The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

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Abstract

MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

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Abstract

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

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Abstract

Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast-cooking and slow-cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant-seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast- and slow-cooking beans due to soaking. Candidate genes identified in the slow-cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall-strengthening enzymes in the slow-cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.

Breast cancer diagnosis and management guided by data augmentation, utilizing an integrated framework of SHAP and random augmentation

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Breast cancer diagnosis and management guided by data augmentation, utilizing an integrated framework of SHAP and random augmentation

The use of SHAP for feature engineering alongside random augmentation for data balancing for the diagnosis of breast cancer (BC) proposed some management strategies for BC before and after diagnosis Developed models that could help in the diagnosis of BC by prediction using various machine learning algorithms.


Abstract

Recent research indicates that early detection of breast cancer (BC) is critical in achieving favorable treatment outcomes and reducing the mortality rate associated with it. With the difficulty in obtaining a balanced dataset that is primarily sourced for the diagnosis of the disease, many researchers have relied on data augmentation techniques, thereby having varying datasets with varying quality and results. The dataset we focused on in this study is crafted from SHapley Additive exPlanations (SHAP)-augmentation and random augmentation (RA) approaches to dealing with imbalanced data. This was carried out on the Wisconsin BC dataset and the effectiveness of this approach to the diagnosis of BC was checked using six machine-learning algorithms. RA synthetically generated some parts of the dataset while SHAP helped in assessing the quality of the attributes, which were selected and used for the training of the models. The result from our analysis shows that the performance of the models used generally increased to more than 3% for most of the models using the dataset obtained by the integration of SHAP and RA. Additionally, after diagnosis, it is important to focus on providing quality care to ensure the best possible outcomes for patients. The need for proper management of the disease state is crucial so as to reduce the recurrence of the disease and other associated complications. Thus the interpretability provided by SHAP enlightens the management strategies in this study focusing on the quality of care given to the patient and how timely the care is.

Occurrence of copper‐resistant Pseudomonas syringae pv. actinidiae strains in kiwifruit orchards of Central Italy

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Abstract

Bacterial isolates belonging to Pseudomonas syringae pv. actinidiae, the causal agent of kiwifruit bacterial canker, have been isolated, during 2021 and 2022, from Actinidia chinensis orchards of Central Italy planted with cultivars Hayward and Zespri G3®. A total of 23 isolates were obtained from twigs and leaves that showed the typical symptoms of bacterial canker, including leaf spotting and twig canker. All of them showed resistance to 1.2 mM copper sulphate added to mannitol–glutamate–yeast extract (MGY) medium. No other Pseudomonas syringae pv. actinidiae strains were isolated from the orchards. The P. s. pv. actinidiae strains that showed resistance to copper have the copA and copD genes that regulate the efflux of copper through the inner membrane and the copper sensor copS gene. They do not possess the cusABC complex that confers resistance to high concentration of copper. Representative copper-resistant strains were proven pathogenic to kiwifruit plants upon artificial inoculation. This is the first record of copper-resistant P. s. pv. actinidiae strains in Italy and, as far as we know, in Europe.

Transmission of Furcraea necrotic streak virus (FNSV) by Olpidium virulentus

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Transmission of Furcraea necrotic streak virus (FNSV) by Olpidium virulentus

Fique plants are source of natural fibre. Furcraea necrotic streak virus (FNSV) causes the most detrimental disease in fique plants, affecting fibre production, and is transmitted by Olpidium virulentus.


Abstract

Furcraea necrotic streak virus (FNSV) is the causative agent of necrotic streak disease, also known as macana in fique crops (Furcraea spp.) resulting in damage to leaf fibres and economic losses. The rhizospheric fungus Olpidium spp. is present in the roots of affected plants and may play a role in the disease transmission. FNSV infection and the role of fungi were examined in macanavirus-diseased plants in Colombia. Spherical, and icosahedral (24.7 ± 1.98 nm), non-enveloped virions with a granular surface were isolated from field fique plants showing signs of macana disease, and the viral genome was completely sequenced. Taxonomic status was assigned through sequence analysis (Macanavirus genus in Tombusviridae family). The variability of the virus pangenome was evaluated in diseased fique plants from ecologically different Andean regions that showed low gene flow. Olpidium virulentus zoospores, identified by internal transcribed spacer (ITS) sequencing and microscopic analysis, were associated with viral particles and resting spores in diseased fique roots. An in vitro virion–zoospore binding assay showed that FNSV and O. virulentus zoospores interacted. Transmission assays in lettuce (Lactuca sativa), a model plant used to study this virus, showed 100% infection when a preincubated mixture of zoospores and FNSV was added to roots, whereas only 33% infection occurred when FNSV was added alone. This demonstrated the ability of O. virulentus to act as a vector for FNSV, potentially enhancing viral transmissibility in field fique crops. This is the first report of FNSV being transmitted by O. virulentus, a rhizosphere fungus.

