Diagnostics of Fusarium wilt in banana: Current status and challenges

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Diagnostics of Fusarium wilt in banana: Current status and challenges

This review highlights challenges in the detection of Fusarium wilt TR4 in banana through a critical assessment of published diagnostic methods and their validation in light of existing genetic diversity in pathogen populations.


Abstract

Global banana production is under threat from the rapidly spreading pathogen Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4), which is pathogenic to Cavendish and many other varieties. Due to the absence of effective control methods and the lack of other market-acceptable resistant cultivars, early diagnostics, containment and quarantine measures are important to limit further spread and impact of this pathogen. Early detection and identification of the pathogen require reliable diagnostic assays. The reliability of a molecular diagnostic assay is directly linked to the rigour applied at validating the assay according to predetermined standards. For specific detection of a target pathogen using molecular diagnostics, a well-resolved taxonomy of the target and related species based on their evolutionary relationships is also required. The advent of sequence-based phylogenetic analysis has given rise to new insights regarding the taxonomic classification of Foc and provided proof for the polyphyletic origin of Foc races, complicating early and reliable detection of the pathogen. Although numerous diagnostic methods for Foc have been developed, choosing a rigorously validated and fit-for-purpose method for adoption is currently challenging as advantages and drawbacks for each assay are not always obvious or put into context with prior methodologies. This review compiles and critically dissects published methods that are reported to detect Foc to date and highlights their benefits and constraints to provide a valuable reference for diagnosticians, researchers and policy makers worldwide.

Volatile organic compounds as potential biomarkers of Cadophora luteo‐olivacea presence on kiwifruits

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Volatile organic compounds as potential biomarkers of Cadophora luteo-olivacea presence on kiwifruits

The results suggested that the volatile compounds are released during the early phase of the interaction between kiwifruit (host) and Cadophora luteo-olivacea (pathogen).


Abstract

Cadophora luteo-olivacea is the causal agent of the skin-pitting disease of kiwifruit, a syndrome that appears after 4–5 months of cold storage. However, it is assumed that the infection takes place in the field during fruit development. The present work takes into consideration the production of volatile organic compounds (VOCs) of Actinidia deliciosa ‘Hayward’ at different phenological phases as potential C. luteo-olivacea infection biomarkers. In vitro assays were conducted to gain knowledge on the effect of kiwifruit VOCs on pathogen conidial germination and mycelial growth. VOCs produced by kiwifruit either inoculated or not with C. luteo-olivacea were analysed at different phenological phases by SPME/GC–MS analysis. In particular, ethanol, o -xylene, d-limonene and acetic acid showed a significant increase in the presence of fungal inoculation. Ethanol and d-limonene were also detected as volatile metabolites of the pathogen. The effect of each compound (ethanol, o -xylene, d-limonene and acetic acid) was tested on the fungal conidial germination at different concentrations, showing a growth stimulation at lower amounts. These results show how the production of some VOCs can contribute to the knowledge of fruit–pathogen interaction in the field with the aim of developing future tools for early disease detection and consequent effective control.

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

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Abstract

Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

Genome‐wide SNP discovery and genotyping delineates potential QTLs underlying major yield‐attributing traits in buckwheat

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Abstract

Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker–trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.

Modelling the displacement and coexistence of clonal lineages of Phytophthora infestans through revisiting past outbreaks

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Modelling the displacement and coexistence of clonal lineages of Phytophthora infestans through revisiting past outbreaks

A simulation model with pathogenesis parameters as inputs was developed to predict the changes in lineage proportions of Phytophthora infestans on potato and tomato crops.


Abstract

The continuous changes in the lineage proportions of populations in the clonal plant pathogen Phytophthora infestans on potato and tomato crops have been perplexing to researchers and disease managers. Sudden outbreaks of newly emergent genotypes are often associated with these rapid composition changes. Modelling can predict the persistence and displacement of pathogen genotypes with differential fitness among hosts. Building upon previous models, we combined analytical and simulation methods to model the outcome of interactions between competing lineages on different hosts. Model inputs include pathogenesis parameters, and the outputs are fitness and lineage proportions within each host. Analytical solutions yielding complete displacement, partial coexistence-displacement and complete coexistence were described. In a retrospective study, the lesion growth rate and sporulation density of P. infestans lineages on potato and tomato from pathogenicity trials were used as inputs. Output lineage frequencies were compared with historical epidemiological situations to check model accuracy. The results showed that pathogenesis traits measured from empirical trials could simulate lineage constituents on potato and tomato and estimate genotypic fitness with reasonable accuracy. The model also showed promise in predicting ongoing lineage displacements in the subsequent year or few years, even when the displaced lineage was still highly prevalent during the time of isolation. However, large uncertainties remain at temporal–spatial scales owing to complex meta-population dynamics in some regions and adaptation to local environmental factors. This simulation model provides a new tool for forecasting pathogen compositions and can be used to identify potentially problematic genotypes based on pathogen life-history traits.

