Category Archives: ORIGINAL ARTICLE

Sensitivity of dominant UK Phytophthora infestans genotypes to a range of fungicide active ingredients

Posted on 13 March 2024 by nJames S. Lynott, nDavid E. L. Cooke, nLouise Sullivan, nAlison K. Leesn

Dominant UK Phytophthora infestans genotypes (EU6, EU36 and EU37) were tested for sensitivity to seven fungicide active ingredients (2019–22). EU37 isolates were insensitive to fluazinam; no insensitivity to other fungicides was found.

Abstract

Late blight, caused by Phytophthora infestans, is a serious disease of potatoes worldwide and is predominantly controlled by repeated prophylactic use of fungicides throughout the growing season. Effective blight management and integrated pest management strategies rely on knowledge of the efficacy of available fungicides to control contemporary genotypes of P. infestans. Between 2019 and 2022, representative isolates of the newer dominant genotypes EU36, EU37 and the older dominant genotype EU6 were sampled from GB crops and tested for sensitivity to seven commonly used fungicide active ingredients (cyazofamid, fluopicolide, mandipropamid, propamocarb, oxathiapiprolin, amisulbrom and mancozeb) used preventatively in detached leaf tests and zoospore motility assays where appropriate. Dose–response curves based on lesion area (mm²) were constructed, and EC₅₀ values calculated. Isolates of P. infestans genotype EU37 were insensitive to fluazinam as previously reported. No insensitivity, or progression towards resistance over time, to any of the other fungicides was observed in any isolates of the genotypes tested, and EC₅₀ values were generally in line with previous testing. Zoospore motility tests with fluopicolide revealed significantly higher MIC values for isolates of genotype EU36 compared with EU37 and EU6, which, whilst not indicative of resistance at the low concentrations of active ingredient tested, may be a factor contributing to the overall dominance of that genotype in the wider population of P. infestans. The evidence suggests that the fungicides tested, with the exception of fluazinam and EU37, are effective for the control of P. infestans genotypes dominant in the GB population up until 2022.

The length of the 3′ UTR of the tomato torrado virus (ToTV) RNA1 affects virus accumulation in Solanum lycopersicum during mechanical passages from plant to plant

Posted on 13 March 2024 by

ToTV-Kra defective genomes with truncated 3′ untranslated region of RNA1 are infectious. Changes in RNA1 length affect viral replication and sap transmission and may have arisen spontaneously or as an adaptation to the mode of viral transmission.

Abstract

Tomato torrado virus (ToTV), a member of the Torradovirus genus, primarily infects tomatoes. Previous analyses revealed high heterogeneity in the 3′ untranslated region (3′ UTR) of RNA1 of isolate ToTV-Kra. In addition to the full-length 3′ UTR RNA1 (a wild-type, wt), four truncated versions (var2, var3, var4 and var5) were identified. Here, we investigated the biological importance of this phenomenon by assessing whether such defective genomes are infectious individually, and how the length of the 3′ UTR influences disease symptoms, virus transmission and viral RNA accumulation. Using the ToTV_pJL-Kra infectious clone, we introduced deletions corresponding to the known RNA1 defective variants and examined their impact on ToTV virulence and sap transmission ability. Viral RNA accumulation was assessed in agroinfiltrated tomatoes, as well as during serial passages. We found that all defective genomes were infectious and the length of the 3′ UTR of RNA1 influenced viral RNA accumulation. Tomatoes agroinfiltrated with var2, var3 or var5 showed the highest copy numbers of genomic RNAs. However, during serial passages, ToTV_pJL-Kra-var1 and -var2 (six nucleotides shorter) showed limited sap transmission ability compared to the other variants, which persisted and replicated well in tomatoes. Plants treated with ToTV_pJL-Kra-var3, -var4 and a mixture of var1–var5 showed the highest viral RNA accumulation, which was not associated with increased symptom severity in comparison to the other variants. Additionally, we identified a further sequence insertion in the 3′ UTR of var3 RNA1. This insertion could have occurred spontaneously or as a result of virus adaptation to the mode of transmission.

Comparative omics analysis for novel target discovery in plant pathogens: A case study for Magnaporthe oryzae

Posted on 13 March 2024 by

A novel strategy, integrating omics and bioinformatics, identifies distinct fungal pathways, revealing a promising target for precision fungicides against Magnaporthe oryzae, causing rice blast disease.

