Category Archives: ORIGINAL ARTICLE

Comparative analysis of Argentinian and European populations of Ramularia collo‐cygni on barley

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Comparative analysis of Argentinian and European populations of Ramularia collo-cygni on barley

Argentinian Ramularia collo-cygni population shows lower diversity and higher structuring than European populations, suggesting the occurrence of a founder effect and an ongoing establishment phase.


Abstract

Ramularia collo-cygni (Rcc) is a major barley pathogen that causes yield and grain quality losses worldwide. The main sources of Rcc inoculum are the seed and asexual airborne spores. In Argentina, Rcc is considered to be an emerging threat to barley crops, especially as most varieties are susceptible to Rcc and have a European genetic background. Here, we describe the population genetic diversity and structure of the Argentinian Rcc population, based on 10 simple-sequence repeat (SSR) markers, in order to compare it with Rcc populations from the Czech Republic and Scotland. The Argentinian Rcc population showed lower genetic diversity, higher level of structuring and higher number of clonal isolates than European populations. Significant differentiation at population origin (country) and region (Europe and South America) level suggests the occurrence of a genetic bottleneck and/or a founder effect on Rcc entry to Argentina and that this population could still be in a state of establishment and emergence. Further research on Rcc genetic structure at local and global scale will be crucial for the understanding of Rcc population dynamics for disease management.

Species diversity of fusarioid genera associated with sweet potato in Brazil, including the description of a new species

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Species diversity of fusarioid genera associated with sweet potato in Brazil, including the description of a new species

This is the first report of Fusarium agrestense, Fusarium annulatum, Fusarium caatingaense, Fusarium elaeidis, Fusarium pernambucanum, Fusarium pseudocircinatum, Neocosmospora falciformis and Neocosmospora suttoniana associated with root and stem rot of sweet potato.


Abstract

The sweet potato is of great socioeconomic importance in Brazil and throughout the world. Among the fungal pathogens associated with root diseases of this crop, Fusarium is of particular importance due to the diversity of species, the pathogenic potential in their various hosts and their ability to survive inside plants as endophytes without apparently causing damage. The objective of this work was to identify fusarioid genera from stems and roots of symptomatic and asymptomatic plants. The identification of fungal species was based on multilocus phylogenetic analysis and morphology. A total of 51 isolates, distributed in the Fusarium incarnatum-equiseti species complex (FIESC), Fusarium fujikuroi species complex (FFSC), Fusarium oxysporum species complex (FOSC)—with a taxonomic novelty—and Neocosmospora were identified. The pathogenicity test on roots showed that 13 of the 14 tested isolates obtained from symptomatic roots and stems and from asymptomatic stems were capable of reproducing the rot symptoms observed in the field. The confirmation of the pathogenicity of isolates from asymptomatic stems corroborates the hypothesis that these fungi can live endophytically in asymptomatic tissue and are capable of causing damage to their hosts in stress situations. This is the first report of Fusarium agrestense, Fusarium annulatum, Fusarium caatingaense, Fusarium elaeidis, Fusarium pernambucanum, Fusarium pseudocircinatum, Neocosmospora falciformis and Neocosmospora suttoniana associated with root and stem rot of sweet potato.

Genetic analysis and molecular mapping of fruit‐bearing habit locus (Bh1) in eggplant (Solanum melongena L.)

