Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

Abstract Wheat rusts, the dreadful fungal diseases caused by members of the Puccinia genus remain as a major threat to global wheat production and food security. The R-gene mediated resistance has been employed as an efficient approach to develop rust resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel genomics assisted molecular players, including non-coding RNAs for rust disease management. MicroRNAs are crucial regulators of genes associated with plant growth, development, abiotic and biotic stress responses. In this study, high throughput small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem rust and leaf rust, together with mock inoculated controls. While miRNA mining in stem rust inoculated libraries revealed a total of twenty-six known and seven novel miRNAs, the search in leaf rust libraries culminated with twenty-two known and four novel miRNAs. The identified candidate miRNAs constituted both guide and passenger miRNA strands along with their isomiRs. Temporal expression pattern of differentially expressed miRNAs pinpoints their possible role during the progress of infection. Comparative analysis provides a better understanding of altered miRNA profiles associated with Sr36 and Lr45 disease resistance genes in response to stem rust and leaf rust, respectively. Also, the disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 with various sub-genomal origins might serve as an important common link between stem rust and leaf rust defense mechanisms downstream to the respective R-genes. Further, cis-regulatory elements that modulate MIR genes, targets of identified miRNAs related to various signal transduction pathways, and miR-SSRs which might be useful for rust disease control, are the emphasized attributes of our results. The outcome from this simultaneous study of miRNA profiles among two rust diseases and further characterization of the identified miRNAs can contribute to the expanding rust disease management programs.

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Resistance of Tangmai 4 wheat to powdery mildew, stem rust, leaf rust, and stripe rust and its chromosome composition

Canadian Journal of Plant Science ◽

10.4141/p03-195 ◽

2004 ◽

Vol 84 (4) ◽

pp. 1015-1023 ◽

Cited By ~ 9

Author(s):

H. J. Li ◽

R. L. Conner ◽

B. D. McCallum ◽

X. M. Chen ◽

H. Su ◽

...

Keyword(s):

Powdery Mildew ◽

Leaf Rust ◽

Stripe Rust ◽

Stem Rust ◽

Northern China ◽

Western Canada ◽

C Banding ◽

Rust Diseases ◽

Hard Red Winter Wheat ◽

Secale Cereale L

The hard red winter wheat Tangmai 4 did not develop symptoms of infection following inoculation with powdery mildew (Erysiphe graminis DC. f. sp. tritici E. Marchal) isolates from regions of western Canada and northern China. Tangmai 4 exhibited resistance to stem rust (Puccinia graminis Pers. f. sp. tritici Eriks. & Henn.) and leaf rust (P. triticina Eriks.) races from western Canada. This wheat line was resistant to individual stripe rust (P. striiformis Westend. f. sp. tritici Eriks.) races from the U.S. and Canada. Sequential C-banding and genomic in situ hybridization (GISH), and electrophoretic analyses of high molecular weight glutenins and gliadins demonstrated that Tangmai 4 carried a pair of T1BL·1RS wheat-rye (Secale cereale L.) translocated chromosomes. Since the genes located on T1BL·1RS are no longer effective in controlling powdery mildew and the rust diseases, Tangmai 4 must carry additional genes for resistance to these diseases, which makes it a valuable resource for the improvement of resistance in wheat against these diseases. Key words: T1BL·1RS translocation, disease resistance, sequential C-banding and GISH, glutenin, gliadin

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Virulence surveillance of wheat black stem rust fungus

Baghdad Science Journal ◽

10.21123/bsj.11.2.803-812 ◽

2014 ◽

Vol 11 (2) ◽

pp. 803-812

Author(s):

Baghdad Science Journal

Keyword(s):

