Application of a U-Net Neural Network to the Puccinia sorghi-Maize Pathosystem.

Computer vision approaches to analyze plant disease data can be both faster and more reliable than traditional, manual methods. However, the requirement of manually annotating training data for the majority of machine learning applications can present a challenge for pipeline development. Here, we describe a machine learning approach to quantify Puccinia sorghi incidence on maize leaves utilizing U-Net convolutional neural network models. We analyzed several U-Net models with increasing amounts of training image data, either randomly chosen from a large data pool or randomly chosen from a subset of disease time course data. As the training dataset size increases, the models perform better, but the rate of performance decreases. Additionally, the use of a diverse training dataset can improve model performance and reduce the amount of annotated training data required for satisfactory performance. Models with as few as 48 whole-leaf training images are able to replicate the ground truth results within our testing dataset. The final model utilizing our entire training dataset performs similarly to our ground truth data, with an intersection over union value of 0.5002 and an F1 score of 0.6669. This work illustrates the capacity of U-Nets to accurately answer real-world plant pathology questions related to quantification and estimation of plant disease symptoms. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Resistance in Maize (Zea mays) to Isolates of Puccinia sorghi from Eastern Australia.

The causal agent of maize common rust (CR), Puccinia sorghi, has increased in incidence and severity in Australia in recent years, prompting the assessment of sources of resistance and a preliminary survey of the diversity of P. sorghi populations. The maize commercial hybrids tested carried no resistance to 14 isolates of P. sorghi and had infection types comparable with that of a susceptible check. The resistance gene Rp1_D that remained effective in the United States for 35 years was ineffective against 7 of the 14 isolates. Maize lines carrying known "resistance to Puccinia" (Rp) genes were inoculated with the five isolates considered most diverse based on year of collection (2018 or 2019), location (Queensland or Victoria), and host from which they were isolated (maize or sweet corn). Lines carrying the resistance genes RpG, Rp5, Rp1_E, Rp1_I, Rp1_L, RpGDJ, RpGJF, and Rp5GCJ were resistant to all five isolates and to isolates collected in many agroecological regions. These lines were recommended as donors of effective resistance for maize breeding programs in Australia. Lines carrying no known resistance or resistance genes Rp8_A, Rp8_B, Rp1_J, Rp1_M, Rp7, and Rpp9 (conferring resistance to P. polysora) were susceptible to all five isolates. Differential lines carrying resistance genes Rp1_B, Rp1_C, Rp1_D, Rp1_F, Rp1_K, Rp3_D, or Rp4_A were either resistant or susceptible depending upon the isolate used, showing that the isolates varied in virulence for these genes. Urediniospore production was reduced on adult compared with juvenile plants, presumably due to changes in plant physiology associated with age or the presence of adult plant resistance.

Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize.

Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1-D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1-D-mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2-infected leaves from the near-isogenic lines H95 and H95:Rp1-D, which differed for the presence of Rp1-D. We observed up-regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up-regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1-D and H95 with an additional H95:Rp1-D-specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1-D-mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance-specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance-specific responses to P. sorghi.

Design, synthesis and fungicidal activity evaluation of novel pyrimidinamine derivatives containing phenyl-thiazole/oxazole moiety.

Diflumetorim is a member of pyrimidinamine fungicides that possess excellent antifungal activities. Nevertheless, as reported that the activity of diflumetorim to corn rust (Puccinia sorghi) was not ideal (EC50 = 53.26 mg/L). Herein, a series of novel pyrimidinamine derivatives containing phenyl-thiazole/oxazole moiety were designed based on our previous study and the structural characteristics of diflumetorim, synthesized and bioassayed to discover novel fungicides with excellent antifungal activities. Among these compounds, T18 gave the optimal fungicidal activity, which respectively offers control effects with EC50 values of 0.93 mg/L against P. sorghi and 1.24 mg/L against E. graminis, significantly superior to commercial fungicides diflumetorim, tebuconazole, and flusilazole. Cell cytotoxicity results suggested that compound T18 has lower toxicities than diflumetorim. Furthermore, DFT calculation indicated that the phenyl-thiazole/oxazole moiety plays an unarguable role in the improvement of activity, which will contribute to designing and developing more potent compounds in the future.

Reaction of maize hybrids to Northern corn leaf blight and common rust, and chemical control of Northern corn leaf blight / Reação de híbridos de milho a helmintosporiose e ferrugem comum, e controle químico de helmintosporiose

Northern corn leaf blight (NCLB) and common rust are among the primary fungal diseases affecting maize production. This study aimed to evaluate the susceptibility of ten maize hybrids to NCLB and to common rust and to verify the efficiency of fungicides in the chemical control of Exserohilum turcicum. In the first experiment, hybrids Pioneer (30F53, P1630H, P2530), Monsanto (AG 8045, AG 9045), Dow AgroSciences (2A550, 2A106 and 2B587) and Syngenta (SYN7205 VIPTERA, SW 3949 TL) were used and in the experiment for effectiveness of fungicides in the control of NCLB. The efficiency of fungicides propiconazole, azoxystrobin, cyproconazole + azoxystrobin, prothioconazole + trifloxystrobin, benzovindiflupir + azoxystrobin, cyproconazole + azoxystrobin + mancozeb were tested in the Pioneer P1630H hybrid. In both experiments, the leaf disease severity (%), yield and the weight of one thousand seeds were evaluated. The experimental design was carried out in randomized blocks with four replicates. The hybrids SYN7205, P2530, SW 3949 TL, 2B587, AG 9045, 2A550, P1630H, 2A106 and AG 8025 showed the smallest areas under the common rust severity progress curve. Hybrids AG9045, 30F53, and 2A550 presented the smallest areas under the NCLB progress curve. Hybrids AG8025, 2B587, P1630H, AG9045, 2A106, 2A550, present the highest yields. The fungicides prothioconazole + trifloxystrobin present the highest chemical control efficiency for NCLB and the lowest area under the disease progress curve (AUDPC).(AU)

