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This dataset was created to investigate the impact of data collection modes and pre-processing techniques on the quality of free comment data related to consumers' sensory perceptions. A total of 200 consumers were recruited and divided into two groups of 100. Each group evaluated six madeleine samples (five distinct samples and one replicate) in a sensory analysis laboratory, using different free comment data collection modes. Consumers in the first group provided only words or short expressions, while those in the second group used complete sentences. Additionally, participants reported their liking for each sample. The collected data provided valuable insights into the effectiveness of the free comment method in sensory evaluation of food products. They emphasized the importance of data pre-processing and demonstrated how the chosen techniques can impact the quality of the results. The dataset is based on real-world consumer data, showcasing how individuals naturally express their subjective perceptions. It features descriptions that reflect authentic consumer language, including informal expressions, incorrect phrasing, spelling errors, and unstructured sentences. This raw textual data has been annotated and translated into English. The dataset can therefore be repurposed to assess and compare the performance of different text mining, natural language processing and sentiment analysis algorithms in both French and English, as well as to drive innovations in AI tools for sensory and consumer research., (© 2024 The Authors.)

Tomato (Solanum lycopersicum L.) is an economically important vegetable susceptible to various fungal diseases, including leaf spot caused by Alternaria spp. from the section Alternaria. In our study, a total of 72 tomato-associated Alternaria spp. strains from Latvia, Lithuania, Estonia, and Algeria were analysed by integrating morphological data, pathogenicity assay, multi-locus phylogeny, and haplotype assignment. Recovered Alternaria spp. strains were characterized by considerable variation in phenotypic diversity, non-pathogenicity to their host of origin and absence of the AAL-toxin biosynthesis gene (ALT1). Multi-locus phylogeny of the RNA polymerase II second largest subunit (rpb2), putative F-box-domain-containing protein (ASA-10), and putative histone-like transcription factor (ASA-19) confirmed the occurrence of both A. alternata and A. arborescens species complexes along with A. longipes and A. postmessia on symptomatic tomatoes. The discordant tree topology among single-gene phylogenies suggested the occurrence of potential recombination between phylogenetic lineages in the section Alternaria, resulting in putative alternata-arborescens and alternata-longipes hybrids. DNA polymorphism analysis of the rpb2, ASA-10, and ASA-19 loci revealed a high level of genetic diversity in the section Alternaria, and the number of single nucleotide polymorphisms (SNPs) and haplotypes varied among loci and lineages studied. A total of 16 and 6 multi-locus haplotypes were assigned in alternata and arborescens lineages, respectively. Global genetic diversity analysis of A. alternata and A. arborescens strains at the rpb2 locus confirmed that major haplotypes described from tomatoes were shared among other hosts of origin., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Plant microbiota appear more and more as potential sources of antagonistic microorganisms. However, the seed microbiota associated with wild plant species has rarely been explored. To identify fungal antagonists to the seed-borne pathogen Alternaria brassicicola , seeds were collected in natural populations of three Brassicaceae species, Arabidopsis thaliana , Capsella bursa-pastoris and Draba verna . A large number of fungal strains reduced the growth of A. brassicicola . The most antagonistic strains belonged to Alternaria , Apiospora , Trichoderma and Aspergillus . Seed-associated fungi tolerated host plant defenses and exhibited lower sensitivity compared to A. brassicicola to indolic compounds such as the phytoalexin camalexin and the glucosinolates (GLS)-breakdown compound indole-3-carbinol. By contrast, antagonistic strains were as inhibited as A. brassicicola in presence of allyl-isothiocyanates (ITC) derived from aliphatic GLS, and more inhibited by benzyl-ITC derived from aromatic GLS. However, all defense compounds could enhance the antagonistic effects of some of the isolated strains on A. brassicicola . The observed potential synergistic effects between defense compounds and seed-associated antagonistic strains emphasize the need for further studies to elucidate the molecular bases of the interactions. A better understanding of the interactions between host plants, pathogens and fungal endophytes is also needed to develop sustainable biocontrol strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lerenard, Aligon, Berruyer, Poupard and Le Corff.)

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices., (© 2023 John Wiley & Sons Ltd.)