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Abstract

In eggplant, two kinds of fruit-bearing habits can be observed, that is, cluster and solitary. The fruits grown in cluster are small in size but contribute towards yield and productivity. In this investigation, we have studied the genetics of fruit-bearing habit and identified the SSR markers linked to this trait. Pusa Safed Baingan 1 (cluster bearer) and Pusa Hara Baingan 1 (solitary bearer) having contrasting traits were crossed to generate F1 (20 plants), F2 (215 plants), B1 (73 plants) and B2 (64 plants). Genetic analysis of the trait was carried out using Chi-square test. The segregation of plants in F2 suggested recessive epistasis with ratio of 9:3:4 (solitary: mixed: cluster) indicating involvement of two genes for controlling the fruit-bearing habit. The parental polymorphic 6 SSR markers were used for genotyping F2 plants and co-segregated with the fruit-bearing habit (Bh 1 ) locus in 1:2:1. A linkage map covering 63.86 cm distance was developed, the SSR marker emf11A03 was closest with a distance of 4.37 cm, emk03O04 at 12.5 cm distance, and emf21O06 at 14.5 cm. The physical positions of the SSR markers emb01J19 and emf11A03 flanking Bh 1 gene were located at 4.77 mb position of contig Sme2.5_05721.1 and 5.18 Mb position of contig Sme2.5_00994.1, respectively. The findings in the present study will be helpful in marker-assisted breeding to enhance yield in eggplant.

Overexpression of an NLP protein family member increases virulence of Verticillium dahliae

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Overexpression of an NLP protein family member increases virulence of Verticillium dahliae

The role of VdNEP, an NLP protein gene, in virulence was investigated by overexpressing the gene in multiple pathotypes and monitoring its cellular localization during infection.


Abstract

Verticillium dahliae is a xylem-invading fungal pathogen that causes vascular wilt in a wide range of angiosperms. The pathogen uses a variety of virulence factors to invade and colonize its hosts. Here, we report that VdNEP, an NLP (Necrosis and ethylene inducing peptide 1-Like Protein), functions as one such factor in multiple hosts. Eggplant leaves treated with VdNEP developed necrotic symptoms. Overexpression of VdNEP by incorporating extra copies of the VdNEP gene increased virulence to cotton, eggplant and tomato plants, suggesting its role as a virulence factor in diverse plants. Increased expression of VdNEP among the transformants did not correlate with the number of VdNEP inserts, suggesting that its expression was affected by the genomic context of the insertion sites. Interestingly, a transformant derived from a defoliating strain with high VdNEP transcript levels caused disease symptoms in tomato plants, whereas the corresponding wild-type strain did not cause visible symptoms. The amount of V. dahliae DNA in plants infected with this VdNEP-overexpressing transformant was 22 times higher than that in plants infected with the wild-type isolate, further supporting the critical role of VdNEP in infection. A VdNEP-EGFP fusion was constructed to follow its localization in fungal cells and during infection.

Unravelling the aetiology of Dickeya zeae using polyphasic approaches for bacterial stalk rot in maize

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Unravelling the aetiology of Dickeya zeae using polyphasic approaches for bacterial stalk rot in maize

This study identifies and molecularly characterizes Dickeya zeae isolates from bacterial stalk rot of maize, using six genomic regions (16S rRNA, recN, gyrB, dnaX, recA and dnaJ) using multiple phylogenetic analyses.


Abstract

Bacterial stalk rot (BSR), caused by Dickeya zeae (syn. Erwinia chrysanthemi pv. zeae), has emerged as a significant disease affecting maize crops worldwide. In this study, symptomatic maize plants were collected from diverse agroclimatic zones in India over the period of kharif 2019–2021. Various approaches, including pathogenicity tests, cultural characteristics, biochemical profiling and molecular analysis, were employed to accurately identify the collected bacterial isolates as Dickeya. Pathogenicity assessments were conducted on 40-day-old maize plants, following Koch's postulates, as well as through potato maceration assays. Furthermore, cross-infectivity studies were conducted on rice, potato, tomato and banana plants. Phenotypic and biochemical characterization confirmed that all the isolates belonged to the Dickeya genus. Additionally, PCR amplification of a pel gene fragment, specific to the genus Dickeya, further verified the pathogenic isolates as Dickeya. Molecular characterization studies were performed on four isolates (UKMDZ-3, PBMDZ-7, TSMDZ-11 and HPMDZ-16), selected to represent distinct maize agroclimatic zones and four states of India, and which caused severe infections on susceptible maize cv. Early Composite. Amplification of six characteristic genome regions (16S rRNA, recN, gyrB, dnaX, recA and dnaJ) from these isolates facilitated individual and concatenated gene phylogenetic analyses, confirming their resemblance to Dickeya zeae. This study represents the first comprehensive molecular analysis of D. zeae isolates from India, providing valuable insights for future crop improvement strategies. The findings contribute to our understanding of the genetic basis of BSR in maize and offer potential avenues for genetic enhancement to mitigate the disease's impact on maize cultivation.