A helmintosporiose e a ferrugem comum estão entre as principais doenças fúngicas que afetam a produção do milho. Os objetivos desse trabalho foram avaliar a suscetibilidade de dez híbridos de milho a helmintosporiose e a ferrugem comum e verificar a eficiência de fungicidas no controle de Exserohilum turcicum. No primeiro experimento utilizaram-se os híbridos Pioneer (30F53, P1630H, P2530), Monsanto (AG 8045, AG 9045), Dow AgroSciences (2A550, 2A106 e 2B587) e Syngenta (SYN7205 VIPTERA, SW 3949 TL), e no experimento de eficiência de fungicidas no controle de helmintosporiose, testou-se a eficiência dos fungicidas propiconazol, azoxistrobina, ciproconazol + azoxistrobina, protioconazol + trifloxistrobina, benzovindiflupir + azoxistrobina, ciproconazol + azoxistrobina + mancozebe, no híbrido Pioneer P1630H. Em ambos os experimentos avaliaram-se a severidade foliar das doenças (%), o rendimento e o peso de mil sementes. O delineamento experimental foi em blocos ao acaso com quatro repetições. Os híbridos SYN7205, P2530, SW 3949 TL, 2B587, AG 9045, 2A550, P1630H, 2A106 e AG 8025 apresentam as menores áreas abaixo da curva de progresso de severidade de ferrugem comum. Os híbridos AG9045, 30F53 e 2A550 apresentam as menores áreas abaixo da curva de progresso de helmintosporiose. Os híbridos AG8025, 2B587, P1630H, AG9045, 2A106 e 2A550 apresentam os maiores rendimentos. Os fungicidas protioconazol + trifloxistrobina apresentam a maior eficiência de controle químico de helmintosporiose e a menor AACPD.(AU)

Combined linkage and association mapping reveal QTL for host plant resistance to common rust (Puccinia sorghi) in tropical maize.

BACKGROUND: Common rust, caused by Puccinia sorghi, is an important foliar disease of maize that has been associated with up to 50% grain yield loss. Development of resistant maize germplasm is the ideal strategy to combat P. sorghi. RESULTS: Association mapping performed using a mixed linear model (MLM), integrating population structure and family relatedness identified 25 QTL (P < 3.12 × 10- 5) that were associated with resistance to common rust and distributed on chromosomes 1, 3, 5, 6, 8, and 10. We identified three QTLs associated with all three disease parameters (final disease rating, mean disease rating, and area under disease progress curve) located on chromosomes 1, 3, and 8. A total of 5 QTLs for resistance to common rust were identified in the RIL population. Nine candidate genes located on chromosomes 1, 5, 6, 8, and 10 for resistance to common rust associated loci were identified through detailed annotation. CONCLUSIONS: Using a diverse set of inbred lines genotyped with high density markers and evaluated for common rust resistance in multiple environments, it was possible to identify QTL significantly associated with resistance to common rust and several candidate genes. The results point to the need for fine mapping common rust resistance by targeting regions identified in common between this study and others using diverse germplasm.

Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust.

Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6Mbdraft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200bppaired-end and 5000bpmate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value⩽e-10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.

Application of "Hydrogen-Bonding Interaction" in Drug Design. Part 2: Design, Synthesis, and Structure-Activity Relationships of Thiophosphoramide Derivatives as Novel Antiviral and Antifungal Agents.

On the basis of the structure of natural product harmine, lead compound 18, and the structure of compounds in part 1, a series of thiophosphoramide derivatives 1-17 were designed and synthesized from various amines in one step. Their antiviral and antifungal activities were evaluated. Most of the compounds showed significantly higher antiviral activity against tobacco mosaic virus (TMV) than commercial virucide ribavirin. Compound (R,R)-17 showed the best anti-TMV activity in vitro (70%/500 µg/mL and 33%/100 µg/mL) and in vivo (inactivation effect, 68%/500 µg/mL and 30%/100 µg/mL; curative effect, 64%/500 µg/mL and 31%/100 µg/mL; protection effect, 66%/500 µg/mL and 31%/100 µg/mL), which is higher than that of ningnanmycin and lead compound 18. The antiviral activity of (R,R)-17·HCl is about similar to that of (R,R)-17. However, the antifungal activity of (R,R)-17·HCl against Puccinia sorghi is slightly lower than that of (R,R)-17. The systematic study provides compelling evidence that these simple thiophosphoramide compounds could become efficient antiviral and antifungal agents.