In addition to absorbing nitrogen from the soil, legumes have the ability to use atmospheric N 2 through symbiotic nitrogen fixation. Therefore, legumes have developed mechanisms regulating nodulation in response to the amount of nitrate in the soil; in the presence of high nitrate concentrations, nodulation is inhibited, while low nitrate concentrations stimulate nodulation and nitrogen fixation. This allows the legumes to switch from soil nitrogen acquisition to symbiotic nitrogen fixation. Recently, particular interest has been given to the nitrate transporters, such as Nitrate Transporter1/Peptide transporter Family (NPF) and Nitrate Transporter 2 (NRT2), having a role in the functioning of nodules. Nitrate transporters of the two model plants, Lotus japonicus and Medicago truncatula , shown to have a positive and/or a negative role in nodule functioning depending on nitrate concentration, are presented in this article. In particular, the following transporters were thoroughly studied: (i) members of NPF transporters family, such as LjNPF8.6 and LjNPF3.1 in L. japonicus and MtNPF1.7 and MtNPF7.6 in M. truncatula , and (ii) members of NRT2 transporters family, such as LjNRT2.4 and LjNRT2.1 in L. japonicus and MtNRT2.1 in M. truncatula . Also, by exploiting available genomic and transcriptomic data in the literature, we have identified the complete PsNPF family in Pisum sativum (69 sequences previously described and 21 new that we have annotated) and putative nitrate transporters candidate for playing a role in nodule functioning in P. sativum .

