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IntroductionChemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology.MethodsThe fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum.Results and DiscussionThe results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm2). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.

IntroductionCodonopsis pilosula is a significant plant in traditional Chinese medicine, valued for its edible and medicinal properties. However, the lack of available genomic resources has hindered further research.MethodsThis study presents the first chromosome-scale genome assembly of C. pilosula using PacBio CLR reads and Hi-C scaffolding technology. Additionally, Ks analysis and syntenic depth analysis were performed to elucidate its evolutionary history.ResultsThe final assembly yielded a high-quality genome of 679.20 Mb, which was anchored to 8 pseudo-chromosomes with an anchoring rate of 96.5% and a scaffold N50 of 80.50 Mb. The genome assembly showed a high completeness of 97.6% based on Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis. Repetitive elements constituted approximately 76.8% of the genome, with long terminal repeat retrotransposons (LTRs) accounting for about 39.17%. Ks and syntenic depth analyses revealed that the polyploidization history of three platycodonoid clade species involved only the γ-WGT event. Karyotype evolutionary analysis identified an ancestral karyotype with 9 protochromosomes for the three platycodonoid clade species. Moreover, non-WGD genes, particularly those arising from tandem duplications, were found to contribute significantly to gene family expansion.DiscussionThese findings provide essential insights into the genetic diversity and evolutionary biology of C. pilosula, aiding its conservation and sustainable use.

Weigela Thunb. is a genus in the family Caprifoliaceae. All species in this genus have high ornamental and medicinal value. However, the genetic divergence between species and the phylogeny within Weigela is still unclear. Therefore, we sequenced and analyzed four plastomes from four different Weigela species to reveal the genetic divergence among species of this genus, and the phylogeny within Weigela. The four plastomes from Weigela ranged from 156,909 bp to 157,739 bp in size, and presented a typical circular quadripartite structure. Each complete plastome contained a pair of inverted repeat regions (23,592~24,957 bp), a larger single-copy (LSC) region (89,922~90,229 bp), and a small single-copy (SSC) region (17,668~20,429 bp). We identified three types of repeats, corresponding to 268 forward repeats, 128 palindromic repeats, and 867 tandem repeats, for a total of 1,263 long repeats. A total of 352 SSRs were identified from the four plastomes, and most of them were concentrated in the LSC region and the noncoding regions. Mononucleotide repeat units were the most frequently detected types of repeats, of which A/T repeat units were the most abundant. Three mutational hotspots (trnH-psbA, trnR-ndhF, and trnN-ndhF) were identified as candidate barcodes for Weigela species. Weigela belongs to Diervilloideae located at an early diverging position in the Caprifoliaceae. Within Weigela, W. japonica and W. floribunda were sister with W. subsessilis and W. florida. This study revealed the plastome structure and variation of four well-known Weigela species, and found three candidate barcodes for further study of four well-known Weigela species. In addition, the phylogenetic location of Weigela within the Caprifoliaceae was identified.

IntroductionPhytohormones play a crucial role in regulating the abscission of plant organs and tissues.MethodsIn this study, the ultrastructure of the sepals of Korla fragrant pears was observed using a transmission electron microscope, and high-performance liquid and gas chromatography were used to analyze the dynamic changes of phytohormones in the abscission zone during the calyx abscission process of Korla fragrant pears, and mass spectrometry imaging was applied to ascertain the spatial distribution of phytohormones.ResultsThe results revealed that the mitochondria in the abscission zone of the decalyx fruits were regularly distributed around the cell wall, and the chloroplasts were moderately present. In contrast, in the persistent calyx fruit, the corresponding parts of the abscission zone showed a scattered distribution of mitochondria within the cells, and there was a higher number of chloroplasts, which also contained starch granules inside. Mass spectrometry imaging revealed that ABA was enriched in the abscission zone of the decalyx fruit, and their ionic signal intensities were significantly stronger than those of the persistent calyx fruit. However, the ionic signal intensities of Indole-3-acetic acid (IAA) and Gibberellin A3 (GA3) of the persistent calyx fruit were significantly stronger than those in the abscission zone of the decalyx fruit and were concentrated in the persistent calyx fruit. 1-Aminocyclopropanecarboxylic Acid (ACC) did not show distinct regional distribution in both the decalyx and persistent calyx fruits. Furthermore, before the formation of the abscission zone, the levels of IAA, GA3, and zeatin (ZT) in the abscission zone of the decalyx fruits were significantly lower than those in the persistent calyx fruits by 37.9%, 57.7%, and 33.0%, respectively, while the levels of abscisic acid (ABA) and ethylene (ETH) were significantly higher by 21.9% and 25.0%, respectively. During the formation of the abscission zone, the levels of IAA, GA3, and ZT in the abscission zone of the decalyx fruits were significantly lower than those in the persistent calyx fruits by 41.7%, 71.7%, and 24.6%, respectively, while the levels of ABA and ETH were significantly higher by 15.2% and 80.0%, respectively. After the formation of the abscission zone, the levels of IAA and GA3 in the abscission zone of the decalyx fruits were lower than those in the persistent calyx fruits by 20.8% and 47.8%, respectively, while the levels of ABA and ETH were higher by 271.8% and 26.9%, respectively. In summary, during the calyx abscission process of Korla fragrant pears, IAA and GA3 in the abscission zone inhibited abscission, while ABA and ETH promoted calyx abscission. These research findings enrich the understanding of the regulatory mechanism of plant hormones on calyx abscission and provide a theoretical basis for the study of exogenous plant growth regulators for regulating calyx abscission in Korla fragrant pear.

