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<jats:p>Traditional treatment of wastewaters is a burden for local governments. Using short rotation coppice willow (SRCW) as vegetal filter has several environmental and economic benefits. Here, we investigated the effect of primary wastewater irrigation on wood structure and composition of the willow cultivar <jats:italic>Salix miyabeana</jats:italic> ‘SX67’ following two years of growth. Compared to unirrigated plants (UI), stem sections of plants irrigated with primary wastewater (WWD) showed an unexpected decrease of hydraulic conductance (K<jats:sub>S</jats:sub>) associated with a decrease in vessel density but not vessel diameter. The majority (86%) of vessels had diameters range groups [20-30[, [30-40[and [40-50[µm and contributed to &amp;gt; 75% of theoretical K<jats:sub>S</jats:sub>, while the group class [50-60[µm (less than 10% of vessels) still accounted for &amp;gt; 20% of total K<jats:sub>S</jats:sub> regardless irrigation treatments. WWD significantly alters the chemical composition of wood with an increase of glucan content by 9 to 16.4% and a decrease of extractives by 35.3 to 36.4% when compared to UI or to plants irrigated with potable water (PW). The fertigation did also increase the proportion of the tension wood which highly correlated with glucan content. In the context of energetic transition and mitigation of climate change, such results are of high interest since WWD effectively permit the phytofiltration of large amounts of organic contaminated effluents without impairing SRCW physiology.</jats:p>

<jats:p>MicroRNAs (miRNAs) mediate the degradation of target mRNA and inhibit mRNA translation to regulate gene expression at the transcriptional and post-transcriptional levels in response to environmental stress in plants. We characterized the post-transcriptional mechanism by deep sequencing small RNA (sRNA) to examine how miRNAs were involved in low night temperature (LNT) stress in tomato and whether the molecular mechanism depended on the abscisic acid (ABA) signaling pathway. We annotated conserved miRNAs and novel miRNAs with four sRNA libraries composed of wild-type (WT) tomato plants and ABA-deficient mutant (<jats:italic>sit</jats:italic>) plants under normal growth and LNT stress conditions. Reverse genetics analysis suggested that miR162 participated in LNT resistance and the ABA-dependent signaling pathway in tomato. miR162-overexpressing (pRI-miR162) and miR162-silenced (pRNAi-miR162) transgenic tomato plants were generated to evaluate miR162 functions in response to LNT stress. miR162 deficiency exhibited high photosynthetic capacity and regulated stomatal opening, suggesting negative regulation of miR162 in the ABA-dependent signaling pathway in response to LNT stress. As feedback regulation, miR162 positively regulated ABA to maintain homeostasis of tomato under diverse abiotic stresses. The mRNA of <jats:italic>DICER-LIKE1</jats:italic> (<jats:italic>DCL1</jats:italic>) was targeted by miR162, and miR162 inhibited DCL1 cleavage in LNT response, including the regulation of miRNA160/164/171a and their targets. The DCL1-deficient mutants (<jats:italic>dcl1</jats:italic>) with CRISPR/Cas9 prevented stomatal opening to influence photosynthesis in the ABA signaling pathway under LNT stress. Finally, we established the regulatory mechanism of ABA-miR162-DCL1, which systematically mediated cold tolerance in tomato. This study suggests that post-transcriptional modulators acted as systemic signal responders <jats:italic>via</jats:italic> the stress hormone signaling pathway, and the model at the post-transcriptional level presents a new direction for research in plant abiotic stress resistance.</jats:p>

<jats:p>Determining response patterns of plant leaf elements to environmental variables would be beneficial in understanding plant adaptive strategies and in predicting ecosystem biogeochemistry processes. Despite the vital role of microelements in life chemistry and ecosystem functioning, little is known about how plant microelement concentrations, especially their bioconcentration factors (BCFs, the ratio of plant to soil concentration of elements), respond to large-scale environmental gradients, such as aridity, soil properties and anthropogenic activities, in drylands. The aim of the present study was to fill this important gap. We determined leaf microelement BCFs by measuring the concentrations of Mn, Fe, Ni, Cu and Zn in soils from 33 sites and leaves of 111 plants from 67 species across the drylands of China. Leaf microelement concentrations were maintained within normal ranges to satisfy the basic requirements of plants, even in nutrient-poor soil. Aridity, soil organic carbon (SOC) and electrical conductivity (EC) had positive effects, while soil pH had a negative effect on leaf microelement concentrations. Except for Fe, aridity affected leaf microelement BCFs negatively and indirectly by increasing soil pH and SOC. Anthropogenic activities and soil clay contents had relatively weak impacts on both leaf microelement concentrations and BCFs. Moreover, leaf microelement concentrations and BCFs shifted with thresholds at 0.89 for aridity and 7.9 and 8.9 for soil pH. Woody plants were positive indicator species and herbaceous plants were mainly negative indicator species of leaf microelement concentrations and BCFs for aridity and soil pH. Our results suggest that increased aridity limits the absorption of microelements by plant leaves and enhances leaf microelement concentrations. The identification of indicator species for the response of plant microelements to aridity and key soil characteristics revealed that woody species in drylands were more tolerant to environmental changes than herbaceous species.</jats:p>

