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<jats:p>Grazing rest during the spring regreening period is the most economical and feasible measure for the ecological restoration of degraded alpine meadows and has been widely popularized and applied in China. The aim of the present study was to undertake a comparative analysis of the effects of grazing rest on the ecological restoration of degraded alpine meadows by plant photosynthesis and respiration. Coverage, height, ground biomass, belowground biomass of degraded alpine meadow vegetation, net photosynthetic rate, stomatal conductance, transpiration rate, intercellular CO<jats:sub>2</jats:sub> concentration, chlorophyll fluorescence parameters, relative chlorophyll content, respiration rate, metabolite content, leaf relative water content, and related mineral element content of the dominant grass <jats:italic>Elymus nutans</jats:italic> Griseb. were measured in degraded alpine grassland with different grazing rest years. The results show that grazing rest during the spring regreening period promoted the ecological restoration of degraded alpine meadows by enhancing the photosynthesis and respiration of the dominant grass <jats:italic>E. nutans</jats:italic> Griseb. Grazing rest enhanced photosynthesis in dominant grass by increasing metabolites related to the Calvin cycle, chlorophyll content, leaf relative water content, and related mineral element content. Grazing at rest enhanced the respiration of dominant grass by increasing metabolites related to the TCA cycle, leaf relative water content, and related mineral element content. This positive effect gradually became stable with increasing years of grazing rest. Our results provide a fundamental basis for the popularization and application of grazing rest during the spring regreening period on degraded Tibetan Plateau grasslands.</jats:p>

<jats:p>Grape growing regions are facing constant warming of the growing season temperature as well as limitations on ground water pumping used for irrigating to overcome water deficits. Trellis systems are utilized to optimize grapevine production, physiology, and berry chemistry. This study aimed to compare 6 trellis systems with 3 levels of applied water amounts based on different replacements of crop evapotranspiration (ET<jats:sub>c</jats:sub>) in two consecutive seasons. The treatments included a vertical shoot position (VSP), two modified VSPs (VSP60 and VSP80), a single high wire (SH), a high quadrilateral (HQ), and a Guyot pruned VSP (GY) combined with 25%, 50%, and 100% ET<jats:sub>c</jats:sub> water replacement. The SH had greater yields, whereas HQ was slower to reach full production potential. At harvest in both years, the accumulation of anthocyanin derivatives was enhanced in SH, whereas VSPs decreased them. As crown porosity increased (mostly VSPs), berry flavonol concentration and likewise molar % of quercetin in berries increased. Conversely, as leaf area increased, total flavonol concentration and molar % of quercetin decreased, indicating a preferential arrangement of leaf area along the canopy for overexposure of grape berry with VSP types. The irrigation treatments revealed linear trends for components of yield, where greater applied water resulted in larger berry size and likewise greater yield. 25% ET<jats:sub>c</jats:sub> was able to increase berry anthocyanin and flavonol concentrations. Overall, this study evidenced the efficiency of trellis systems for optimizing production and berry composition in Californian climate, also, the feasibility of using flavonols as the indicator of canopy architecture.</jats:p>

<jats:p>Hull color of foxtail millet is an important indicator of certain nutritional quality parameters. An F<jats:sub>2:6</jats:sub> recombinant inbred line (RIL) population developed by crossing a yellow-hulled cultivar Yugu 5 and a brown-hulled cultivar Jigu 31 was used to determine the genetic control of the hull color trait. This population segregated for yellow and brown hull colors in a ratio of 2:1, indicating that hull color is regulated by multiple genetic loci. A bulk segregant analysis-RNA sequencing (BSR-Seq) approach performed using the RNA bulks from 30 lines with brown and yellow hull colors each identified three genomic regions on chromosomes 1 (4,570,517-10,698,955 bp), 2 (40,301,380-46,168,003 bp), and 3 (44,469,860-50,532,757 bp). A new QTL for brown hull color of Jigu 31, <jats:italic>QHC.czas1</jats:italic>, was detected between bin markers Block43 and Block697 on chromosome 1 with the genetic linkage map constructed by re-sequencing a subset of the 147 RILs. This QTL explained a high level of phenotypic variation ranging from 28.0% to 47.0%. The corresponding genomic region of this QTL in the foxtail millet reference genome overlapped with that detected on chromosome 1 by the BSR-Seq analysis. Nineteen genes associated with biosynthesis of anthocyanin were annotated in this genomic region. Gene <jats:italic>Si1g06530</jats:italic> encoding a SANT/Myb domain protein was highly expressed in developing panicles and seeds, which warrants further verification as the candidate gene for the brown color hull of Jigu 31. Moreover, several annotated genes for biosynthesis of anthocyanin were identified in the genomic regions of chromosomes 2 and 3.</jats:p>