Abstract

The central concern surrounding chemical pesticide application is its potential adverse effects on non-target organisms. For fungal pathogens, the search for specific targets has been complicated by the similarities in pathways shared between these pathogens and humans. We present a comprehensive strategy, integrating comparative omics and bioinformatics, to pinpoint precise targets for fungicides effective against the fungal pathogen Magnaporthe oryzae, responsible for rice blast disease. Our approach involves subtractive metabolic pathways, homology screening and target prioritization. Through subtractive metabolic analysis, we identified three unique M. oryzae pathways, distinct from human and rice. Nonredundant protein sequences were subsequently subjected to BLASTP screening against human and rice, as well as other databases from diverse organisms. Target subcellular localization was predicted using eight tools, including artificial intelligence and a deep-learning method. A comprehensive examination of biological processes was conducted, including gene expression, protein–protein interactions, network enrichment, broad-spectrum activity and physicochemical analysis. Glutamate 5-kinase emerged as the prime candidate for targeted fungicide development, promising progress in precision-oriented solutions.

Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon

Posted on 10 March 2024 by nDennis N. Katuuramu, nAmnon Levi, nWilliam P. Wechtern

Abstract

Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.

Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba

Posted on 10 March 2024 by

Abstract

4-Coumarate-CoA ligase (4CL) gene plays vital roles in plant growth and development, especially the regulation of lignin metabolism and flavonoid synthesis. To investigate the potential function of 4CL in the lignin biosynthesis of Ginkgo biloba, this study identified two 4CL genes, Gb4CL1 and Gb4CL2, from G. biloba genome. Based on the phylogenetic tree analysis, Gb4CL1 and Gb4CL2 protein were classified into Class I, which has been confirmed to be involved in lignin biosynthesis. Therefore, it can be inferred that these two genes may also participate in lignin metabolism. The tissue-specific expression patterns of these two genes revealed that Gb4CL1 was highly expressed in microstrobilus, whereas Gb4CL2 was abundant in immature leaves. The onion transient expression assay indicated that Gb4CL1 was predominantly localized in the nucleus, indicating its potential involvement in nuclear functions, while Gb4CL2 was observed in the cell wall, suggesting its role in cell wall-related processes. Phytohormone response analysis revealed that the expression of both genes was upregulated in response to indole acetic acid, while methyl jasmonate suppressed it, gibberellin exhibited opposite effects on these genes. Furthermore, Gb4CL1 and Gb4CL2 expressed in all tissues containing lignin that showed a positive correlation with lignin content. Thus, these findings suggest that Gb4CL1 and Gb4CL2 are likely involved in lignin biosynthesis. Gb4CL1 and Gb4CL2 target proteins were successfully induced in Escherichia coli BL21 with molecular weights of 85.5 and 89.2 kDa, proving the integrity of target proteins. Our findings provided a basis for revealing that Gb4CL participated in lignin synthesis in G. biloba.

Mining exotic germplasm for genetic improvement of protein quantity and quality in soybean (Glycine max)

Posted on 6 March 2024 by nRenan Souza, nBlair Buckley, nM. A. Rouf Mian, nZenglu Lin

Abstract

Soybean meal is the main protein source for animal feed, but it has low content of the essential amino acids cysteine (Cys) and methionine (Met). In this research, an exotic germplasm (PI 399000) was crossed with ‘Woodruff’ to develop an F₅-derived recombinant inbred line (RIL) population for mapping quantitative trait loci for seed composition. The population was grown in six environments, and protein, oil, Cys, and Met were determined with near-infrared spectroscopy. RILs were genotyped with the SoySNP6K BeadChip, and 1865 SNPs were used for analysis. QTL analysis identified three loci on chromosomes (Chrs) 6, 15 and 17 in at least five environments for protein; two QTLs on Chrs 14 and 17 in all environments for oil; three QTLs on Chrs 3, 6 and 10 for Cys and Met in at least three environments; and two QTLs for seed size on Chrs 17 and 20 in all environments. Stacking of protein and Cys + Met QTLs can increase both traits simultaneously, and 13 breeding lines were identified with improved seed composition. The markers linked to the QTLs can be used to assist the development of cultivars with improved meal quality.

Selective autophagy receptor‐encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection

Posted on 6 March 2024 by nValeriy K. Vishnichenkon

Shallot homologues of Nicotiana benthamiana and Oryza sativa P3IP selective autophagy receptors (SARs) have the ability to bind the shallot virus X p11 movement protein and initiate its autophagic degradation, thus carrying dual function as SAR and negative regulators of programmed cell death.

Abstract

Plant host tolerance is a key plant defence response to parasites, including viruses. This complex genetic trait involves multiple molecular mechanisms and, in particular, selective autophagy. Experimental data on the role of various selective autophagy factors and, in particular, cargo receptors in plant tolerance to viral infection are extremely limited. In this communication, I present the results of in silico identification of sequences in the shallot transcriptome encoding homologues of several selective autophagy receptors (SARs) related to the immune response and their expression patterns in response to asymptomatic infection of shallot virus X, a member of the genus Allexivirus, subgenus Acarallexivirus, within the family Alphaflexiviridae. The results obtained, together with the relevant literature data, suggest that some SARs likely to be involved in the regulation of the unfolded protein response and programmed cell death may play an active role in the formation of the state of tolerance of the host plant to allexivirus infection.