<jats:p>Bitter gourd is an important vegetable crop grown throughout the tropics mainly because of its high nutritional value. Sex expression and identification of gynoecious trait in cucurbitaceous vegetable crops has facilitated the hybrid breeding programme in a great way to improve productivity. In bitter gourd, gynoecious sex expression is poorly reported and detailed molecular pathways involve yet to be studied. The present experiment was conducted to study the inheritance, identify the genomic regions associated with gynoecious sex expression and to reveal possible candidate genes through QTL-seq. Segregation for the gynoecious and monoecious sex forms in the F<jats:sub>2</jats:sub> progenies indicated single recessive gene controlling gynoecious sex expression in the genotype, PVGy-201. Gynoecious parent, PVGy-201, Monoecious parent, Pusa Do Mausami (PDM), and two contrasting bulks were constituted for deep-sequencing. A total of 10.56, 23.11, 15.07, and 19.38 Gb of clean reads from PVGy-201, PDM, gynoecious bulk and monoecious bulks were generated. Based on the ΔSNP index, 1.31 Mb regions on the chromosome 1 was identified to be associated with gynoecious sex expression in bitter gourd. In the QTL region 293,467 PVGy-201 unique variants, including SNPs and indels, were identified. In the identified QTL region, a total of 1019 homozygous variants were identified between PVGy1 and PDM genomes and 71 among them were non-synonymous variants (SNPS and INDELs), out of which 11 variants (7 INDELs, 4 SNPs) were classified as high impact variants with frame shift/stop gain effect. In total twelve genes associated with male and female gametophyte development were identified in the QTL-region. Ethylene-responsive transcription factor 12, Auxin response factor 6, Copper-transporting ATPase RAN1, CBL-interacting serine/threonine-protein kinase 23, ABC transporter C family member 2, DEAD-box ATP-dependent RNA helicase 1 isoform X2, Polygalacturonase QRT3-like isoform X2, Protein CHROMATIN REMODELING 4 were identified with possible role in gynoecious sex expression. Promoter region variation in 8 among the 12 genes indicated their role in determining gynoecious sex expression in bitter gourd genotype, DBGy-1. The findings in the study provides insight about sex expression in bitter gourd and will facilitate fine mapping and more precise identification of candidate genes through their functional validation.</jats:p>

<jats:p>Biodiversity is essential for the provision of multiple ecosystem functions simultaneously (ecosystem multifunctionality EMF). Yet, it remains unclear whether and how dominant plant species impact EMF. Here, we aimed at disentangling the direct from indirect above- and belowground pathways by which dominant plant species influence EMF. We evaluated the effects of two dominant plant species (<jats:italic>Dasiphora fruticosa</jats:italic>, and the toxic perennial plant <jats:italic>Ligularia virgaurea</jats:italic>) with expected positive and negative impacts on the abiotic environment (soil water content and pH), surrounding biological communities (plant and nematode richness, biomass, and abundance in the vicinity), and on the EMF of alpine meadows, respectively. We found that the two dominant plants enhanced EMF, with a positive effect of <jats:italic>L. virgaurea</jats:italic> on EMF greater than that of <jats:italic>D</jats:italic>. <jats:italic>fruticosa</jats:italic>. We also observed that dominant plants impacted on EMF through changes in soil water content and pH (indirect abiotic effects), but not through changes in biodiversity of surrounding plants and nematodes (indirect biotic pathway). Our study suggests that dominant plants may play an important role in promoting EMF, thus expanding the pervasive mass-ratio hypothesis originally framed for individual functions, and could mitigate the negative impacts of vegetation changes on EMF in the alpine meadows.</jats:p>