Plant architecture determines canopy coverage, photosynthetic efficiency, and ultimately productivity in soybean (Glycine max). Optimizing plant architecture is a major goal of breeders to develop high yield soybean varieties. Over the past few decades, the yield per unit area of soybean has not changed significantly; however, rice and wheat breeders have succeeded in achieving high yields by generating semi‐dwarf varieties. Semi-dwarf crops have the potential to ensure yield stability in high-density planting environments because they can significantly improve responses to fertilizer input, lodging resistance, and enhance resistance to various abiotic and biotic stresses. Soybean has a unique plant architecture, with leaves, inflorescences, and pods growing at each node; internode number greatly affects the final yield. Therefore, producing high-yielding soybean plants with an ideal architecture requires the coordination of effective node formation, effective internode formation, and branching. Dozens of quantitative trait loci (QTLs) controlling plant architecture have been identified in soybean, but only a few genes that control this trait have been cloned and characterized. Here, we review recent progress in understanding the genetic basis of soybean plant architecture. We provide our views and perspectives on how to breed new high-yielding soybean varieties.

IntroductionArbuscular mycorrhizal fungi (AMF) and dark septate endophytic fungi (DSEs) generally coexist in the roots of plants. However, our understanding of the effects of their coexistence on plant growth and stress resistance is limited.MethodsIn the present study, the effects of single and dual inoculation of AMF and DSE on the growth, photosynthetic physiology, glutathione (GSH) metabolism, endogenous hormones, and cadmium (Cd) content of maize under 25 mg•kg-1 Cd stress were investigated.ResultsCompared with that after the non-inoculation treatment, AMF+DSE co-inoculation significantly increased the photosynthetic rate (Pn) of maize leaves; promoted root GSH metabolism; increased the root GSH concentration and activity of γ-glutamyl cysteine synthase (γ-GCS), ATP sulfatase (ATPS) and sulfite reductase (SIR) by 215%, 117%, 50%, and 36%, respectively; and increased the concentration of endogenous hormones in roots, with increases in zeatin (ZR), indole-3 acetic acid (IAA), and abscisic acid (ABA) by 81%, 209%, and 72%, respectively. AMF inoculation, DSE inoculation and AMF+DSE co-inoculation significantly increased maize biomass, and single inoculation with AMF or DSE increased the Cd concentration in roots by 104% or 120%, respectively. Moreover, significant or highly significant positive correlations were observed between the contents of ZR, IAA, and ABA and the activities of γ-GCS, ATPS, and SIR and the glutathione (GSH) content. There were significant or highly significant positive interactions between AMF and DSE on the Pn of leaves, root GSH metabolism, and endogenous hormone contents according to two-way analysis of variance. Therefore, the coexistence of AMF and DSE synergistically enhanced the Cd tolerance of maize.

