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<jats:p>Root system architecture (RSA) and tiller are important agronomic traits. However, the mechanisms of the IGT family genes regulate RSA and tiller development in different rice varieties remain unclear. In this study, we demonstrated that 38 rice varieties obtained from Yuanyang Hani’s terraced fields with different RSA and could be classified into six groups based on the ratio of root length and width. We found a positive correlation between RSA (including root width, length, and area) and tiller number in most of rice varieties. Furthermore, the IGT family genes <jats:italic>Deeper Rooting 1</jats:italic> (<jats:italic>DRO1</jats:italic>), <jats:italic>LAZY1</jats:italic>, <jats:italic>TAC1</jats:italic>, and <jats:italic>qSOR1</jats:italic> showed different expression patterns when rice grown under irrigation and drought conditions. Moreover, the <jats:italic>qSOR1</jats:italic> gene had higher levels in the roots and tillers, and accompanied with higher levels of <jats:italic>PIN1b</jats:italic> gene in roots when rice grown under drought environmental condition. <jats:italic>DRO1</jats:italic> gene had two single nucleotide polymorphisms (SNPs) in the exon 3 sequences and showed different expression patterns in the roots and tillers of the 38 rice varieties. Overexpression of <jats:italic>DRO1</jats:italic> with a deletion of exon 5 caused shorter root length, less lateral roots and lower levels of <jats:italic>LAZY1</jats:italic>, <jats:italic>TAC1</jats:italic>, and <jats:italic>qSOR1</jats:italic>. Further protein interaction network, microRNA targeting and co-expression analysis showed that <jats:italic>DRO1</jats:italic> plays a critical role in the root and tiller development associated with auxin transport. These data suggest that the RSA and tiller development are regulated by the IGT family genes in an intricate network way, which is tightly related to rice genetic background in rice adapting to different environmental conditions.</jats:p>

<jats:p>CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling through receptor-like kinases (RLKs) regulates developmental transitions and responses to biotic and abiotic inputs by communicating the physiological state of cells and tissues. CLE peptides have varying signaling ranges, which can be defined as the distance between the source, i.e., the cells or tissue that secrete the peptide, and their destination, i.e., cells or tissue where the RLKs that bind the peptide and/or respond are expressed. Case-by-case analysis substantiates that CLE signaling is predominantly autocrine or paracrine, and rarely endocrine. Furthermore, upon CLE reception, the ensuing signaling responses extend from cellular to tissue, organ and whole organism level as the downstream signal gets amplified. CLE-RLK-mediated effects on tissue proliferation and differentiation, or on subsequent primordia and organ development have been widely studied. However, studying how CLE-RLK regulates different stages of proliferation and differentiation at cellular level can offer additional insights into these processes. Notably, CLE-RLK signaling also mediates diverse non-developmental effects, which are less often observed; however, this could be due to biased experimental approaches. In general, CLEs and RLKs, owing to the sequence or structural similarity, are prone to promiscuous interactions at least under experimental conditions in which they are studied. Importantly, there are regulatory mechanisms that suppress CLE-RLK cross-talk <jats:italic>in vivo,</jats:italic> thereby eliminating the pressure for co-evolving binding specificity. Alternatively, promiscuity in signaling may also offer evolutionary advantages and enable different CLEs to work in combination to activate or switch off different RLK signaling pathways.</jats:p>

<jats:p><jats:italic>Polygala fallax</jats:italic> Hemsl. (Polygalaceae), a traditional Chinese medicinal species, requires optimal growth conditions for artificial cultivation. Irradiance is one of the primary environmental factors that affects the growth and survival of <jats:italic>P. fallax</jats:italic> Hemsl. plants, which seemingly grow better under weak irradiance conditions. However, the optimum light intensity for growing <jats:italic>P. fallax</jats:italic> Hemsl. is not clear. To determine the optimum light intensity for cultivating this medicinal plant species, <jats:italic>P. fallax</jats:italic> Hemsl. plants from two different habitats were grown and exposed to three shade treatments (50% shade, 70% shade and 90% shade, which resulted in photosynthetically active radiation amounts equal to 662 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>, 401 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>, and 131 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>, respectively) to evaluate survival, growth, leaf photosynthesis, and the main pharmacological active ingredients (saponins) in response to shade. Our results revealed that the <jats:italic>P. fallax</jats:italic> Hemsl. plants in the different habitats consistently exhibited relatively high photosynthesis rates, biomass, survival rates and saponins under 662 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup> created by the 50% shade treatment. We concluded that photosynthetically active radiation of approximately 662 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup> is suitable for the cultivation of <jats:italic>P. fallax</jats:italic> Hemsl. plants.</jats:p>