The proliferation of wireless and other telecommunications equipment brought about by technological advances in the communication industry has substantially increased the radiofrequency radiation levels in the environment. The emphasis is, therefore, placed on investigating the potential impacts of radiofrequency radiation on biota. In this work, the impact of 2850 MHz electromagnetic field radiation (EMF-r) on early development, photosynthetic pigments, and the metabolic profile of two Brassica oleracea L. cultivars (red and green cabbage) was studied. On a daily basis for seven days, seedlings were exposed to homogeneous EMF-r for one, two, and four hours, and observations were carried out at 0-h, 1-h, and 24-h following the final dose. Irrespective of the duration of harvest, exposure to EMF-r resulted in a dose-dependent reduction in both root (from 6.3 cm to 4.0 cm in red; 6.1 cm to 3.8 cm in green) and shoot lengths (from 5.3 cm to ⁓3.1 cm in red; 5.1 cm to 3.1 cm in green), as well as a decrease in biomass (from 2.9 mg to ⁓1.1 mg in red; 2.5 to 0.9 mg in green) of the seedlings when compared to control samples. Likewise, the chlorophyll (from 6.09 to ⁓4.94 mg g -1 d.wt in red; 7.37 to 6.05 mg g -1 d.wt. in green) and carotenoid (from 1.49 to 1.19 mg g -1 d.wt. in red; 1.14 to 0.51 mg g -1 d.wt. in green) contents of both cultivars decreased significantly when compared to the control. Additionally, the contents of phenolic (28.99‒45.52 mg GAE g -1 in red; 25.49‒33.76 mg GAE g -1 in green), flavonoid (21.7‒31.8 mg QE g -1 in red; 12.1‒19.0 mg QE g -1 in green), and anthocyanin (28.8‒43.6 mg per 100 g d.wt. in red; 1.1‒2.6 mg per 100 g d.wt. in green) in both red and green cabbage increased with exposure duration. EMF-r produced oxidative stress in the exposed samples of both cabbage cultivars, as demonstrated by dose-dependent increases in the total antioxidant activity (1.33‒2.58 mM AAE in red; 1.29‒2.22 mM AAE in green), DPPH activity (12.96‒78.33% in red; 9.62‒67.73% in green), H 2 O 2 content (20.0‒77.15 nM g -1 f.wt. in red; 14.28‒64.29 nM g -1 f.wt. in green), and MDA content (0.20‒0.61 nM g -1 f.wt. in red; 0.18‒0.51 nM g -1 f.wt. in green) compared to their control counterparts. The activity of antioxidant enzymes, i.e., superoxide dismutases (3.83‒8.10 EU mg -1 protein in red; 4.19‒7.35 EU mg -1 protein in green), catalases (1.81‒7.44 EU mg -1 protein in red; 1.04‒6.24 EU mg -1 protein in green), and guaiacol peroxidases (14.37‒47.85 EU mg -1 protein in red; 12.30‒42.79 EU mg -1 protein in green), increased significantly compared to their control counterparts. The number of polyphenols in unexposed and EMF-r exposed samples of red cabbage was significantly different. The study concludes that exposure to 2850 MHz EMF-r affects the early development of cabbage seedlings, modifies their photosynthetic pigments, alters polyphenol content, and impairs their oxidative metabolism., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Depending on the questions to be answered, water flow in the xylem can be modelled following different approaches with varying spatial and temporal resolution. When focussing on the influence of hydraulic architecture upon flow dynamics, distribution of water potentials in a tree crown or questions of vulnerability of the hydraulic system, functional-structural plant models, which link representations of morphological structure with simulated processes and with a virtual environment, can be a promising tool. Such a model will then include a network of idealized xylem segments, each representing the conducting part of a stem or branch segment, and a numerical machinery suitable for solving a system of differential equations on it reflecting the hydrodynamic laws, which are the basis of the broadly accepted cohesion-tension theory of water flow in plants. We will discuss functional-structural plant models, the simplifications that are useful for hydraulic simulations within this framework, the deduction of the used differential equations from basic physical conservation laws, and their numerical solution, as well as additional necessary models of radiation, photosynthesis, and stomatal conductance. In some supplementary notes, we are shortly addressing some related questions, for example, about root systems or about the relation between macro-scale hydraulic parameters and fine-grained (anatomical) xylem structure., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Poor grain-filling initiation in inferior spikelets severely impedes rice yield improvement, while photo-assimilates from source leaves can greatly stimulate the initiation of inferior grain-filling (sink). To investigate the underlying mechanism of source-sink interaction, a two-year field experiment was conducted in 2019 and 2020 using two large-panicle rice cultivars (CJ03 and W1844). The treatments included intact panicles and partial spikelet removal. These two cultivars showed no significant difference in the number of spikelets per panicle. However, after removing spikelet, W1844 showed higher promotion on 1000-grain weight and seed-setting rate than CJ03, particularly for inferior spikelets. The reason was that the better sink activity of W1844 led to a more effective initiation of inferior grain-filling compared to CJ03. The inferior grain weight of CJ03 and W1844 did not show a significant increase until 8 days poster anthesis (DPA), which follows a similar pattern to the accumulation of photo-assimilates in leaves. After removing spikelets, the source leaves of W1844 exhibited lower photosynthetic inhibition compared to CJ03, as well as stronger metabolism and transport of photo-assimilates. Although T6P levels remained constant in both cultivars under same conditions, the source leaves of W1844 showed notable downregulation of SnRK1 activity and upregulation of phytohormones (such as abscisic acid, cytokinins, and auxin) after removing spikelets. Hence, the high sink strength of inferior spikelets plays a role in triggering the enhancement of source strength in rice leaves, thereby fulfilling grain-filling initiation demands., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Blumeria graminis f. sp. tritici ( Bgt ) is an obligate biotrophic fungal pathogen responsible for powdery mildew in bread wheat ( Triticum aestivum ). Upon Bgt infection, the wheat plant activates basal defense mechanisms, namely PAMP-triggered immunity, in the leaves during the first few days. Understanding this early stage of quantitative resistance is crucial for developing new breeding tools and evaluating plant resistance inducers for sustainable agricultural practices. In this sense, we used a combination of transcriptomic and metabolomic approaches to analyze the early steps of the interaction between Bgt and the moderately susceptible wheat cultivar Pakito. Bgt infection resulted in an increasing expression of genes encoding pathogenesis-related (PR) proteins ( PR1 , PR4 , PR5 , and PR8 ) known to target the pathogen, during the first 48 h postinoculation. Moreover, RT-qPCR and metabolomic analyses pointed out the importance of the phenylpropanoid pathway in quantitative resistance against Bgt . Among metabolites linked to this pathway, hydroxycinnamic acid amides containing agmatine and putrescine as amine components accumulated from the second to the fourth day after inoculation. This suggests their involvement in quantitative resistance via cross-linking processes in cell walls for reinforcement, which is supported by the up-regulation of PAL (phenylalanine ammonia-lyase), PR15 (oxalate oxidase) and POX (peroxidase) after inoculation. Finally, pipecolic acid, which is considered a signal involved in systemic acquired resistance, accumulated after inoculation. These new insights lead to a better understanding of basal defense in wheat leaves after Bgt infection., Competing Interests: The author(s) declare no conflict of interest.

