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<jats:title>SUMMARY</jats:title><jats:p>2,4‐dichlorophenoxyacetic acid (2,4‐D) is a synthetic analogue of the plant hormone auxin that is commonly used in many <jats:italic>in vitro</jats:italic> plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole‐3‐acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4‐D analogues to test the structure–activity relationship with respect to the capacity to induce SE and auxinic activity in <jats:italic>Arabidopsis thaliana</jats:italic>. Four analogues induced SE as effectively as 2,4‐D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4‐D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4‐position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3‐position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4‐D analogues was consistent with their simulated TIR1‐Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4‐D‐induced SE and stress both require TIR1/AFB auxin co‐receptor function. Our data indicate that the stress‐related effects triggered by 2,4‐D and considered important for SE induction are downstream of auxin signalling.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Plant growth and morphogenesis are determined by the mechanical properties of its cell walls. Using atomic force microscopy, we have characterized the dynamics of cell wall elasticity in different tissues in developing roots of several plant species. The elongation growth zone of roots of all species studied was distinguished by a reduced modulus of elasticity of most cell walls compared to the meristem or late elongation zone. Within the individual developmental zones of roots, there were also significant differences in the elasticity of the cell walls of the different tissues, thus identifying the tissues that limit root growth in the different species. In cereals, this is mainly the inner cortex, whereas in dicotyledons this function is performed by the outer tissues—rhizodermis and cortex. These differences result in a different behaviour of the roots of these species during longitudinal dissection. Modelling of longitudinal root dissection using measured properties confirmed the difference shown. Thus, the morphogenesis of monocotyledonous and dicotyledonous roots relies on different tissues as growth limiting, which should be taken into account when analyzing the localization of associated molecular events. At the same time, no matrix polysaccharide was found whose immunolabelling in type I or type II cell walls would predict their mechanical properties. However, assessment of the degree of anisotropy of cortical microtubules showed a striking correlation with the elasticity of the corresponding cell walls in all species studied.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Despite the identification of clubroot resistance genes in various Brassica crops our understanding of the genetic basis of immunity to <jats:italic>Plasmodiophora brassicae</jats:italic> infection in the model plant <jats:italic>Arabidopsis thaliana</jats:italic> remains limited. To address this issue, we performed a screen of 142 natural accessions and identified 11 clubroot‐resistant Arabidopsis lines. Genome‐wide association analysis identified several genetic loci significantly linked with resistance. Three genes from two of these loci were targeted for deletion by CRISPR/Cas9 mutation in resistant accessions Est‐1 and Uod‐1. Deletion of <jats:italic>Resistance to Plasmodiophora brassicae 1</jats:italic> (<jats:italic>RPB1</jats:italic>) rendered both lines susceptible to the <jats:italic>P. brassicae</jats:italic> pathotype P1+. Further analysis of <jats:italic>rpb1</jats:italic> knock‐out Est‐1 and Uod‐1 lines showed that the RPB1 protein is required for activation of downstream defence responses, such as the expression of phytoalexin biosynthesis gene <jats:italic>CYP71A13</jats:italic>. RPB1 has recently been shown to encode a cation channel localised in the endoplasmic reticulum. The clubroot susceptible Arabidopsis accession Col‐0 lacks a functional <jats:italic>RPB1</jats:italic> gene; when Col‐0 is transformed with <jats:italic>RPB1</jats:italic> expression driven by its native promoter it is capable of activating <jats:italic>RPB1</jats:italic> transcription in response to infection, but this is not sufficient to confer resistance. Transient expression of <jats:italic>RPB1</jats:italic> in <jats:italic>Nicotiana tabacum</jats:italic> induced programmed cell death in leaves. We conclude that RPB1 is a critical component of the defence response to <jats:italic>P. brassicae</jats:italic> infection in Arabidopsis, acting downstream of pathogen recognition but required for the elaboration of effective resistance.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Dihydrochalcones (DHCs) including phlorizin (phloretin 2′‐<jats:italic>O</jats:italic>‐glucoside) and its positional isomer trilobatin (phloretin 4′‐<jats:italic>O</jats:italic>‐glucoside) are the most abundant phenylpropanoids in apple (<jats:italic>Malus</jats:italic> spp.). Transcriptional regulation of DHC production is poorly understood despite their importance in insect‐ and pathogen‐plant interactions in human physiology research and in pharmaceuticals. In this study, segregation in hybrid populations and bulked segregant analysis showed that the synthesis of phlorizin and trilobatin in <jats:italic>Malus</jats:italic> leaves are both single‐gene‐controlled traits. Promoter sequences of <jats:italic>PGT1</jats:italic> and <jats:italic>PGT2</jats:italic>, two glycosyltransferase genes involved in DHC glycoside synthesis, were shown to discriminate <jats:italic>Malus</jats:italic> with different DHC glycoside patterns. Differential <jats:italic>PGT1</jats:italic> and <jats:italic>PGT2</jats:italic> promoter activities determined DHC glycoside accumulation patterns between genotypes. Two transcription factors containing MYB‐like DNA‐binding domains were then shown to control DHC glycoside patterns in different tissues, with PRR2L mainly expressed in leaf, fruit, flower, stem, and seed while MYB8L mainly expressed in stem and root. Further hybridizations between specific genotypes demonstrated an absolute requirement for DHC glycoside production in <jats:italic>Malus</jats:italic> during seed development which explains why no <jats:italic>Malus</jats:italic> spp. with a null DHC chemotype have been reported.