<jats:p>Secondary growth of the woody tree stem is governed by meristematic cell division and differentiation in the vascular cambium. Multiple hormonal signals and endogenous developmental programs regulate vascular cambium activity. Brassinosteroids (BRs) significantly promote secondary stem growth and wood formation in poplar trees. However, the underlying regulatory mechanisms of BRs within the vascular tissue remain unclear. Genetic and anatomical approaches were used here to elucidate the role of <jats:italic>PagDET2</jats:italic>, the rate-limiting enzyme for BRs biosynthesis, in regulating secondary vascular cambium activity in <jats:italic>Populus</jats:italic>. This study showed that the elevated endogenous castasterone (CS) levels in tree stems through overexpressing <jats:italic>PagDET2</jats:italic> could enhance cambium meristem cell activity and xylem (XY) differentiation to promote secondary stem growth. RNA-seq analysis revealed that genes involved in BRs response, vascular cambium cell division, XY differentiation, and secondary cell wall synthesis were up-regulated.</jats:p>

<jats:p>MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20–24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level <jats:italic>via</jats:italic> cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.</jats:p>

<jats:p>Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in <jats:italic>Pogostemon cablin</jats:italic>. In this study, the full-length cDNA of the FPP synthase gene from <jats:italic>P. cablin</jats:italic> (<jats:italic>PcFPPS</jats:italic>) was cloned and characterized. The expressions of <jats:italic>PcFPPS</jats:italic> are different among different tissues (highly in <jats:italic>P. cablin</jats:italic> flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal <jats:italic>FPPS</jats:italic> deletion mutation in yeast CC25. Transient overexpression of <jats:italic>PcFPPS</jats:italic> in <jats:italic>P. cablin</jats:italic> leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of <jats:italic>PcFPPS</jats:italic> in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of <jats:italic>PcFPPS</jats:italic> can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of <jats:italic>PcWRKY44</jats:italic> in <jats:italic>P. cablin</jats:italic> upregulated the expression levels of <jats:italic>PcFPPS</jats:italic> and patchoulol synthase gene (<jats:italic>PcPTS</jats:italic>), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the <jats:italic>PcFPPS</jats:italic> and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.</jats:p>

<jats:p>To adapt to variable natural conditions, plants have evolved several strategies to respond to different environmental stresses. MicroRNA (miRNA)-mediated gene regulation is one of such strategies. Variants, e.g., single nucleotide polymorphisms (SNPs) within the mature miRNAs or their target sites may cause the alteration of regulatory networks and serious phenotype changes. In this study, we proposed a novel approach to construct a miRNA–miRNA crosstalk network in <jats:italic>Arabidopsis thaliana</jats:italic> based on the notion that two cooperative miRNAs toward common targets are under a strong pressure to be inherited together across ecotypes. By performing a genome-wide scan of the SNPs within the mature miRNAs and their target sites, we defined a “regulation fate profile” to describe a miRNA–target regulation being static (kept) or dynamic (gained or lost) across 1,135 ecotypes compared with the reference genome of Col-0. The cooperative miRNA pairs were identified by estimating the similarity of their regulation fate profiles toward the common targets. The reliability of the cooperative miRNA pairs was supported by solid expressional correlation, high PPImiRFS scores, and similar stress responses. Different combinations of static and dynamic miRNA–target regulations account for the cooperative miRNA pairs acting on various biological characteristics of miRNA conservation, expression, homology, and stress response. Interestingly, the targets that are co-regulated dynamically by both cooperative miRNAs are more likely to be responsive to stress. Hence, stress-related genes probably bear selective pressures in a certain group of ecotypes, in which miRNA regulations on the stress genes reprogram. Finally, three case studies showed that reprogramming miRNA–miRNA crosstalk toward the targets in specific ecotypes was associated with these ecotypes’ climatic variables and geographical locations. Our study highlights the potential of miRNA–miRNA crosstalk as a genetic basis underlying environmental adaptation in natural populations.</jats:p>

