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<jats:p>The myeloblastosis (MYB) proteins perform key functions in mediating cadmium (Cd) tolerance of plants. <jats:italic>Ipomoea aquatica</jats:italic> has strong adaptability to Cd Stress, while the roles of the <jats:italic>I. aquatica MYB</jats:italic> gene family with respect to Cd stress are still unclear. Here, we identified a total of 183 <jats:italic>MYB</jats:italic> genes in the <jats:italic>I. aquatica</jats:italic> genome (<jats:italic>laMYB</jats:italic>), which were classified into 66 1R-type <jats:italic>IaMYB</jats:italic>, 112 2R-type <jats:italic>IaMYB</jats:italic>, four 3R-type <jats:italic>IaMYB</jats:italic>, and one 4R-type <jats:italic>IaMYB</jats:italic> based on the number of the MYB repeat in each gene. The analysis of phylogenetic tree indicated that most of <jats:italic>IaMYB</jats:italic> genes are associated with the diverse biological processes including defense, development and metabolism. Analysis of sequence features showed that the <jats:italic>IaMYB</jats:italic> genes within identical subfamily have the similar patterns of the motif distributions and gene structures. Analysis of gene duplication events revealed that the dispersed duplication (DSD) and whole-genome duplication (WGD) modes play vital roles in the expansion of the <jats:italic>IaMYB</jats:italic> gene family. Expression profiling manifests that approximately 20% of <jats:italic>IaMYB</jats:italic> genes had significant role in the roots of <jats:italic>I. aquatica</jats:italic> under Cd stress. Promoter profiling implied that the differentially expressed genes might be induced by environmental factors or inherent hormones and thereby execute their function in Cd response. Remarkably, the 2R-type <jats:italic>IaMYB157</jats:italic> with abundant light-responsive element G-box and ABA-responsive element ABRE in its promoter region exhibited very strong response to Cd stress. Taken together, our findings provide an important candidate <jats:italic>IaMYB</jats:italic> gene for further deciphering the molecular regulatory mechanism in plant with respect to Cd stress.</jats:p>

<jats:p>The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.</jats:p>

<jats:p>FERONIA (FER) receptor kinase plays versatile roles in plant growth and development, biotic and abiotic stress responses, and reproduction. Autophagy is a conserved cellular recycling process that is critical for balancing plant growth and stress responses. Target of Rapamycin (TOR) has been shown to be a master regulator of autophagy. Our previous multi-omics analysis with loss-of-function <jats:italic>fer-4</jats:italic> mutant implicated that FER functions in the autophagy pathway. We further demonstrated here that the <jats:italic>fer-4</jats:italic> mutant displayed constitutive autophagy, and FER is required for TOR kinase activity measured by S6K1 phosphorylation and by root growth inhibition assay to TOR kinase inhibitor AZD8055. Taken together, our study provides a previously unknown mechanism by which FER functions through TOR to negatively regulate autophagy.</jats:p>

<jats:p>Growth-regulating factors (GRFs) play crucial roles in plant growth and stress response. To date, there have been no reports of the analysis and identification of the GRF transcription factor family in alfalfa. In this study, we identified 27 GRF family members from alfalfa (<jats:italic>Medicago sativa</jats:italic> L.) “Xinjiang Daye”, and analyzed their physicochemical properties. Based on phylogenetic analysis, these <jats:italic>MsGRFs</jats:italic> were divided into five subgroups, each with a similar gene structure and conserved motifs. <jats:italic>MsGRFs</jats:italic> genes are distributed on 23 chromosomes, and all contain QLQ and WRC conserved domains. The results of the collinearity analysis showed that all <jats:italic>MsGRFs</jats:italic> are involved in gene duplication, including multiple whole-genome duplication or segmental duplication and a set of tandem duplication, indicating that large-scale duplication is important for the expansion of the GRF family in alfalfa. Several hormone-related and stress-related <jats:italic>cis</jats:italic>-acting elements have been found in the promoter regions of <jats:italic>MsGRFs</jats:italic>. Some <jats:italic>MsGRFs</jats:italic> were highly expressed in young leaves and stems, and their expression decreased during development. In addition, the leaf size of different varieties was found to vary, and <jats:italic>MsGRF1</jats:italic> to <jats:italic>4</jats:italic>, <jats:italic>MsGRF18</jats:italic> to <jats:italic>20</jats:italic>, and <jats:italic>MsGRF22</jats:italic> to <jats:italic>23</jats:italic> were differentially expressed in large and small leaf alfalfa varieties, suggesting that they are critical in the regulation of leaf size. The results of this study can benefit further exploration of the regulatory functions of <jats:italic>MsGRFs</jats:italic> in growth and development, and can identify candidate genes that control leaf size development.</jats:p>