Woody plant encroachment (WPE), a widespread ecological phenomenon globally, has significant impacts on ecosystem structure and functions. However, little is known about how WPE affects phenology in wetland ecosystems of middle and high latitudes. Here, we investigated the regional-scale effects of WPE on the start (SOS), peak (POS), end (EOS), and length (GSL) of the growing season in boreal wetland ecosystems, and their underlying mechanisms, using remote sensing dataset during 2001–2016. Our results showed that WPE advanced the annual SOS and POS, while delaying EOS and extending GSL in boreal wetlands with these impacts increasing over time. When boreal wetland ecosystems were fully encroached by woody plants, the SOS and POS were advanced by 12.17 and 5.65 days, respectively, the EOS was postponed by 2.74 days, and the GSL was extended by 15.21 days. We also found that the impacts of WPE on wetland SOS were predominantly attributed to the increased degree of WPE (α), while climatic factors played a more significant role in controlling the POS and EOS responses to WPE. Climate change not only directly influenced phenological responses of wetlands to WPE but also exerted indirect effects by regulating soil moisture and α. Winter precipitation and spring temperature primarily determined the effects of WPE on SOS, while its impacts on POS were mainly controlled by winter precipitation, summer temperature, and precipitation, and the effects on EOS were mainly determined by winter precipitation, summer temperature, and autumn temperature. Our findings offer new insights into the understanding of the interaction between WPE and wetland ecosystems, emphasizing the significance of considering WPE effects to ensure accurate assessments of phenology changes.

Zucchini fruit are notably susceptible to chilling injury when stored at low temperatures. The purpose of this experimental investigation was to assess the influence of strigolactone (ST) (5 μmol L-1) on mitigating chilling injury and the metabolic changes in amino acids, ascorbic acid, and abscisic acid in zucchini fruit stored at 4°C. Research findings demonstrated that ST-treated zucchini fruit displayed a significantly higher tolerance to chilling stress compared to the control group. Postharvest ST treatment led to a decrease in weight loss, accompanied by reduced levels of malondialdehyde and relative ion leakage compared to the untreated group. ST immersion significantly boosted the metabolic pathways associated with proline and arginine, affecting both the enzymatic reactions and gene expressions, thus cumulatively increasing the internal concentrations of these amino acids in zucchini fruit. Zucchini treated with ST exhibited an increased concentration of γ-aminobutyric acid (GABA) as a result of augmented activities and elevated transcriptional levels of glutamate decarboxylase (GAD), GABA transaminase (GAT), and succinate semialdehyde dehydrogenase (SSD). In the ST-treated sample, the elevated enzymatic activities and enhanced gene expressions within the ascorbic acid (AsA) biosynthesis pathway worked together to sustain AsA accumulation. The application of ST resulted in a rise in abscisic acid (ABA) concentration, which correspondingly correlated with the induction of both activities and gene expression levels of crucial enzymes involved in ABA metabolism. Our findings revealed that submerging zucchini fruit in ST could be a highly effective strategy for boosting their chilling tolerance. The alleviation in chilling injury induced by ST may be attributed to the modulation of proline, arginine, GABA, AsA and ABA metabolism.

Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified in Arabidopsis, little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report that Arabidopsis TZF1 is a bona-fide stress granule protein. Ectopic expression of TZF1 (TZF1 OE), but not an mRNA binding-defective mutant (TZF1H186Y OE), enhances salt stress tolerance in Arabidopsis. RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes in TZF1 OE plants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3’-UTRs, we hypothesized that TZF1—ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of the autoinhibited Ca2+-ATPase 11 (ACA11) mRNA, which encodes a tonoplast-localized calcium pump that extrudes calcium and dampens signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated in aca11 null mutants. Collectively, our findings demonstrate that TZF1 binds and initiates degradation of specific mRNAs to enhance salt stress tolerance.

Carbon (C), nitrogen (N), and phosphorus (P) stoichiometry serve as valuable indices for plant nutrient utilization and biogeochemical cycling within ecosystems. However, the allocation of these nutrients among different plant organs and the underlying drivers in dynamic riparian ecosystems remain inadequately understood. In this study, we gathered plant samples from diverse life forms (annuals and perennials) and organs (leaves, stems, and roots) in the riparian zone of the Three Gorges Reservoir Region (TGRR) in China—a novel ecosystem subject to winter flooding. We used random forest analysis and structural equation modeling to find out how flooding, life forms, plant communities, and soil variables affect organs C, N, and P levels. Results showed that the mean concentrations of plant C, N, and P in the riparian zone of the TGRR were 386.65, 19.31, and 5.27 mg/g for leaves respectively, 404.02, 11.23, and 4.81 mg/g for stems respectively, and 388.22, 9.32, and 3.27 mg/g for roots respectively. The C:N, C:P and N:P ratios were 16.15, 191.7 and 5.56 for leaves respectively; 26.98, 273.72 and 4.6 for stems respectively; and 16.63, 223.06 and 4.77 for roots respectively. Riparian plants exhibited nitrogen limitation, with weak carbon sequestration, low nutrient utilization efficiency, and a high capacity for nutrient uptake. Plant C:N:P stoichiometry was significantly different across life forms and organs, with higher N and P concentrations in leaves than stems and roots, and higher in annuals than perennials. While flooding stress triggered distinct responses in the C, N, and P concentrations among annual and perennial plants, they maintained similar stoichiometric ratios along flooding gradients. Furthermore, our investigation identified soil properties and life forms as more influential factors than plant communities in shaping variations in C:N:P stoichiometry in organs. Flooding indirectly impacts plant C:N:P stoichiometry primarily through alterations in plant community composition and soil factors. This study underscores the potential for hydrologic changes to influence plant community composition and soil nutrient dynamics, and further alter plant ecological strategies and biogeochemical cycling in riparian ecosystems.