Rice leaf disease detection based on enhanced feature fusion and target adaptation

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Rice leaf disease detection based on enhanced feature fusion and target adaptation

The proposed EFFTAN model was validated for robustness and generalization of four rice leaf spot data plus maize data samples, and the experimental data demonstrated the significance and validity of the research work.


Abstract

Intelligent rice disease recognition methods based on deep neural networks can predict the degree of disease on the basis of, for example, the number of disease spots on an image, so that preventive measures can be taken. Currently, intelligent recognition methods for rice diseases suffer from the disadvantages of poor versatility and low accuracy. This paper uses eight common image classification networks to classify and identify four rice diseases. ResNet50 was selected as the feature extraction network and an enhanced feature fusion and target adaptive network (EFFTAN), referred to as EFFTAN, is proposed. The EFFTAN was used to detect four rice spot diseases in the rice leaf disease image samples dataset; the mean average precision of the final detection was 95.3%, and effective detection was also achieved for the dense spot features.

Influence of berry ripening on susceptibility to Coniella diplodiella infection in grapevine

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Influence of berry ripening on susceptibility to Coniella diplodiella infection in grapevine

The data from in vitro and in vivo trials showed that grape clusters were susceptible to infection by Coniella diplodiella for a long period; effective disease control therefore requires interventions from early berry development.


Abstract

White rot, caused by the fungus Coniella diplodiella, is an important but poorly studied disease that mainly affects grapevine clusters. White rot control typically involves the repeated application of fungicides, which may be unjustified in some cases given that the key period of berry susceptibility to infection remains unclear and controversial. In this study, germination of C. diplodiella conidia and mycelium growth were investigated on water agar (conidial germination only) and artificial media similar to berry juice at five growth stages from pea-sized to berries ripe for harvest. On water agar, conidia germinated from 10°C to 35°C (with an optimum of 20–30°C) with >2 h of moisture incubation. Both conidial germination and mycelial growth were higher on agar similar to berry juice at véraison to berry softening than at other stages, with the lowest values detected for the ripe berries. The berries were also artificially inoculated with conidia at the different growth stages, showing that grape clusters were susceptible to infection for a long period, albeit with varying degrees of susceptibility at different stages. This implies that effective disease control requires interventions from early berry development, whenever weather conditions are conducive to infection. Further development of a predictive model accounting for weather conditions and berry susceptibility dynamics would facilitate the dynamic estimation of the disease risk during the grapevine-growing season and contribute to a risk-based application of fungicides for white rot control.

Differential expression of antimicrobial metabolites, phenylpropanoid and phytohormone metabolic pathway genes determines resistance or susceptibility to Ascochyta rabiei in chickpea

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Differential expression of antimicrobial metabolites, phenylpropanoid and phytohormone metabolic pathway genes determines resistance or susceptibility to Ascochyta rabiei in chickpea

Defence to Ascochyta rabiei in chickpea is composed of a two-tier system separated by time wherein jasmonic acid, phenylpropanoids, antimicrobial peptides and defence genes govern resistance and abscisic acid susceptibility.


