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<jats:p>Wheat crop has to compete with several weeds including <jats:italic>Avena fatua</jats:italic>, a noxious weed that alone is responsible for 30–70% losses in the yield annually. Because of the environmental concerns associated with conventional methods, researchers are on a continuous hunt to find clean alternatives in order to manage weeds. Fungi have shown promising weedicide potential in lab studies. The current study aimed to isolate endophytic fungi from wheat plants which can promote wheat growth and inhibit the growth of common weed, <jats:italic>A. fatua</jats:italic>. Of several isolates, GW (grayish white) was selected for its promising features, and the strain was identified as <jats:italic>Fusarium oxisporum</jats:italic> through ITS sequencing technique. This fungus released a number of compounds including Isovitexin, Calycosin, quercetagetin, and dihydroxy-dimethoxyisoflavone that inhibited the growth of <jats:italic>A. fatua</jats:italic> but did not influence the growth of wheat seedlings. Biomass of this fungus in the soil also reduced growth parameters of the weed and promoted the growth of wheat. For instance, the vigor index of <jats:italic>A. fatua</jats:italic> seedlings was reduced to only 6% of the control by this endophyte. In contrast, endophyte-associated wheat seedlings showed a higher vigor index than the control. Behind this differential response of the two plants were their contrasting physiological and biochemical status. Lower growth phenotypes of <jats:italic>A. fatua</jats:italic> seedlings had reduced levels of IAA, GAs, and SA and higher the levels of JA and ABA. Besides, their ROS scavenging ability was also compromised as evident from relatively lower activities of catalase, peroxidase, and ascorbic acid oxidase, as well as higher accumulation of ROS in their leaves. Wheat seedlings response to GW was opposite to the <jats:italic>A. fatua</jats:italic>. It may be concluded that <jats:italic>F. oxysporum</jats:italic> GW has the ability to differentially modulate physiology and biochemistry of the two hosts leading to contrasting phenotypic responses.</jats:p>

<jats:p>The transcription factor <jats:italic>WRINKLED1</jats:italic> (<jats:italic>WRI1</jats:italic>) is known as a master regulator of fatty acid synthesis in developing oilseeds of <jats:italic>Arabidopsis thaliana</jats:italic> and other species. <jats:italic>WRI1</jats:italic> is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by <jats:italic>WRI</jats:italic>1. To shortlist possible gene targets for future <jats:italic>in-planta</jats:italic> experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in <jats:italic>A. thaliana</jats:italic> were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the <jats:italic>in vitro</jats:italic> assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase (<jats:italic>FRK</jats:italic>3) and of phosphoglucose isomerase (<jats:italic>PGI</jats:italic>1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.</jats:p>

<jats:p>Tree thinning affects the light environment, which in turn affects the growth and survival of understory vegetation, thus improving species diversity and nutrient cycling, as well as the ecological habitat factors. However, the response of understory vegetation to the thinning intensity and short-time effects in the temperate broadleaf-conifer mixed forest is not completely clear. In this study, four permanent plots with a total area of 4 hm<jats:sup>2</jats:sup> were established in a mixed broadleaf-conifer forest in northeast China, with thinning intensities of 20% (light thinning, LT), 35% (medium thinning, MT), 55% (heavy thinning, HT) and the unthinned plot (CK), respectively, in accordance with the basal area. The responses of species diversity to changes in understory vegetation were conducted by a structural equation model (SEM). The results showed that compared with CK, thinning significantly increased the photosynthetically active radiation (PAR) and the light quality (R/FR) (<jats:italic>p</jats:italic> &amp;lt; 0.05), while decreased the contents of soil total nitrogen (TN), total phosphorous (TP), organic matter (OM), nitrate nitrogen (NN), ammonia nitrogen (AN) and <jats:italic>pH</jats:italic>. The degree of fragmentation of light factors among the treatment plots gradually decreased as thinning intensity increased. Among all the thinning treatments, PAR and R/FR were found to be the optimal light condition when the forest thinning intensity was 55%. The light condition was found to have a significant negative correlation with soil TN, TP, OM, and AN. While the soil nutrients were positively correlated with herbaceous layer diversity but negatively correlated with shrub layer diversity. The soil nutrients were lost after thinning in a short time and herb diversity decreased, but shrub diversity increased significantly compared with unthinned plots. For the understory vegetation, the species diversity of shrub and herb layer were showed to be more sensitive to soil nutrients than light environment.</jats:p>