<jats:p>Embryonic and endosperm development are important biological events during <jats:italic>Arabidopsis</jats:italic> seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the <jats:italic>naa15</jats:italic> mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of <jats:italic>Arabidopsis</jats:italic>, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted <jats:italic>naa15</jats:italic> seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from <jats:italic>naa15-1</jats:italic>/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and <jats:italic>naa15</jats:italic>. The heatmap and qPCR analyses showed that auxin response genes (<jats:italic>ARFs</jats:italic>), auxin transport genes (<jats:italic>PINs</jats:italic>) cytokinin synthesis genes (<jats:italic>LOGs</jats:italic>), cytokinin dehydrogenase genes (<jats:italic>CKXs</jats:italic>), cytokinin receptor, transcription factors (<jats:italic>MYB</jats:italic>, <jats:italic>bHLH</jats:italic>, <jats:italic>MADS-box</jats:italic>, and <jats:italic>ERF</jats:italic>) were significantly downregulated in <jats:italic>naa15</jats:italic> compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of <jats:italic>naa15</jats:italic> were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of <jats:italic>naa15</jats:italic>. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.</jats:p>

<jats:p>Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (<jats:italic>i.e.</jats:italic>, robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (<jats:italic>i.e.</jats:italic>, cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (<jats:italic>i.e.</jats:italic>, bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that <jats:italic>Actinobacteria</jats:italic> and <jats:italic>Ascomycota</jats:italic> were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla <jats:italic>Proteobacteria</jats:italic> and <jats:italic>Ascomycota</jats:italic> dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities’ assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles.</jats:p>

<jats:p>Horticultural plants such as vegetables, fruits, and ornamental plants are crucial to human life and socioeconomic development. Gibberellins (GAs), a class of diterpenoid compounds, control numerous developmental processes of plants. The roles of GAs in regulating growth and development of horticultural plants, and in regulating significant progress have been clarified. These findings have significant implications for promoting the quality and quantity of the products of horticultural plants. Here we review recent progress in determining the roles of GAs (including biosynthesis and signaling) in regulating plant stature, axillary meristem outgrowth, compound leaf development, flowering time, and parthenocarpy. These findings will provide a solid foundation for further improving the quality and quantity of horticultural plants products.</jats:p>

<jats:p>The <jats:italic>bZIP</jats:italic> transcription factor family plays important roles in plant growth and development, response to stress, and regulation of secondary metabolite biosynthesis. The identification and molecular function of <jats:italic>bZIP</jats:italic> gene have been deeply studied in the model plant <jats:italic>Arabidopsis thaliana</jats:italic>, but it has not been reported in the medicinal plant <jats:italic>Isatis indigotica</jats:italic>. In this study, 65 <jats:italic>IibZIP</jats:italic> genes were identified in the genome of <jats:italic>I. indigotica</jats:italic>, which were distributed on seven chromosomes, were highly conserved, could be classified into 11 subgroups. Transcriptomic and metabolomic data for leaves of <jats:italic>I. indigotica</jats:italic> exposed to salt stress were analyzed to construct an <jats:italic>IibZIP</jats:italic> gene co-expression network and metabolite correlation network. Seventeen <jats:italic>IibZIP</jats:italic> genes were co-expressed with 79 transcription factors, and GO and KEGG enrichment analysis showed that most of these genes were associated with abiotic stress and hormone responses of plants. 17 <jats:italic>IibZIP</jats:italic> genes regulated 110 metabolites through 92 transcription factor associations. In addition, <jats:italic>IibZIP23</jats:italic>, <jats:italic>IibZIP38</jats:italic> and <jats:italic>IibZIP51</jats:italic> were associated with six metabolites including three alkaloids (quinoline alkaloid stylopine, indole alkaloids tabersonine and indole-3-acetic acid), flavonoid myricetin 3-O-galactoside, and two primary metabolites 2-hydroxy-6-aminopurine, 3-dehydroshikimic acid were strongly correlated. This study provides data for identification of the <jats:italic>IibZIP</jats:italic> gene family and their regulation of metabolites in response to salt stress.</jats:p>