Abstract

Blight caused by Ascochyta rabiei is a major constraint in the productivity of chickpea (Cicer arietinum). The mechanisms governing resistance/susceptibility to blight in chickpea are poorly understood. We used a blight-resistant (HC1) and a blight-susceptible (GPF2) genotype of chickpea and genes of pathogenesis-related proteins (PRPs), phenylpropanoid pathway metabolites, abscisic acid (ABA), gibberellic acid (GA) and jasmonic acid (JA) to understand the role of these in A. rabiei resistance/susceptibility. The JA, ABA and GA biosynthesis genes of chickpea were retrieved, characterized and gene-specific primers were used for transcriptional studies. Gene expression revealed that chickpea activated its defences rather quickly and well before initiation of spore germination. In resistant HC1, the majority of the JA, GA and phenylpropanoid pathway genes had peak maxima at 2 h post-inoculation (hpi) whereas PRPs/defence genes had peak maxima at 24/36 hpi implying that defence to A. rabiei in chickpea is composed of a two-tier system separated by time: immediately after spore attachment and at or just prior to host penetration. Unlike HC1, susceptible GPF2 was late in activation of defence responses or did not activate them. Another striking difference between HC1 and GPF2 was up-regulation of ABA biosynthesis genes in inoculated GPF2 and down-regulation in HC1. This study revealed that phenylpropanoids, PRPs, JA, 8-(1R,2R)-3-oxo-2-(Z)-pent-2-enyl cyclopentyl octanoate, (15Z)-12-oxophyto-10,15-dienoic acid and methyl-jasmonate govern resistance to A. rabiei in chickpea whereas ABA governs susceptibility.

Transcriptional profiling identifies the early responses to Puccinia triticina infection in the adult plant leaf rust resistant wheat variety Toropi

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Transcriptional profiling identifies the early responses to Puccinia triticina infection in the adult plant leaf rust resistant wheat variety Toropi

The wheat cv. Toropi displays a durable leaf rust resistance that is associated with a prehaustorial resistance phenotype and rapid changes in wheat gene expression following Puccinia triticina inoculation.


Abstract

Leaf rust, caused by Puccinia triticina (Pt), is a major disease of wheat and a significant problem for wheat production in Brazil. The Brazilian variety Toropi, released in 1965, has maintained high levels of field, adult plant resistance (APR) to leaf rust across global locations, while microscopic studies have indicated prehaustorial resistance mechanisms. Analyses of gene expression in flag leaves of Toropi, during the early stages of Pt infection, were undertaken to explore the mechanisms behind the APR in Toropi. Differential expression of wheat genes was undertaken, comparing Pt- to mock-inoculated and Pt- to Pt-inoculated time points. Analysis of gene expression indicated a strong response to Pt, which was fully active by 6 h after inoculation (hai). More genes were downregulated than upregulated, particularly at 6 and 12 hai. Gene Ontology enrichment analysis indicated a shutting down of RNA and protein synthesis and an early effect on photosynthesis, with disruption of the electron transfer chain. Analyses of upregulated genes identified genes involved in ATP-binding and protein kinase activity at 6 hai, supporting a rapid metabolic response to Pt infection. A general upregulation of genes involved in transport and metabolism indicated the need to relocate protein and organic-based resources. Alignment of differentially expressed genes with the genomic regions defining four leaf rust APR quantitative trait loci (QTLs) in Toropi identified candidate resistance genes, including a sugar transporter, a receptor kinase and a seven-transmembrane MLO family protein. In addition, 60 Pt genes were identified, 11 being annotated as potential effector proteins.

Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection

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Abstract

Effects of individual single-nucleotide polymorphism (SNP) markers and the size of “training” and “test” populations affect prediction accuracy in genomic selection (GS). This study evaluated 11 subsets of 4932 SNPs using six genetic additive methods to understand marker density in GS prediction in alfalfa (Medicago sativa L.). In the GS methods, the effect of “training” to “test” population size was also evaluated. Fourteen alfalfa populations sampled from long-term grazing sites were genotyped using genotyping by sequencing for the identification of SNPs. These populations were also phenotyped for six agromorphological and three nutritive traits from 2018 to 2020. The accuracy of GS prediction improved across six GS methods when the ratio of “training” to “test” population size increased. However, the prediction accuracy of the six GS methods reduced to a range of −0.27 to 0.11 when random, uninformative SNPs were used. In this study, five Bayesian methods and ridge-regression best linear unbiased prediction (rrBLUP) method had similar GS accuracies for “training” sets, but rrBLUP tended to outperform Bayesian methods in independent “test” sets when SNP subsets with high mean-squared-estimated-marker effect were used. These findings can enhance the application of GS in alfalfa genetic improvement.