The presented RNAseq data were obtained from Arabidopsis seeds dry and 6h imbibed to describe, in wild-type and glucosinolate (GSL)-deficient genotypes, the response at the RNA level to nitrogen compounds, i.e ., potassium nitrate (KNO 3 , 10mM), potassium thiocyanate (KSCN, 8µM). The cyp79B2 cyp79B3 (cyp79B2/B3) double mutant deficient in Indole GSL, the myb28 myb29 (myb28/29) double mutant deficient in aliphatic GSL, the quadruple mutant cyp79B2 cyp79B3 myb28 myb29 (qko) deficient in total GSL in the seed and the WT reference genotype in Col-0 background were used for the transcriptomic analysis. Total ARN was extracted using NucleoSpin® RNA Plant and Fungi kit. Library construction and sequencing were performed with DNBseq™ technology at Beijing Genomics Institute. FastQC was used to check reads quality and mapping analysis were made using a quasi-mapping alignment from Salmon. Gene expression changes in mutant seeds compared to WT were calculated using DESeq2 algorithms. This comparison with the qko, cyp79B2/B3 and myb28/29 mutants made it possible to identify 30220, 36885 and 23807 differentially expressed genes (DEGs), respectively. Mapping rate result was merge into a single report using MultiQC; graphic results were illustrated through Veen diagrams and volcano plots. Fastq raw data and count files from 45 samples are available in the repository Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) and can be consulted with the data identification number GSE221567 at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221567., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Author(s).)

Alternaria leaf blight, caused by the fungus Alternaria dauci , is the most damaging foliar disease of carrot. Some carrot genotypes exhibit partial resistance to this pathogen and resistance Quantitative Trait Loci (rQTL) have been identified. Co-localization of metabolic QTL and rQTL identified camphene, α-pinene, α-bisabolene, β-cubebene, caryophyllene, germacrene D and α-humulene as terpenes potentially involved in carrot resistance against ALB. By combining genomic and transcriptomic analyses, we identified, under the co-localization regions, terpene-related genes which are differentially expressed between a resistant and a susceptible carrot genotype. These genes include five terpene synthases and twenty transcription factors. In addition, significant mycelial growth inhibition was observed in the presence of α-humulene and caryophyllene.

Phosphonate-based products have demonstrated diverse abilities to protect crops against pests, with various modes of action proposed. In this article, we specifically investigated potassium phosphonate (KHP) on apple crops. Its performance to control three major apple bioagressors ( Venturia inaequalis , Erwinia amylovora , and Dysaphis plantaginea ) was evaluated under semicontrolled conditions. The product was able to confer significant protection rates (40 to 75% for apple scab, 40% for fire blight, and 30% for rosy aphid), which can be explained by its more or less efficient biocidal activity against the three pests, and by its ability to induce apple immunity (pathogenesis-related proteins and secondary metabolites genes). A cumulative effect of treatments as well as the systemic behavior of the product was demonstrated. Fields trials against apple scab and the postharvest disease bull's eyes rot ( Neofabraea vagabunda ) were performed on different apple varieties by applying KHP combined with light pest management programs either reducing (dessert orchards) or suppressing (cider orchards) fungicide applications. KHP was able to reduce apple scab by 70 to 90% on shoots and young and harvested fruit, and bull's eyes rot by 70 to 90% on harvested fruit. Overall, our results indicate that KHP is useful for the protection of apple trees against its major pests by direct effect and by triggering the host defense system.