<jats:p>As a fungus with both medicinal and edible value, <jats:italic>Wolfiporia cocos</jats:italic> (F. A. Wolf) Ryvarden &amp;amp; Gilb. has drawn more public attention. Chemical components’ content fluctuates in wild and cultivated <jats:italic>W. cocos</jats:italic>, whereas the accumulation ability of chemical components in different parts is different. In order to perform a quality assessment of <jats:italic>W. cocos</jats:italic>, we proposed a comprehensive method which was mainly realized by Fourier transform near-infrared (FT-NIR) spectroscopy and ultra-fast liquid chromatography (UFLC). A qualitative analysis means was built a residual convolutional neural network (ResNet) to recognize synchronous two-dimensional correlation spectroscopy (2DCOS) images. It can rapidly identify samples from wild and cultivated <jats:italic>W. cocos</jats:italic> in different parts. As a quantitative analysis method, UFLC was used to determine the contents of three triterpene acids in 547 samples. The results showed that a simultaneous qualitative and quantitative strategy could accurately evaluate the quality of <jats:italic>W. cocos</jats:italic>. The accuracy of ResNet models combined synchronous FT-NIR 2DCOS in identifying wild and cultivated <jats:italic>W. cocos</jats:italic> in different parts was as high as 100%. The contents of three triterpene acids in Poriae Cutis were higher than that in Poria, and the one with wild Poriae Cutis was the highest. In addition, the suitable habitat plays a crucial role in the quality of <jats:italic>W. cocos</jats:italic>. The maximum entropy (MaxEnt) model is a common method to predict the suitable habitat area for <jats:italic>W. cocos</jats:italic> under the current climate. Through the results, we found that suitable habitats were mostly situated in Yunnan Province of China, which accounted for approximately 49% of the total suitable habitat area of China. The research results not only pave the way for the rational planting in Yunnan Province of China and resource utilization of <jats:italic>W. cocos</jats:italic>, but also provide a basis for quality assessment of medicinal fungi.</jats:p>

<jats:p>Productivity decline of <jats:italic>Casuarina equisetifolia</jats:italic> plantation and difficulty in natural regeneration remains a serious problem because of allelopathy. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) are the major allelochemicals of the <jats:italic>C. equisetifolia</jats:italic> litter exudates. The production of these allelochemicals may derive from decomposition of litter or from the litter endophyte and microorganisms adhering to litter surfaces. In the present study, we aimed to evaluate the correlation between allelochemicals in litter and endophytic and epiphytic fungi and bacteria from litter. A total of 100 fungi and 116 bacteria were isolated from the interior and surface of litter of different forest ages (young, half-mature, and mature plantation). Results showed that the fermentation broth of fungal genera <jats:italic>Mycosphaerella</jats:italic> sp. and <jats:italic>Pestalotiopsis</jats:italic> sp., and bacterial genera <jats:italic>Bacillus amyloliquefaciens</jats:italic>, <jats:italic>Burkholderia-Paraburkholderia</jats:italic>, and <jats:italic>Pantoea ananatis</jats:italic> had the strongest allelopathic effect on <jats:italic>C. equisetifolia</jats:italic> seeds. Allelochemicals, such as 2,4-DTBP and its analogs were identified in the fermentation broths of these microorganisms using GC/MS analysis. These results indicate that endophytic and epiphytic fungi and bacteria in litters are involved in the synthesis of allelochemicals of <jats:italic>C. equisetifolia</jats:italic>. To further determine the abundance of the allelopathic fungi and bacteria, Illumina MiSeq high-throughput sequencing was performed. The results showed that bacterial genera with strong allelopathic potential were mainly distributed in the young and half-mature plantation with low abundance, while the abundance of fungal genera <jats:italic>Mycosphaerella</jats:italic> sp. and <jats:italic>Pestalotiopsis</jats:italic> sp. were higher in the young and mature plantations. In particular, the abundance of <jats:italic>Mycosphaerella</jats:italic> sp. in the young and mature plantations were 501.20% and 192.63% higher than in the half-mature plantation, respectively. Overall, our study demonstrates that the litter fungi with higher abundance in the young and mature plantation were involved in the synthesis of the allelochemical 2,4-DTBP of <jats:italic>C. equisetifolia.</jats:italic> This finding may be important for understanding the relationship between autotoxicity and microorganism and clarifying the natural regeneration problem of <jats:italic>C. equisetifolia.</jats:italic></jats:p>

<jats:p>Research has generally outlined that the Neolithic East Asian farmers expanded into Southeast Asia, leading to substantial social and cultural transformations. However, the associated archaeobotanical evidence until now has been insufficient to clarify the exact timing, dispersal route, and farming package of the emergence of agriculture in Mainland Southeast Asia. To clarify these issues, the micro-plant remains of phytolith and starch from three Neolithic sites in Ha Long Bay were extracted and analyzed. This study validates the earliest evidence of co-cropping in northern Vietnam, involving the cultivation of rice together with foxtail millet at 4000 years BP or slightly earlier. Moreover, the results indicate that at least two patterns of subsistence strategy were practiced simultaneously during the initial farming phase in the region. The Trang Kenh people, a regional variant of the Phung Nguyen cultural group often have been seen as the first farmers in northern Vietnam, and they mainly practiced a cereal-based subsistence strategy with more vital cultural characteristics of southern China origin. Meanwhile, the Ha Long people, mainly composed of indigenous hunter-gatherer descendants, continued to utilize a wide range of their preferred plant resources such as taros, yams, and acorns, while they absorbed and incorporated new elements such as millet and rice into their food system. This study provides solid information to understand the diverse economic systems among different cultural groups in Vietnam.</jats:p>