<jats:p>Elucidating the effects of atmospheric nitrogen (N) deposition on the photosynthetic capacity of plants is critical to understand forest growth and conservation under global change. However, studies on this topic generally consider only understory N addition, which ignores the effect of canopy interception. In this study, we conducted a field experiment in a subtropical forest to compare the effects of canopy vs. understory N addition on the photosynthetic rate of canopy and understory species. We found that canopy N addition enhanced the photosynthetic rate of canopy species by increasing leaf hydraulic conductivity and shortening the distance of CO<jats:sub>2</jats:sub> transportation. In contrast, understory N addition had non-significant effects on the photosynthetic rate of canopy species. Moreover, the photosynthetic rate of understory species was not affected by canopy or understory N addition. Interestingly, changes in hydraulic conductivity contributed more to accelerating the photosynthetic rate than changes in CO<jats:sub>2</jats:sub> transport distance. Our results provide important insights into the dissimilar effects of canopy and understory N addition on the photosynthetic rates of species in subtropical forests. Based on our findings, we highlighted the urgent need to consider canopy processes in future studies on N deposition.</jats:p>

<jats:p>A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for <jats:italic>Corydalis</jats:italic> DC., a species-rich (&amp;gt; 500 species), ecologically and medically important, but taxonomically notoriously difficult genus. Here, we constructed backbone phylogeny and estimated the divergence of <jats:italic>Corydalis</jats:italic> based on the plastome data from 39 <jats:italic>Corydalis</jats:italic> species (32 newly sequenced), which represent ca. 80% of sections and series across this genus. Our phylogenetic analyses recovered six fully supported main clades (I–VI) and provided full support for the majority of lineages within <jats:italic>Corydalis</jats:italic>. Section <jats:italic>Archaeocapnos</jats:italic> was unexpectedly turned out to be sister to the rest of the subg. <jats:italic>Corydalis</jats:italic> s. l. (clades IV–VI), thus treating as a distinct clade (clade III) to render all the main clades monophyletic. Additionally, some unusual plastome structural rearrangements were constantly detected within <jats:italic>Corydalis</jats:italic> and were proven to be lineage-specific in this study, which, in turn, provided further support to our phylogeny. A segment containing five genes (<jats:italic>trnV-UAC</jats:italic>–<jats:italic>rbcL</jats:italic>) in the plastome's LSC region was either normally located downstream of the <jats:italic>ndhC</jats:italic> gene in clade I species or translocated downstream of the <jats:italic>atpH</jats:italic> gene in clade II species or translocated to downstream of the <jats:italic>trnK-UUU</jats:italic> gene in clade III–VI species. The unique large inversion (ca. 50 kb) in the plastome LSC region of clade III species, representing an intermediate stage of the above translocation in clades IV–VI, firmly supported clade III as a distinct and early diverged clade within this large lineage (clades III–VI). Our phylogeny contradicted substantially with the morphology-based taxonomy, rejected the treatment of tuberous species as an independent evolutionary group, and proved that some commonly used diagnostic characters (e.g., root and rhizome) were results of convergent evolution, suggestive of unreliability in <jats:italic>Corydalis</jats:italic>. We dated the origin of crown <jats:italic>Corydalis</jats:italic> to the early Eocene (crown age 49.08 Ma) and revealed possible explosive radiation around 25 Ma, coinciding with the drastic uplift of the Qinghai-Tibetan Plateau in Oligocene and Miocene. This study provided the most reliable and robust backbone phylogeny of <jats:italic>Corydalis</jats:italic> to date and shed some new insights on the evolution of <jats:italic>Corydalis</jats:italic>.</jats:p>