Leaf Rust ◽

Disease Severity ◽

Stem Rust ◽

Yellow Rust ◽

Rust Fungus ◽

The North ◽

Rust Diseases ◽

Northern Regions ◽

Infection Disease ◽

Wheat Rust

General survey for wheat rust diseases in Iraqi fields was done during the seasons of 2010, 2011 and 2012. The survey covered different fields in southern, middle and northern regions. Results of the first season indicated that most of Iraqi cultivars such as Tmmoze2, IPA 99 and Mexipak showed different types of susceptibility to both yellow and leaf rust infection. Disease severity increased when the conditions were favorable for infections with using susceptible cultivars. The severity of leaf rust was less in the north region comparing with the middle and south regions. Most of the introduced cultivars such as Sham6 and Cimmyto showed susceptible reaction to yellow and leaf rust. Yellow rust was in epiphytotic form at the Iraqi-Syrian-Turkish triangle where the disease severity was 100%. Low disease severity of stem rust was observed on some cultivars (1-5%), except for the cultivar Mexipak which showed 40%S in Najaf. Rusts at season of 2011 were restricted mostly in Baghdad and the yellow rust was dominant. The AUDPC of 15 wheat cultivars showed that Sawa and Sali were highly susceptible to the three types of rusts while Babil113 and Tamoze2 were resistant. No rusts were detected at season 2012.

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Seedling resistances to rust diseases in international triticale germplasm

Crop and Pasture Science ◽

10.1071/cp10252 ◽

2010 ◽

Vol 61 (12) ◽

pp. 1036 ◽

Cited By ~ 8

Author(s):

J. Zhang ◽

C. R. Wellings ◽

R. A. McIntosh ◽

R. F. Park

Keyword(s):

Leaf Rust ◽

Stripe Rust ◽

Plant Resistance ◽

Stem Rust ◽

Rust Resistance ◽

Adult Plant Resistance ◽

Stem Rust Resistance ◽

Adult Plant ◽

Seedling Resistance ◽

Rust Diseases

Seedling resistances to stem rust, leaf rust and stripe rust were evaluated in the 37th International Triticale Screening Nursery, distributed by the International Wheat and Maize Improvement Centre (CIMMYT) in 2005. In stem rust tests, 12 and 69 of a total of 81 entries were postulated to carry Sr27 and SrSatu, respectively. When compared with previous studies of CIMMYT triticale nurseries distributed from 1980 to 1986 and 1991 to 1993, the results suggest a lack of expansion in the diversity of stem rust resistance. A total of 62 of 64 entries were resistant to five leaf rust pathotypes. In stripe rust tests, ~93% of the lines were postulated to carry Yr9 alone or in combination with other genes. The absence of Lr26 in these entries indicated that Yr9 and Lr26 are not genetically associated in triticale. A high proportion of nursery entries (63%) were postulated to carry an uncharacterised gene, YrJackie. The 13 lines resistant to stripe rust and the 62 entries resistant to leaf rust represent potentially useful sources of seedling resistance in developing new triticale cultivars. Field rust tests are needed to verify if seedling susceptible entries also carry adult plant resistance.

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Genetic diversity, antifungal evaluation and molecular docking studies of Cu-chitosan nanoparticles as prospective stem rust inhibitor candidates among some Egyptian wheat genotypes

PLoS ONE ◽

10.1371/journal.pone.0257959 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0257959

Author(s):

Hanaa S. Omar ◽

Abdullah Al Mutery ◽

Neama H. Osman ◽

Nour El-Houda A. Reyad ◽

Mohamed A. Abou-Zeid

Keyword(s):