<jats:p>Changes in net primary productivity (NPP) to global change have been studied, yet the relative impacts of global change on grassland productivity at large scales remain poorly understood. Using 182 grassland samples established in 17 alpine meadows (AM) and 21 desert steppes (DS) in China, we show that NPP of AM was significantly higher than that of DS. NPP increased significantly with increasing leaf nitrogen content (LN) and leaf phosphorus content (LP) but decreased significantly with increasing leaf dry matter content (LDMC). Among all abiotic factors, soil nutrient factor was the dominant factor affecting the variation of NPP of AM, while the NPP of DS was mainly influenced by the changing of precipitation. All abiotic factors accounted for 62.4% of the spatial variation in the NPP of AM, which was higher than the ability to explain the spatial variation in the NPP of DS (43.5%). Leaf traits together with soil nutrients and climatic factors determined the changes of the grassland productivity, but the relative contributions varied somewhat among different grassland types. We quantified the effects of biotic and abiotic factors on grassland NPP, and provided theoretical guidance for predicting the impacts of global change on the NPP of grasslands.</jats:p>

<jats:p>China has implemented a series of policies to reduce the usage of chemical pesticides to maintain food production safety and to reduce water and soil pollution. However, there is still a huge gap in developing biological pesticides to replace chemical agents or managing pests to prevent crop production loss. It is necessary to predict the future use of chemical pesticides and to exploit the potential ways to control pests and crop diseases. Pesticide usage is affected by seasonal changes and analyzed by using a seasonal autoregressive integrated moving average (ARIMA) model (a statistical model that predicts future trends using time-series data). The future development of biopesticides in China was predicted using the compound annual growth rate (CAGR), which is calculated <jats:italic>via</jats:italic> the equation [(Final value/Starting value)<jats:sup>1/years</jats:sup> – 1] according to the annual growth rate of target products over time. According to the reducing trend of pesticide and biological pesticide usage annually, China is predicted possibly step into the era of pesticide-free agriculture in 2050 based on the analysis of the ARIMA model. With CAGR calculation, China will produce from 500 thousand to one million tons of biopesticides in 2050, which can meet the need to replace chemical pesticides in agriculture to prevent the present crop production loss. To achieve the goal, China still has the greatest challenges to develop biopesticides and use various strategies to control pest and crop diseases. China may step into the dawn of chemical pesticide-free agriculture in 2050 if biopesticides can be developed smoothly and pests can be controlled well using various strategies.</jats:p>

<jats:p>Due to advances in the industrial development of light-emitting diodes (LEDs), much research has been conducted in recent years to get a better understanding of how plants respond to these light sources. This study investigated the effects of different LED-based light regimes on strawberry plant development and performance. The photosynthetic pigment content, biochemical constituents, and growth characteristics of strawberry plants were investigated using a combination of different light intensities (150, 200, and 250 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>), qualities (red, green, and blue LEDs), and photoperiods (14/10 h, 16/8 h, and 12/12 h light/dark cycles) compared to the same treatment with white fluorescent light. Plant height, root length, shoot fresh and dry weight, chlorophyll <jats:italic>a</jats:italic>, total chlorophyll/carotenoid content, and most plant yield parameters were highest when illuminated with LM7 [intensity (250 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>) + quality (70% red/30% blue LED light combination) + photoperiod (16/8 h light/dark cycles)]. The best results for the effective quantum yield of PSII photochemistry Y(II), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained with LM8 illumination [intensity (250 μmol m<jats:sup>−2</jats:sup> s<jats:sup>−1</jats:sup>) + quality (50% red/20% green/30% blue LED light combination) + photoperiod (12 h/12 h light/dark cycles)]. We conclude that strawberry plants require prolonged and high light intensities with a high red-light component for maximum performance and biomass production.</jats:p>