Damage on grapevine cv. Niagara Rosada leaves caused by the combined effect of temperature and Asian grapevine leaf rust (Neophysopella tropicalis)

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Damage on grapevine cv. Niagara Rosada leaves caused by the combined effect of temperature and Asian grapevine leaf rust (Neophysopella tropicalis)

Inoculated plants kept at 30°C presented cell alterations that blocked colonization, reducing lesion density and severity. However, accelerated leaf senescence due to temperature raise may increase leaf damage and reduce yield.


Abstract

Asian grapevine leaf rust (AGLR), caused by Neophysopella tropicalis, is a problem for viticulture, especially in latitudes lower than 25° S, which include the most significant production regions in Brazil. Climate change has raised new concerns in agriculture as temperature can affect the resistance of plants to pathogens. With the aim of understanding how air temperature rise affects the AGLR pathosystem, measurements of leaf gas exchange and epidemiological and histopathological analyses were carried out on control and inoculated leaves of Vitis labrusca ‘Niagara Rosada’ grown at 25°C and 30°C. The lesion density and rust severity were higher at 25°C than 30°C, and the ratio between adaxial surface necrosis and the abaxial surface area occupied by pustules was >1 only at 30°C, presenting a necrosis not associated to the pathogen lesion. In fact, leaf necrosis was identified on control plants kept at 30°C and associated with gerontoplasts, representing accelerated leaf senescence. The AGLR pathogen reduced gas exchange and photosystem II activities at 25°C, with no difference between control and inoculated plants at 30°C. Our results indicate that AGLR is sensitive to increasing air temperature. However, the accelerated leaf senescence caused by the combination of N. tropicalis infection and temperature on Niagara Rosada can lead to high leaf damage.

Double trouble: Co‐infection of potato with the causal agents of late and early blight

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Double trouble: Co-infection of potato with the causal agents of late and early blight

Alternaria solani directly inhibits Phytophthora infestans growth in vitro and co-inoculation of potato with both pathogens favours A. solani, even when P. infestans arrives first/simultaneously.


Abstract

Global potato production is plagued by multiple pathogens, amongst which are Phytophthora infestans and Alternaria solani, the causal agents of potato late blight and early blight, respectively. Both these pathogens have different lifestyles and are successful pathogens of potato, but despite observations of both pathogens infecting potato simultaneously in field conditions, the tripartite interactions between potato and these two pathogens are so far poorly understood. Here we studied the interaction of A. solani and P. infestans first in vitro and subsequently in planta both in laboratory and field settings. We found that A. solani can inhibit P. infestans in terms of growth in vitro and also infection of potato in both laboratory experiments and in an agriculturally relevant field setting. A. solani had a direct inhibitory effect on P. infestans in vitro and compounds secreted by A. solani had both an inhibitory and disruptive effect on sporangia and mycelium of P. infestans in vitro. In planta infection bioassays revealed that simultaneous co-inoculation of both pathogens resulted in larger necrotic lesions than single inoculations; however, consecutive inoculations only resulted in larger lesions when A. solani was inoculated after P. infestans. These results indicate that the order in which these pathogens attempt to colonize potato is important for the disease outcome and that the influence of plant pathogens on each other should be accounted for in the design of future disease control strategies in crops such as potato.

Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

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Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

Genome sequence of 123 global Venturia isolates shows genetic diversity and population structure but does not find population genetic differentiation between North America and Europe/central Asia due to geographic separation.


Abstract

Venturia inaequalis, the causal fungal pathogen of apple scab, has evolved with its Malus hosts during apple domestication. This co-evolution has resulted in a genetic structure in V. inaequalis populations from Europe and central Asia based on host species and geographic isolation. However, it is not yet clear if geographic isolation has led to population differentiation in North American isolates. We resequenced the genomes of 54 V. inaequalis isolates from North America and analysed them with publicly available genome sequences of 90 European and central Asian isolates for variant discovery and population structure. A total of 204,566 high-quality single-nucleotide polymorphisms (SNPs) were identified and used to assess population genetic structure and genomic diversity across 123 Venturia spp. isolates from around the world. Population genetic analysis identified four clusters based on Malus and non-Malus hosts and Venturia species; this differentiation was supported by genetic diversity parameters including F ST, Nei's π and Tajima's D. Genetic structure analysis did not reveal a distinct subpopulation of North American V. inaequalis isolates within the global isolates. Additionally, structure was not observed in V. inaequalis isolates collected on M. × domestica between North America and Europe. These observations indicate that geographical isolation has not contributed to the population differentiation between North America and Europe/central Asia. These results will enhance our understanding of the evolution of V. inaequalis, the emergence of virulent isolates and their implications for managing apple scab effectively.