<jats:p>Four near-isogenic lines (NILs) with different allele combinations of the <jats:italic>starch branching enzyme 3</jats:italic> (<jats:italic>SBE3</jats:italic>) and <jats:italic>granule-bound starch synthase 1</jats:italic> (<jats:italic>GBSS1</jats:italic>) were developed by crossing the <jats:italic>japonica</jats:italic> rice cultivars “Dodamssal” and “Hwayeong.” The associations between sequence variations in <jats:italic>SBE3</jats:italic> and <jats:italic>GBSS1</jats:italic>, and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS). <jats:italic>SBE3</jats:italic> and <jats:italic>GBSS1</jats:italic> showed genetic interaction in regulating AAC and RS. Gene expression profiling of panicle tissues revealed significant differences in expression levels of <jats:italic>GBSS1</jats:italic>, <jats:italic>SBE3</jats:italic>, and other starch-related genes among the four NILs, indicating that variations in <jats:italic>GBSS1</jats:italic> and <jats:italic>SBE3</jats:italic> changed the expression level of starch-related genes. These variations contributed to the changes observed in AAC, RS, and physico-chemical characteristics of the rice starch from the NILs.</jats:p>

<jats:p>Salt stress seriously affects plant growth and crop yield, and has become an important factor that threatens the soil quality worldwide. In recent years, the cultivation of salt-tolerant plants such as <jats:italic>Sesbania rostrata</jats:italic> has a positive effect on improving coastal saline-alkali land. Microbial inoculation and GABA addition have been shown to enhance the plant tolerance in response to the abiotic stresses, but studies in green manure crops and the revelation of related mechanisms are not clear. In this study, the effects of inoculation with <jats:italic>Azorhizobium caulinodans</jats:italic> ORS571 and exogenous addition of γ-Aminobutyric Acid (GABA; 200 mg·L<jats:sup>−1</jats:sup>) on the growth and development of <jats:italic>S. rostrata</jats:italic> under salt stress were investigated using potting experiments of vermiculite. The results showed that inoculation with ORS571 significantly increased the plant height, biomass, chlorophyll content, proline content (PRO), catalase (CAT) activity, and superoxide dismutase (SOD) activity of <jats:italic>S. rostrata</jats:italic> and reduced the malondialdehyde (MDA) level of leaves. The exogenous addition of GABA also increased the height, biomass, and CAT activity and reduced the MDA and PRO level of leaves. In addition, exogenous addition of GABA still had a certain improvement on the CAT activity and chlorophyll content of the ORS571-<jats:italic>S. rostrata</jats:italic> symbiotic system. In conclusion, ORS571 inoculation and GABA application have a positive effect on improving the salt stress tolerance in <jats:italic>S. rostrata</jats:italic>, which are closely associated with increasing chlorophyll synthesis and antioxidant enzyme activity and changing the amino acid content. Therefore, it can be used as a potential biological measure to improve the saline-alkali land.</jats:p>

<jats:p>The development of plant tissues and organs during post-embryonic growth occurs through the activity of both primary and secondary meristems. While primary meristems (root and shoot apical meristems) promote axial plant growth, secondary meristems (vascular and cork cambium or phellogen) promote radial thickening and plant axes strengthening. The vascular cambium forms the secondary xylem and phloem, whereas the cork cambium gives rise to the periderm that envelops stems and roots. Periderm takes on an increasingly important role in plant survival under climate change scenarios, but it is also a forest product with unique features, constituting the basis of a sustainable and profitable cork industry. There is established evidence that epigenetic mechanisms involving histone post-translational modifications, DNA methylation, and small RNAs play important roles in the activity of primary meristem cells, their maintenance, and differentiation of progeny cells. Here, we review the current knowledge on the epigenetic regulation of secondary meristems, particularly focusing on the phellogen activity. We also discuss the possible involvement of DNA methylation in the regulation of periderm contrasting phenotypes, given the potential impact of translating this knowledge into innovative breeding programs.</jats:p>