Phenylpropanoids and flavonoids are specialized metabolites frequently reported as involved in plant defense to biotic or abiotic stresses. Their biosynthetic accumulation may be constitutive and/or induced in response to external stimuli. They may participate in plant signaling driving plant defense responses, act as a physical or chemical barrier to prevent invasion, or as a direct toxic weapon against microbial or insect targets. Their protective action is described as the combinatory effect of their localization during the host's interaction with aggressors, their sustained availability, and the predominance of specific compounds or synergy with others. Their biosynthesis and regulation are partly deciphered; however, a lot of gaps in knowledge remain to be filled. Their mode of action on microorganisms and insects probably arises from an interference with important cellular machineries and structures, yet this is not fully understood for all type of pests and pathogens. We present here an overview of advances in the state of the art for both phenylpropanoids and flavonoids with the objective of paving the way for plant breeders looking for natural sources of resistance to improve plant varieties. Examples are provided for all types of microorganisms and insects that are targeted in crop protection. For this purpose, fields of phytopathology, phytochemistry, and human health were explored.

Many fungal pathogens are carried and transmitted by seeds. These pathogens affect germination and seed quality. Their transmission from the germinating seed to seedling causes many diseases in crops. Seed defense mechanisms during germination are poorly documented. RNA-seq experiments were used to describe the molecular mechanisms involved in seed interaction with a necrotrophic fungus. Here the Arabidopsis thaliana/Alternaria brassicicola pathosystem was used to perform dual-transcriptomic approach. Arabidopsis thaliana seeds and necrotrophic fungus transcripts were identified at critical germination and seedling establishment stages. Total RNA was extracted from healthy and infected germinating seeds and seedlings at 3, 6 and 10 days after sowing. Transcript libraries were made and sequenced, then fungal and plant short reads were mapped and quantified respectively against Arabidopsis thaliana and Alternaria brassicicola reference transcriptomes. This dual-transcriptomic approach revealed that 3409, 7506 and 8589 Arabidopsis thaliana genes showed a differential expression at respectevely 3, 6 and 10 days after sowing between healthy and infected seeds, including 1192 genes differentially expressed at the three studied stages. Moreover, in this experiement, we also identified the dynamic of the transcript changes occurring at the same stages in the necrotrophic fungus concomitantly during germination and seedling establishment., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors. Published by Elsevier Inc.)

Legumes are suitable for the development of sustainable agroecosystems because of their ability to use atmospheric N 2 through symbiotic nitrogen fixation (SNF). However, a basic NO 3 - input is necessary before SNF takes place to ensure successful seedling establishment. Since Rhizobia not only induce nodulation but also affect root branching by stimulating the development of lateral roots, and NO 3 - as a signal also modulates root system architecture, we investigated whether Rhizobium -derived signals interfere in nitrate signaling. Here, we bring evidence that (i) Rhizobium -altered NO 3 - -mediated processes in pea expressions of major players in NO 3 - transport, sensing, and signaling were affected, and (ii) the characteristic limitation of root foraging and branching in response to NO 3 - supply was abolished. The number of tertiary roots per secondary root was higher in infected compared to uninfected peas, thus indicating that the Rhizobium effect allows for favorable management of trade-offs between nodules growth for nitrogen capture and root foraging for water and other nutrient uptake in pea. The outcome of this basic research can be used to produce molecular tools for breeding pea genotypes able to develop deep-foraging and branched root systems, and more competitive architectures and molecular levels for soil NO 3 - absorption during seedling establishment without jeopardizing nodulation.