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p><jats:italic>Bougainvillea</jats:italic> is a typical tropical flower of great ornamental value due to its colorful bracts. The molecular mechanism behind color formation is not well‐understood. Therefore, this research conducted metabolome analysis, transcriptome analysis, and multi‐flux full‐length sequencing in two color bracts of <jats:italic>Bougainvillea × buttiana</jats:italic> ‘Chitra’ to investigate the significantly different metabolites (SDMs) and differentially expressed genes (DEGs). Overall, 261 SDMs, including 62 flavonoids and 26 alkaloids, were detected, and flavonols and betalains were significantly differentially accumulated among the two bracts. Furthermore, the complete‐length transcriptome of <jats:italic>Bougainvillea × buttiana</jats:italic> was also developed, which contained 512 493 non‐redundant isoforms. Among them, 341 210 (66.58%) displayed multiple annotations in the KOG, GO, NR, KEGG, Pfam, Swissprot, and NT databases. RNA‐seq findings revealed that 3610 DEGs were identified between two bracts. Co‐expression analysis demonstrated that the DEGs and SDMs involved in flavonol metabolism (such as <jats:italic>CHS</jats:italic>, <jats:italic>CHI</jats:italic>, <jats:italic>F3H</jats:italic>, <jats:italic>FLS</jats:italic>, <jats:italic>CYP75B1</jats:italic>, kaempferol, and quercetin) and betacyanin metabolism (<jats:italic>DODA</jats:italic>, betanidin, and betacyanins) were the main contributors for the canary yellow and red bract formation, respectively. Further investigation revealed that several putative transcription factors (TFs) might interact with the promoters of the genes mentioned above. The expression profiles of the putative TFs displayed that they may positively and negatively regulate the structural genes' expression profiles. The data revealed a potential regulatory network between important genes, putative TFs, and metabolites in the flavonol and betacyanin biosynthesis of <jats:italic>Bougainvillea × buttiana</jats:italic> ‘Chitra’ bracts. These findings will serve as a rich genetic resource for future studies that could create new color bracts.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Structural determinants of substrate recognition remain inadequately defined in broad specific cell‐wall modifying enzymes, termed xyloglucan xyloglucosyl transferases (XETs). Here, we investigate the <jats:italic>Tropaeolum majus</jats:italic> seed TmXET6.3 isoform, a member of the GH16_20 subfamily of the GH16 network. This enzyme recognises xyloglucan (XG)‐derived donors and acceptors, and a wide spectrum of other chiefly saccharide substrates, although it lacks the activity with homogalacturonan (pectin) fragments. We focus on defining the functionality of carboxyl‐terminal residues in TmXET6.3, which extend acceptor binding regions in the GH16_20 subfamily but are absent in the related GH16_21 subfamily. Site‐directed mutagenesis using double to quintuple mutants in the carboxyl‐terminal region – substitutions emulated on barley XETs recognising the XG/penta‐galacturonide acceptor substrate pair – demonstrated that this activity could be gained in TmXET6.3. We demonstrate the roles of semi‐conserved Arg238 and Lys237 residues, introducing a net positive charge in the carboxyl‐terminal region (which complements a negative charge of the acidic penta‐galacturonide) for the transfer of xyloglucan fragments. Experimental data, supported by molecular modelling of TmXET6.3 with the XG oligosaccharide donor and penta‐galacturonide acceptor substrates, indicated that they could be accommodated in the active site. Our findings support the conclusion on the significance of positively charged residues at the carboxyl terminus of TmXET6.3 and suggest that a broad specificity could be engineered <jats:italic>via</jats:italic> modifications of an acceptor binding site. The definition of substrate specificity in XETs should prove invaluable for defining the structure, dynamics, and function of plant cell walls, and their metabolism; these data could be applicable in various biotechnologies.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>In the marine environment, distance signaling based on water‐borne cues occurs during interactions between macroalgae and herbivores. In the brown alga <jats:italic>Laminaria digitata</jats:italic> from North‐Atlantic Brittany, oligoalginates elicitation or grazing was shown to induce chemical and transcriptomic regulations, as well as emission of a wide range of volatile aldehydes, but their biological roles as potential defense or warning signals in response to herbivores remain unknown. In this context, bioassays using the limpet <jats:italic>Patella pellucida</jats:italic> and <jats:italic>L. digitata</jats:italic> were carried out for determining the effects of algal transient incubation with 4‐hydroxyhexenal (4‐HHE), 4‐hydroxynonenal (4‐HNE) and dodecadienal on algal consumption by grazers. Simultaneously, we have developed metabolomic and transcriptomic approaches to study algal molecular responses after treatments of <jats:italic>L. digitata</jats:italic> with these chemical compounds. The results indicated that, unlike the treatment of the plantlets with 4‐HNE or dodecadienal, treatment with 4‐HHE decreases algal consumption by herbivores at 100 ng.ml<jats:sup>−1</jats:sup>. Moreover, we showed that algal metabolome was significantly modified according to the type of aldehydes, and more specifically the metabolite pathways linked to fatty acid degradation. RNAseq analysis further showed that 4‐HHE at 100 ng.ml<jats:sup>−1</jats:sup> can activate the regulation of genes related to oxylipin signaling pathways and specific responses, compared to oligoalginates elicitation. As kelp beds constitute complex ecosystems consisting of habitat and food source for marine herbivores, the algal perception of specific aldehydes leading to targeted molecular regulations could have an important biological role on kelps/grazers interactions.</jats:p>