<jats:p>Foxtail millet (<jats:italic>Setaria italica</jats:italic>), a short-day plant, is one of the important crops for food security encountering climate change, particularly in regions where it is a staple food. Under the short-day condition in Taiwan, the heading dates (HDs) of foxtail millet accessions varied by genotypes and ambient temperature (AT). The allelic polymorphisms in flowering time (FT)–related genes were associated with HD variations. AT, in the range of 13°C–30°C that was based on field studies at three different latitudes in Taiwan and observations in the phytotron at four different AT regimes, was positively correlated with growth rate, and high AT promoted HD. To elucidate the molecular mechanism of foxtail millet HD, the expression of 14 key FT-related genes in four accessions at different ATs was assessed. We found that the expression levels of <jats:italic>SiPRR95</jats:italic>, <jats:italic>SiPRR1</jats:italic>, <jats:italic>SiPRR59</jats:italic>, <jats:italic>SiGhd7-2</jats:italic>, <jats:italic>SiPHYB</jats:italic>, and <jats:italic>SiGhd7</jats:italic> were negatively correlated with AT, whereas the expression levels of <jats:italic>SiEhd1</jats:italic>, <jats:italic>SiFT11</jats:italic>, and <jats:italic>SiCO4</jats:italic> were positively correlated with AT. Furthermore, the expression levels of <jats:italic>SiGhd7-2</jats:italic>, <jats:italic>SiEhd1</jats:italic>, <jats:italic>SiFT</jats:italic>, and <jats:italic>SiFT11</jats:italic> were significantly associated with HD. A coexpression regulatory network was identified that shown genes involved in the circadian clock, light and temperature signaling, and regulation of flowering, but not those involved in photoperiod pathway, interacted and were influenced by AT. The results reveal how gene × temperature and gene × gene interactions affect the HD in foxtail millet and could serve as a foundation for breeding foxtail millet cultivars for shift production to increase yield in response to global warming.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>The flower buds of <jats:italic>Lonicera japonica</jats:italic> Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new <jats:italic>L. japonica</jats:italic> varieties.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of <jats:italic>Lonicera</jats:italic> in China using simplified genome sequencing technology.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>A total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of <jats:italic>Lonicera</jats:italic> were divided into four subgroups, and the population structure and genetic relationships among existing <jats:italic>Lonicera</jats:italic> germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 <jats:italic>Lonicera</jats:italic> varieties.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>To our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of <jats:italic>Lonicera</jats:italic> varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of <jats:italic>Lonicera</jats:italic>. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.</jats:p></jats:sec>

<jats:p>Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (<jats:italic>Medicago sativa</jats:italic> L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that <jats:italic>MPK3</jats:italic>, <jats:italic>MPK9</jats:italic>, <jats:italic>WRKY22</jats:italic> (downstream target gene of <jats:italic>MPK3</jats:italic>), and TGACG-binding factor 1 (<jats:italic>TGA1)</jats:italic> are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce <jats:italic>MPK3</jats:italic> to regulate <jats:italic>WRKY22</jats:italic> to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (<jats:italic>NPR1)</jats:italic>, <jats:italic>TGA1</jats:italic>, pathogenesis-related 1 <jats:italic>(PR1)</jats:italic>, superoxide dismutase (<jats:italic>SOD)</jats:italic>, peroxidase <jats:italic>(POD)</jats:italic>, ascorbate peroxidase (<jats:italic>APX)</jats:italic>, glutathione-S-transferase <jats:italic>(GST)</jats:italic>, and heat shock protein <jats:italic>(HSP)</jats:italic>. This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Alfalfa (<jats:italic>Medicago sativa L.</jats:italic>) is a highly nutritious leguminous forage that plays an essential role in animal husbandry. In the middle and high latitudes of the northern hemisphere, there are problems with its low rates of overwintering and production. The application of phosphate (P) is an important measure to improve the cold resistance and production of alfalfa, but little is known about the mechanism of P in improving the cold resistance of alfalfa.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>This study integrated the transcriptome and metabolome to explain the mechanism of alfalfa in response to low-temperature stress under two applications of P (50 and 200 mg kg<jats:sup>-1</jats:sup>) and a control of none applied.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The application of P fertilizer improved the root structure and increased the content of soluble sugar and soluble protein in the root crown. In addition, there were 49 differentially expressed genes (DEGs) with 23 upregulated and 24 metabolites with 12 upregulated when 50 mg kg<jats:sup>-1</jats:sup> of P was applied. In contrast, there were 224 DEGs with 173 upregulated and 12 metabolites with 6 upregulated in the plants treated with 200 mg kg<jats:sup>-1</jats:sup> of P compared with the Control Check (CK). These genes and metabolites were significantly enriched in the biosynthesis of other secondary metabolites and the metabolic pathways of carbohydrates and amino acids. The integration of the transcriptome and metabolome indicated that P affected the biosynthesis of N-acetyl-L-phenylalanine, L-serine, lactose, and isocitrate during the period of increasing cold. It could also affect the expression of related genes that regulate cold tolerance in alfalfa.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Our findings could contribute to a deeper understanding of the mechanism that alfalfa uses to tolerate cold and lay a theoretical foundation for breeding alfalfa that is highly efficient at utilizing phosphorus.</jats:p></jats:sec>