Plant architecture determines yield (fruit or flowers) and product quality in many horticultural species. It results from growth and branching processes and is dependent on genetic and environmental factors such as light quality. Highly significant genotype and light quality effects and their interaction have been demonstrated on the architecture of rose. Far-red (FR) light is known for its favourable effect on plant growth and development. We evaluated the effect of FR on rose growth and development and its interaction with the genotype through architectural, eco-physiological (net photosynthesis rate) and biochemical (sugar and hormone concentrations) approaches. Two cultivars ('The Fairy' - TF - and Knock Out ® Radrazz - KO) with contrasting architectures were grown in a climate chamber under FR or in the absence of FR at an average photosynthetic photon flux density (400-700 nm) of 181.7 ± 12.8 μmol m -2 s -1 for 16 h. A significant effect of FR on the architecture of TF was demonstrated, marked by greater stem elongation, shoot branching and flowering, while KO remained insensitive to FR, supporting a genotype x FR interaction. The response of TF to FR was associated with improved photosynthetic capabilities, while KO exhibited an elevated level of abscisic acid (ABA) in its leaves. FR-dependent ABA accumulation might inhibit photosynthesis and prevent the increased plant carbon status required for growth. From a practical perspective, these findings argue in favour of a better reasoning of the choice of the cultivars grown in lighted production systems. Further investigations will be necessary to better understand these genotype-specific responses to FR and to unravel their molecular determinants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Crespel, Le Bras, Amoroso, Dubuc, Citerne, Perez-Garcia and Sakr.)

The transmission of seed-borne pathogens by the germinating seed is responsible for major crop diseases. The immune responses of the seed facing biotic invaders are poorly documented so far. The Arabidopsis thaliana / Alternaria brassicicola patho-system was used to describe at the transcription level the responses of germinating seeds and young seedling stages to infection by the necrotrophic fungus. RNA-seq analyses of healthy versus inoculated seeds at 3 days after sowing (DAS), stage of radicle emergence, and at 6 and 10 DAS, two stages of seedling establishment, identified thousands of differentially expressed genes by Alternaria infection. Response to hypoxia, ethylene and indole pathways were found to be induced by Alternaria in the germinating seeds. However, surprisingly, the defense responses, namely the salicylic acid (SA) pathway, the response to reactive oxygen species (ROS), the endoplasmic reticulum-associated protein degradation (ERAD) and programmed cell death, were found to be strongly induced only during the latter post-germination stages. We propose that this non-canonical immune response in early germinating seeds compared to early seedling establishment was potentially due to the seed-to-seedling transition phase. Phenotypic analyses of about 14 mutants altered in the main defense pathways illustrated these specific defense responses. The unexpected germination deficiency and insensitivity to Alternaria in the glucosinolate deficient mutants allow hypothesis of a trade-off between seed germination, necrosis induction and Alternaria transmission to the seedling. The imbalance of the SA and jasmonic acid (JA) pathways to the detriment of the JA also illustrated a non-canonical immune response at the first stages of the seedling.

Coordinating growth and patterning is essential for eukaryote morphogenesis. In plants, auxin is a key regulator of morphogenesis implicated throughout development. Despite this central role, our understanding of how auxin coordinates cell fate and growth changes is still limited. Here, we addressed this question using a combination of genomic screens to delve into the transcriptional network induced by auxin at the earliest stage of flower development, prior to morphological changes. We identify a shoot-specific network suggesting that auxin initiates growth through an antagonistic regulation of growth-promoting and growth-repressive hormones, quasi-synchronously to floral fate specification. We further identify two DNA-binding One Zinc Finger (DOF) transcription factors acting in an auxin-dependent network that could interface growth and cell fate from the early stages of flower development onward., Competing Interests: The authors declare that they have no competing interest., (© 2022 The Authors.)

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination., Competing Interests: IL was employed by company MBCC Group. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sano, Lounifi, Cueff, Collet, Clément, Balzergue, Huguet, Valot, Galland and Rajjou.)

Alternaria dauci is a Dothideomycete fungus, causal agent of carrot leaf blight. As a member of the Alternaria genus, known to produce a lot of secondary metabolite toxins, A. dauci is also supposed to synthetize host specific and non-host specific toxins playing a crucial role in pathogenicity. This study provides the first reviewing of secondary metabolism genetic basis in the Alternaria genus by prediction of 55 different putative core genes. Interestingly, aldaulactone, a phytotoxic benzenediol lactone from A. dauci, was demonstrated as important in pathogenicity and in carrot partial resistance to this fungus. As nothing is known about aldaulactone biosynthesis, bioinformatic analyses on a publicly available A. dauci genome data set that were reassembled, thanks to a transcriptome data set described here, allowed to identify 19 putative secondary metabolism clusters. We exploited phylogeny to pinpoint cluster 8 as a candidate in aldaulactone biosynthesis. This cluster contains AdPKS7 and AdPKS8, homologs with genes encoding a reducing and a non-reducing polyketide synthase. Clusters containing such a pair of PKS genes have been identified in the biosynthesis of resorcylic acid lactones or dihydroxyphenylacetic acid lactones. AdPKS7 and AdPKS8 gene expression patterns correlated with aldaulactone production in different experimental conditions. The present results highly suggest that both genes are responsible for aldaulactone biosynthesis., (© 2022. The Author(s).)