<jats:p>With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.</jats:p>

<jats:p>As a sessile organism, plants hold elaborate transcriptional regulatory systems that allow them to adapt to variable surrounding environments. Current understanding of plant regulatory mechanisms is greatly constrained by limited knowledge of transcription factor (TF)–DNA interactions. To mitigate this problem, a Plant-DTI predictor (<jats:bold>Plant D</jats:bold>BD-<jats:bold>T</jats:bold>FBS <jats:bold>I</jats:bold>nteraction) was developed here as the first machine-learning model that covered the largest experimental datasets of 30 plant TF families, including 7 plant-specific DNA binding domain (DBD) types, and their transcription factor binding sites (TFBSs). Plant-DTI introduced a novel TFBS feature construction, called TFBS base-preference, which enhanced the specificity of TFBS to DBD types. The proposed model showed better predictive performance with the TFBS base-preference than the simple binary representation. Plant-DTI was validated with 22 independent ChIP-seq datasets. It accurately predicted the measured DBD-TFBS pairs along with their TFBS motifs, and effectively predicted interactions of other TFs containing similar DBD types. Comparing to the existing state-of-art methods, Plant-DTI prediction showed a figure of merit in sensitivity and specificity with respect to the position weight matrix (PWM) and TSPTFBS methods. Finally, the proposed Plant-DTI model helped to fill the knowledge gap in the regulatory mechanisms of the cassava sucrose synthase 1 gene (MeSUS1). Plant-DTI predicted MeERF72 as a regulator of MeSUS1 in consistence with the yeast one-hybrid (Y1H) experiment. Taken together, Plant-DTI would help facilitate the prediction of TF-TFBS and TF-target gene (TG) interactions, thereby accelerating the study of transcriptional regulatory systems in plant species.</jats:p>

<jats:p>Cell wall integrity is tightly regulated and maintained given that non-physiological modification of cell walls could render plants vulnerable to biotic and/or abiotic stresses. Expansins are plant cell wall-modifying proteins active during many developmental and physiological processes, but they can also be produced by bacteria and fungi during interaction with plant hosts. Cell wall alteration brought about by ectopic expression, overexpression, or exogenous addition of expansins from either eukaryote or prokaryote origin can in some instances provide resistance to pathogens, while in other cases plants become more susceptible to infection. In these circumstances altered cell wall mechanical properties might be directly responsible for pathogen resistance or susceptibility outcomes. Simultaneously, through membrane receptors for enzymatically released cell wall fragments or by sensing modified cell wall barrier properties, plants trigger intracellular signaling cascades inducing defense responses and reinforcement of the cell wall, contributing to various infection phenotypes, in which expansins might also be involved. Here, we review the plant immune response activated by cell wall surveillance mechanisms, cell wall fragments identified as responsible for immune responses, and expansin’s roles in resistance and susceptibility of plants to pathogen attack.</jats:p>

<jats:p>The non-uniform growth and development of crops within Chinese Solar Greenhouses (CSG) is directly related to the micro-light climate within canopy. In practice, reflective films are used to improve micro-light climate within plant canopy by homogenizing light distribution and so increasing total plant light interception. However, as to our knowledge, the contributions to light distribution within canopy have not been investigated for passive reflector like reflective films. Field experiments dealing with light conditions and growth behavior over time, are complicated to carry out, time-consuming and hard to control, while however, accurate measurements of how reflective films influence the micro-light climate of canopy are an essential step to improve the growth conditions for any crop. Here, we propose a supplementary light strategy using reflective films to improve light distribution within plant canopy. Based on the example of CSG, a 3D greenhouse model including a detailed 3D tomato canopy structure was constructed to simulate the influence of supplementary reflective films to improve micro-light climate. Comparison of measured solar radiation intensity with predicted model data demonstrated that the model could precisely predict light radiation intensity over time with different time points and positions in the greenhouse. A series of reflective film configurations were investigated based on features analysis of light distribution in the tomato canopy on sunny days using the proposed model. The reflective film configuration scheme with the highest impact significantly improved the evenness of horizontal and vertical light distribution in tomato canopy. The strategy provided here can be used to configure reflective films that will enhance light conditions in CSG, which can be applied and extended in different scenarios.</jats:p>

<jats:p>The tree of heaven, <jats:italic>Ailanthus altissima</jats:italic> (<jats:sc>MILL</jats:sc>.) <jats:sc>SWINGLE</jats:sc>, is a globally invasive plant known to secrete allelopathic metabolites called quassinoids. Quassinoids are highly modified triterpenoids. So far, nothing has been known about the biochemical basis of quassinoid biosynthesis. Here, based on transcriptome and metabolome data of <jats:italic>Ailanthus altissima</jats:italic>, we present the first three steps of quassinoid biosynthesis, which are catalysed by an oxidosqualene cyclase and two cytochrome P450 monooxygenases, resulting in the formation of the protolimonoid melianol. Strikingly, these steps are identical to the first steps of the biosynthesis of limonoids, structurally different triterpenoids from sister plant families within the same order Sapindales. Our results are therefore not only important to fully understand the biosynthesis of complex triterpenoids in plants, but also confirm the long-standing hypothesis that quassinoids and limonoids share an evolutionary origin. In addition, our transcriptome data for <jats:italic>Ailanthus altissima</jats:italic> will be beneficial to other researchers investigating the physiology and ecology of this invasive tree.</jats:p>

<jats:p>The commercialization of hybrid rice has greatly contributed to the increase in rice yield, with the improvement of its seed production capacity having played an important role. The stigma exsertion rate (SER) is a key factor for improving the outcrossing of the sterile line and the hybrid rice seed production. We used the Zhenshan 97B × IRAT109 recombinant inbred population comprising 163 lines and a natural population of 138 accessions to decipher the genetic foundation of SER over 2 years in three environments. Additionally, we detected eight QTLs for SER on chromosomes 1, 2, and 8 via linkage mapping. We also identified seven and 19 significant associations for SER using genome-wide association study in 2016 and 2017, respectively. Interestingly, we located two lead SNPs (sf0803343504 and sf083344610) on chromosome 8 in the <jats:italic>qTSE8</jats:italic> QTL region that were significantly associated with total SER. After transcriptomic analysis, quantitative real-time PCR, and haplotype analysis, we found 13 genes within this reliable region as important candidate genes. Our study results will be beneficial to molecular marker-assisted selection of rice lines with high outcrossing rate, thereby improving the efficiency of hybrid seed production.</jats:p>