Genetic Diversity ◽

Molecular Docking ◽

Disease Control ◽

Leaf Rust ◽

Stem Rust ◽

Chitosan Nanoparticles ◽

Docking Studies ◽

Rust Disease ◽

Wheat Genotypes ◽

Main Cluster

Wheat has a remarkable importance among cereals worldwide. Wheat stem and leaf rust constitute the main threats that destructively influence grain quality and yield production. Pursuing resistant cultivars and developing new genotypes including resistance genes is believed to be the most effective tool to overcome these challenges. This study is the first to use molecular markers to evaluate the genetic diversity of eighteen Egyptian wheat genotypes. Moreover, the molecular docking analysis was also used to assess the Cu-chitosan nanoparticle (CuChNp) treatment and its mode of action in disease control management. The tested genotypes were categorized into two main cluster groups depending on the similarity matrix, i.e the most resistant and susceptible genotypes to stem and leaf rust races. The results of SCoT primers revealed 140 polymorphic and 5 monomorphic bands with 97% polymorphism. While 121 polymorphic and 74 monomorphic bands were scored for SRAP primers (99% polymorphism). The genotypes Sakha 94, Sakha 95, Beni Sweif 4, Beni Sweif 7, Sohag 4 and Sohag 5 were resistant, while Giza 160 was highly susceptible to all stem rust races at the seedling stage. However, in the adult stage, the 18 genotypes were evaluated for stem and leaf rust-resistant in two different locations, i.e. Giza and Sids. In this investigation, for the first time, the activity of CuChNp was studied and shown to have the potential to inhibit stem and leaf rust in studied Egyptian wheat genotypes. The Spraying Cu-chitosan nanoparticles showed that the incubation and latent periods were increased in treated plants of the tested genotypes. Molecular modeling revealed their activity against the stem and leaf rust development. The SRAP and SCoT markers were highly useful tools for the classification of the tested wheat genotypes, although they displayed high similarities at the morphological stage. However, Cu-chitosan nanoparticles have a critical and effective role in stem and leaf rust disease control.

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RUST: A Robust, User-Friendly Script Tool for Rapid Measurement of Rust Disease on Cereal Leaves

Plants ◽

10.3390/plants9091182 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1182

Author(s):

Luis M. Gallego-Sánchez ◽

Francisco J. Canales ◽

Gracia Montilla-Bascón ◽

Elena Prats

Keyword(s):

Leaf Rust ◽

Disease Assessment ◽

Infection Frequency ◽

Rust Disease ◽

Sources Of Resistance ◽

High Throughput Analysis ◽

Automated Evaluation ◽

Rust Diseases ◽

Color Transformation ◽

User Friendly

Recently, phenotyping has become one of the main bottlenecks in plant breeding and fundamental plant science. This is particularly true for plant disease assessment, which has to deal with time-consuming evaluations and the subjectivity of visual assessments. In this work, we have developed an open source Robust, User-friendy Script Tool (RUST) for semi-automated evaluation of leaf rust diseases. RUST runs under the free Fiji imaging software (developed from ImageJ), which is a well-recognized software among the scientific community. The script enables the evaluation of leaf rust diseases using a color transformation tool and provides three different automation modes. The script opens images sequentially and records infection frequency (pustules per area) (semi-)automatically for high-throughput analysis. Furthermore, it can manage several scanned leaf segments in the same image, consecutively selecting the desired segments. The script has been validated with nearly 900 samples from 80 oat genotypes ranging from resistant to susceptible and from very light to heavily infected leaves showing a high accuracy with a Lin’s concordance correlation coefficient of 0.99. The analysis show a high repeatability as indicated by the low variation coefficients obtained when repeating the measurement of the same samples. The script also has optional steps for calibration and training to ensure accuracy, even in low-resolution images. This script can evaluate efficiently hundreds of leaves facilitating the screening of novel sources of resistance to this important cereal disease.

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Comparison of Genomic Prediction Methods for Yellow, Stem, and Leaf Rust Resistance in Wheat Landraces from Afghanistan

Plants ◽

10.3390/plants10030558 ◽

2021 ◽

Vol 10 (3) ◽

pp. 558

Author(s):

Muhammad Massub Tehseen ◽

Zakaria Kehel ◽

Carolina P. Sansaloni ◽

Marta da Silva Lopes ◽

Ahmed Amri ◽

...