Older people with excess body weight are not spared from undernutrition. They may face appetite decline which may lead to insufficient nutrient intake. They also have a higher risk of developing chronic diseases which may have a negative impact on protein-anabolic pathways. The present study aimed to determine the prevalence of undernutrition in overweight and obese older people from a secondary analysis on data collected through two French surveys among people aged 65 or over ( n = 782; 31% men; 65-103 years old). Undernutrition was assessed using the MNA screening tool (Mini-Nutritional Assessment). Results showed that 2% of the respondents with a BMI over 25 were undernourished (MNA score below 17/30) and 23% were at risk of undernutrition (MNA score of 17-23.5). Specifically, 18% of overweight and 29% of obese respondents were at risk of undernutrition. Taking into account the most recent French census data, it can be estimated that in France, around 1,7 million people aged over 65 with a BMI over 25 are undernourished or at risk of undernutrition. Given the worldwide increase in the number of overweight/obese individuals in the last few decades, further research will be needed to develop strategies to tackle nutritional risk in overweight/obese older adults., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sulmont-Rossé, Van Wymelbeke-Delannoy and Maître.)

Shoot branching is regulated by multiple signals. Previous studies have indicated that sucrose may promote shoot branching through suppressing the inhibitory effect of the hormone strigolactone (SL). However, the molecular mechanisms underlying this effect are unknown. Here, we used molecular and genetic tools to identify the molecular targets underlying the antagonistic interaction between sucrose and SL. We showed that sucrose antagonizes the suppressive action of SL on tillering in rice and on the degradation of D53, a major target of SL signalling. Sucrose inhibits the gene expression of D3, the orthologue of the Arabidopsis F-box MAX2 required for SL signalling. Overexpression of D3 antagonizes sucrose inhibition of D53 degradation and enables the SL inhibition of tillering under high sucrose. Sucrose prevents SL-induced degradation of D14, the SL receptor involved in D53 degradation. In contrast to D3, D14 overexpression enhances D53 protein levels and sucrose-induced tillering, even in the presence of SL. Our results show that sucrose inhibits SL response by affecting key components of SL signalling and, together with previous studies reporting the inhibition of SL synthesis by nitrate and phosphate, demonstrate the central role played by SLs in the regulation of plant architecture by nutrients., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

RNA interference is a mechanism of suppressing gene expression in plants, animals and fungi. This regulation mechanism involves three main enzymes, Dicers (Dcr), Argonautes (Ago) and RNA Dependent RNA Polymerases (Rdrp) allowing to produce smallRNAs. RNA interference and smallRNAs have a role in the plant-microorganisms interaction, either in a pathogenic or in a symbiotic relationships. Alternaria brassicicola is a pathogenic fungus of the Brassicaceae plants. During plant infection, it is able to transmit itself vertically and horizontally, giving advantages for new infection and dissemination. To investigate RNA interference and the presence of smallRNAs in A. brassicicola, an in silico analysis was achieved. Two DCR, 4 AGO and 3 RDRP genes were identified comforting the presence of smallRNAs in A. brassicicola. SmallRNA sequencing from wild-type strain and DCR deleted mutants allowed the identifcation of 17 miRNAs in A. brassicicola. The synthesis of these miRNAs is only weakly influenced by the inactivation of DCR genes suggesting the possible existence of an alternative Dicer-independent miRNA synthesis pathway. Target's prediction of A. brassicicola miRNAs identified genes in the fungus and in the plant model Arabidopsis thaliana. Some miRNAs were predicted to target A. thaliana genes involved in the methylation of histone and in the disease resistance., (Copyright © 2022 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)