Unveiling mechanisms for induced systemic resistance, resistance breeding and molecular marker‐assisted breeding against Phomopsis blight of Solanum melongena

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Unveiling mechanisms for induced systemic resistance, resistance breeding and molecular marker-assisted breeding against Phomopsis blight of Solanum melongena

This paper reviews resistance in eggplant (brinjal) cultivars against Phomopsis vexans via heterosis breeding, induced resistance, grafting and marker-assisted techniques.


Abstract

Phomopsis vexans is one of the most destructive fungal pathogens associated with eggplant and currently poses a significant threat to eggplant production worldwide. The detrimental impact of P. vexans on eggplant yield has been extensively explored by various mycologists who have conducted thorough studies on the diversity, pathology and biological aspects of the pathogen. However, achieving enduring resistance or effective management has proven to be a challenge thus far. PCR-based detection and molecular association of Phomopsis resistance use molecular markers to examine the potential for heterosis in various crosses, aiming for premium hybrids with genetic resistance and high-yielding capabilities. The latest genome sequencing methods and availability of a wider range of genetic diversity has enabled the breeding of resistant varieties of eggplant. This review provides a detailed description on P. vexans including its epidemiology, dispersal methods, symptomology, colony characteristics, taxonomy and evolution of its strains. Different resistance breeding techniques including heterosis breeding, host plant resistance, identification of resistant sources, inheritance pattern for Phomopsis resistance, importance of grafting to impart resistance, significance of induced resistance, PCR-based detection and molecular association of Phomopsis resistance are explained. Future approaches include molecular marker techniques such as genome-wide association studies, sequence-characterized amplified regions (SCAR), role of biotic inducers, pathogenesis-related proteins and plant growth-promoting rhizobacteria against Phomopsis blight of eggplant.

Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

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Abstract

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.

First insights into the quantitative genetic composition of the female seed yield for an efficient hybrid seed production in wheat (Triticum aestivum L.)

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Abstract

Hybrid breeding of wheat (Triticum aestivum L.) is limited by its self-pollinating nature. Past cross-pollination improvements mostly focused on optimizing male traits. We tested the hybrid seed yield of 100 diverse elite lines treated with a chemical hybridization agent (CHA) and pollinated by non-sterilized male plants in multi-environmental field trials. Plant height and phenological traits of female plants were also assessed. In parallel, control experiments without CHA sterilization were conducted to measure per se yield of the tested material. Hybrid seed yield variation is of quantitative genetic nature, and, despite the large environmental influence, this trait has a strong genotypic component and is highly heritable (h 2 = .77). The lack of correlation between hybrid seed yield and per se yield suggests a non-shared genetic control. Phenological traits and their interactions are important factors explaining together ~1/3 of hybrid seed yield variation. In contrast to plant height and flowering traits, which are influenced by major genetic factors, no significant marker–trait associations were found for the hybrid seed yield, thus suggesting a highly polygenic genetic architecture and the need of larger populations to investigate female hybrid seed yield.

Control of crown rot with potassium carbonate in banana cv. Enano Gigante

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Control of crown rot with potassium carbonate in banana cv. Enano Gigante

Incidence of banana postharvest crown rot caused by artificial infection with Colletotrichum musae can be reduced by 91.6% with treatments of potassium carbonate, a ‘generally recognized as safe’ (GRAS) substance, at 175 mM.


Abstract

The postharvest antifungal activity of potassium carbonate (PC) against crown rot (CR) was investigated in banana cv. Enano Gigante by artificially inoculating with Colletotrichum musae (Cm) and incubating at 25 ± 1°C for 7 days. PC treatments were tested by in vitro and in vivo primary experiments. The in vivo preliminary concentration of 175 mM PC was selected as the most effective and was used in subsequent experiments on the influence of dip temperature on the effectiveness of PC. Curative dip treatments of 175 mM PC at 40°C for 20 min applied alone or combined with low doses of thiabendazole (TBZ) were evaluated on CR. Finally, the effect of PC on banana fruit quality was determined. PC at 150 and 200 mM totally inhibited mycelial growth and conidial germination of Cm. In in vivo primary experiments, 175 mM PC significantly reduced both the incidence (33.3% reduction) and the severity (90.5% reduction) of CR, but only in curative treatments. When the 175 mM PC dip for 20 min was tested at different temperatures, the curative dip at 40°C was the most effective, reducing CR incidence and severity by 91.6% and 98.8%, respectively, and was used for subsequent experiments. PC combined with TBZ at 225 μL L−1 did not improve the curative control effectiveness on CR compared to PC alone. PC did not affect the quality of banana fruit.