<jats:p>The components and structure of cell wall are closely correlated with aluminum (Al) toxicity and tolerance for plants. However, the cell wall assembly and function construction in response to Al is not known. Brefeldin A (BFA), a macrolide, is used to disrupt cell wall polysaccharide components, and nitric oxide (NO), a signal molecule, is used to modify the cell wall structure. Pretreatment with BFA accelerated Al accumulation in root tips and Al-induced inhibition of root growth of two rice genotypes of Nipponbare and Zhefu 802, and significantly decreased the cell wall polysaccharide content including pectin, hemicellulose 1, and hemicellulose 2, indicating that BFA inhibits the biosynthesis of components in the cell wall and makes the root cell wall lose the ability to resist Al. The addition of NO donor (SNP) significantly alleviated the toxic effects of Al on root growth, Al accumulation, and oxidative damage, and decreased the content of pectin polysaccharide and functional groups of hydroxyl, carboxyl, and amino in the cell wall <jats:italic>via</jats:italic> FTIR analysis, while had no significant effect on hemicellulose 1 and hemicellulose 2 content compared with Al treatment. Furthermore, NO didn't change the inhibition effect of BFA-induced cell wall polysaccharide biosynthesis and root growth. Taken together, BFA disrupts the integrity of cell wall and NO modifies partial cell wall composition and their functional groups, which change the Al tolerance in rice.</jats:p>

<jats:p>Potassium (K<jats:sup>+</jats:sup>) is essential for crop growth. Increasing the K<jats:sup>+</jats:sup> content can often directly promote the improvement of crop yield and quality. Heterosis plays an important role in genetic improvement and leads to genetic gains. We found that the K<jats:sup>+</jats:sup> content of tobacco showed significant heterosis, which is highly significant for cultivating tobacco varieties with high K<jats:sup>+</jats:sup> content. However, the mechanism by which K<jats:sup>+</jats:sup> content heterosis occurs in tobacco leaves is not clear. In this study, a comprehensive comparative transcriptome sequencing analysis of root samples from the hybrid G70 × GDH11 and its parental inbred lines G70 and GDH11 was performed to elucidate the importance of the root uptake capacity of K<jats:sup>+</jats:sup> in the formation of heterosis. The results showed that 29.53% and 60.49% of the differentially expressed genes (DEGs) exhibited dominant and over-dominant expression patterns, respectively. These non-additive upregulated DEGs were significantly enriched in GO terms, such as metal ion transport and reaction, ion balance and homeostasis, ion channel activity, root meristem growth, and regulation of root hairs. The KEGG annotation results indicated that these genes were mainly involved in the pathways such as energy metabolism, carbohydrate formation, amino acid metabolism, and signal transduction. Further analysis showed that probable potassium transporter 17 (<jats:italic>NtKT17</jats:italic>) and potassium transporter 5-like (<jats:italic>NtKT5</jats:italic>), associated with potassium ion absorption, glutamate receptor 2.2-like and glutamate receptor 2.8-like, associated with ion channel activity, LOC107782957, protein detoxification 42-like, and probable glutamate carboxypeptidase 2, associated with root configuration, showed a significantly higher expression in the hybrids. These results indicated that the over-dominant expression pattern of DEGs played a key role in the heterosis of K<jats:sup>+</jats:sup> content in tobacco leaves, and the overexpression of the genes related to K<jats:sup>+</jats:sup> uptake, transport, and root development in hybrids helped to improve the K<jats:sup>+</jats:sup> content of plants, thus showing the phenomenon of heterosis.</jats:p>