Keyword(s):

Leaf Rust ◽

Stem Rust ◽

Ridge Regression ◽

Genomic Prediction ◽

Bayesian Models ◽

Predictive Ability ◽

Rust Diseases ◽

Wheat Landraces ◽

Gp Model ◽

Wheat Rust

Wheat rust diseases, including yellow rust (Yr; also known as stripe rust) caused by Puccinia striiformis Westend. f. sp. tritici, leaf rust (Lr) caused by Puccinia triticina Eriks. and stem rust (Sr) caused by Puccinia graminis Pres f. sp. tritici are major threats to wheat production all around the globe. Durable resistance to wheat rust diseases can be achieved through genomic-assisted prediction of resistant accessions to increase genetic gain per unit time. Genomic prediction (GP) is a promising technology that uses genomic markers to estimate genomic-assisted breeding values (GBEVs) for selecting resistant plant genotypes and accumulating favorable alleles for adult plant resistance (APR) to wheat rust diseases. To evaluate GP we compared the predictive ability of nine different parametric, semi-parametric and Bayesian models including Genomic Unbiased Linear Prediction (GBLUP), Ridge Regression (RR), Least Absolute Shrinkage and Selection Operator (LASSO), Elastic Net (EN), Bayesian Ridge Regression (BRR), Bayesian A (BA), Bayesian B (BB), Bayesian C (BC) and Reproducing Kernel Hilbert Spacing model (RKHS) to estimate GEBV’s for APR to yellow, leaf and stem rust of wheat in a panel of 363 bread wheat landraces of Afghanistan origin. Based on five-fold cross validation the mean predictive abilities were 0.33, 0.30, 0.38, and 0.33 for Yr (2016), Yr (2017), Lr, and Sr, respectively. No single model outperformed the rest of the models for all traits. LASSO and EN showed the lowest predictive ability in four of the five traits. GBLUP and RR gave similar predictive abilities, whereas Bayesian models were not significantly different from each other as well. We also investigated the effect of the number of genotypes and the markers used in the analysis on the predictive ability of the GP model. The predictive ability was highest with 1000 markers and there was a linear trend in the predictive ability and the size of the training population. The results of the study are encouraging, confirming the feasibility of GP to be effectively applied in breeding programs for resistance to all three wheat rust diseases.

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Adult plant resistance of selected Kenyan wheat cultivars to leaf rust and stem rust diseases

Cereal Research Communications ◽

10.1556/0806.44.2016.052 ◽

2017 ◽

Vol 45 (1) ◽

pp. 68-82 ◽

Cited By ~ 3

Author(s):

S. Figlan ◽

T.A. Baloyi ◽

T. Hlongoane ◽

T.G. Terefe ◽

H. Shimelis ◽

...

Keyword(s):

Leaf Rust ◽

Plant Resistance ◽

Stem Rust ◽

Adult Plant Resistance ◽

Adult Plant ◽

Wheat Cultivars ◽

Rust Diseases

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Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

Rice ◽

10.1186/s12284-021-00461-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kieu Thi Xuan Vo ◽

Md Mizanor Rahman ◽

Md Mustafizur Rahman ◽

Kieu Thi Thuy Trinh ◽

Sun Tae Kim ◽

...

Keyword(s):

Stress Responses ◽

Biotic Stress ◽

Defense Mechanisms ◽

Defense Responses ◽

Global Changes ◽

Biotic Stresses ◽

Novel Proteins ◽

Stress Agent ◽

Global Food ◽

Shed Light

AbstractBiotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.

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Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover

Plants ◽

10.3390/plants10020267 ◽

2021 ◽

Vol 10 (2) ◽

pp. 267

Author(s):

Axel J. Giudicatti ◽

Ariel H. Tomassi ◽

Pablo A. Manavella ◽

Agustin L. Arce

Keyword(s):

Small Rna ◽

Stress Responses ◽

Cellular Localization ◽

Mirna Biogenesis ◽

Small Rna Sequencing ◽

Sequencing Data ◽

Extensive Analysis ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Argonaute 1

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.

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