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was observed in both the rhizosphere and root endosphere of Fp‐infected wheat. SR80 reached 3.7 × 107 cells g−1 in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defence genes in top leaves. Upon re‐introduction in soils, SR80 enhanced plant growth, both the below‐ground and above‐ground, and induced strong disease resistance by boosting plant defence in the above‐ground plant parts, but only when the pathogen was present.Together, the bacterium SR80 seems to have acted as an early warning system for plant defence. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system. [ABSTRACT FROM AUTHOR]