Meiotic pairing and morphological and yield characterisation of three advanced lines of hexaploid tritordeum (×Tritordeum martini)

Posted on 5 March 2024 by nAna Carvalho, nJosé Lima‐Briton

Abstract

Hexaploid tritordeum [×Tritordeum martinii A. Pujadas (Poaceae) nothosp. nov.; H^chH^chAABB] resulted from crosses between wild barley (Hordeum chilense Roem et. Schultz) and durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.]. Tritordeum (HT) presents interesting agronomic traits that can be transferred to cultivated wheat. Through the years, several HT lines were developed and characterised. Genomic stability and fertility are expected for advanced HT lines with multiple self-fertilisation generations. In this work, we analysed the meiotic chromosomal pairing in pollen mother cells (PMCs) of three advanced lines of hexaploid tritordeum (HT9, HT31 and HT67) after fluorescence in situ hybridisation (FISH) performed with genomic DNA from H. chilense and the bread wheat cloned rDNA sequence, pTa71, as probes, and characterised nine morphological and yield-related traits for three consecutive years in adult plants. As expected, all HT lines showed regular meiotic chromosomal pairing, ensuring plant fertility as previously confirmed by the characterisation of morphological and yield-related traits in adult plants of preceding generations. Globally, tritordeum is interesting for wheat breeding and has potential as an alternative crop.

Identification and pathogenicity of Colletotrichum species associated with twig dieback of citrus in Western Australia

Posted on 4 March 2024 by

Citrus twig dieback in Western Australia was shown to be caused by Colletotrichum gloeosporioides, C. karstii and C. novae-zelandiae.

Abstract

Up to 32 Colletotrichum species have been reported to be associated with pre- or postharvest diseases of citrus globally, while in Australia, six species have been reported to cause citrus leaf and fruit disease. Twig or shoot dieback has recently been observed as an emerging disease in citrus orchards in Western Australia. Colletotrichum species were isolated from diseased twigs showing dieback (withertip) or lesions, with or without gummosis, collected from 12 varieties of orange, mandarin and lemon. Colletotrichum gloeosporioides sensu stricto, Colletotrichum karstii and Colletotrichum novae-zelandiae were identified using a polyphasic approach that included multigene phylogenetic analysis using sequences of internal transcribed spacer and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (gapdh), β-tubulin (tub2), actin (act) and histone (his3) for isolates in the boninense species complex, and Apn2–Mat1–2 intergenic spacer and partial mating type (Mat1–2) (ApMat) and glutamine synthetase (gs) for isolates in the gloeosporioides species complex, as well as morphological characteristics. C. gloeosporioides was the most prevalent species associated with twig dieback in Western Australia, while C. novae-zelandiae was reported for the first time in Australia. Pathogenicity tests on shoot twigs from lemon and orange trees confirmed C. gloeosporioides, C. karstii and C. novae-zelandiae as the cause of twig dieback, with C. gloeosporioides being the most aggressive species. Knowledge of the species causing twig dieback and their lifestyle will assist the development of integrated control methods.

Comparative genomics identifies genetic markers linked to structural variations that differentiate Puccinia graminis tritici and secalis formae speciales

Posted on 29 February 2024 by

Newly available genome sequence data were harnessed to design four simple PCR-based assays able to distinguish Puccina graminis formae speciales.

Abstract

Stem rust is a serious disease of many gramineous plants including small grain staples such as wheat, barley, rye and triticale. Separate formae speciales (ff. spp.) of the causal fungus, Puccinia graminis, predominantly infect certain host plant genera. However, despite these taxonomic subdivisions, many P. graminis ff. spp. are genetically too similar to distinguish using existing genetic markers. For those infecting cereals, this is particularly challenging for P. graminis f. sp. tritici (Pgt) and P. graminis f. sp. secalis (Pgs). Herein we harnessed newly available genomic data for 39 Pgt and Pgs isolates and identified four regions of structural variation that were used to design four simple PCR-based assays to distinguish the aforementioned formae speciales. These genomic regions display large presence/absence variation between Pgt and Pgs isolates, and yet a high degree of sequence conservation within shared neighbouring regions, facilitating primer design. We also confirmed lack of amplification in host plant genera analysed, which included assessment of the shared alternate host of Pgt and Pgs, Berberis vulgaris. Accurate classification of P. graminis ff. spp. infections on B. vulgaris is exceptionally valuable to rapidly define plants harbouring P. graminis inoculum when adjacent to cereal crops. Finally, we demonstrated utility of these four genetic markers to correctly distinguish a genetically diverse array of Pgt and Pgs isolates. This strategy could now be readily applied to other pathogens of interest, which will be of increasing value as genomic resources continue to rapidly expand for many key biotic threats to agricultural productivity.