IntroductionClimate change-related CO2 increases and different forms of nitrogen deposition are thought to affect the performance of plants, but their interactions have been poorly studied.MethodsThis study investigated the responses of photosynthesis and growth in two invasive maple species, amur maple (Acer ginnala Maxim.) and boxelder maple (Acer negundo L.), to elevated CO2 (400 µmol mol-1 (aCO2) vs. 800 µmol mol-1 (eCO2) and different forms of nitrogen fertilization (100% nitrate, 100% ammonium, and an equal mix of the two) with pot experiment under controlled conditions.Results and discussionThe results showed that eCO2 significantly promoted photosynthesis, biomass, and stomatal conductance in both species. The biochemical limitation of photosynthesis was switched to RuBP regeneration (related to Jmax) under eCO2 from the Rubisco carboxylation limitation (related to Vcmax) under aCO2. Both species maximized carbon gain by lower specific leaf area and higher N concentration than control treatment, indicating robust morphological plasticity. Ammonium was not conducive to growth under aCO2, but it significantly promoted biomass and photosynthesis under eCO2. When nitrate was the sole nitrogen source, eCO2 significantly reduced N assimilation and growth. The total leaf N per tree was significantly higher in boxelder maple than in amur maple, while the carbon and nitrogen ratio was significantly lower in boxelder maple than in amur maple, suggesting that boxelder maple leaf litter may be more favorable for faster nutrient cycling. The results suggest that increases in ammonium under future elevated CO2 will enhance the plasticity and adaptation of the two maple species.

IntroductionRice (Oryza sativa L.) is a pivotal cereal crop worldwide. It relies heavily on the presence of iron plaque on its root surfaces for optimal growth and enhanced stress resistance across diverse environmental conditions.MethodTo study the crystallographic aspects of iron plaque formation on rice roots, the concentrations of Fe2+ and PO43- were controlled in this study. The effects of these treatments were assessed through comprehensive analyzes encompassing root growth status, root surface iron concentration, root vitality, enzyme activities, and microstructural characteristics using advanced techniques such as root analysis, scanning electron microscopy (SEM), and ultrathin section transmission electron microscopy (TEM).ResultsThe results demonstrated that an increase in the Fe2+ concentration or a decrease in the PO43- concentration in the nutrient solution led to improvements in various root growth indicators. There was an elevation in the DCB (dithionite-citrate–bicarbonate) iron content within the roots, enhanced root vitality, and a significant increase in the activities of the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) enzymes. Moreover, as the Fe2+ concentration increased, amorphous iron oxide minerals on the root surface were gradually transformed into ferrihydrite particles with sizes of approximately 200 nm and goethite particles with sizes of approximately 5 μm. This study showed that an increase in the Fe2+ concentration and a decrease in the PO43- concentration led to the formation of substantial iron plaque on the root surfaces. It is noteworthy that there was a distinct gap ranging from 0.5 to 3 μm between the iron plaque formed through PO43- treatment and the cellular layer of the root surface.DiscussionThis study elucidated the impacts of Fe2+ and PO43- treatments on the formation, structure, and morphology of the iron plaque while discerning variations in the spatial proximity between the iron plaque and root surface under different treatment conditions.

Salinity is one of the major abiotic stresses besides drought and cold stress. The application of plant growth regulators (PGRs) is an effective method to mitigate yield losses caused by salinity. However, we investigated the effects of exogenous regulatory substances (γ-aminobutyric acid (GABA), salicylic acid (SA), and brassinolide (BR) on the growth and development of “Kyoho” grapevine under salt stress. The results showed that exogenous regulators GABA, SA, and BR alleviated the inhibition of grape growth by saline stress and regulated the effects of salinity stress on grape fruit development and quality. All three regulators significantly increased fruit set, cross-sectional diameter, weight per unit, and anthocyanin content. In conclusion, this study provides a theoretical basis for grape production practices by using exogenous aminobutyric acid (GABA), salicylic acid (SA), and brassinolide (BR) to mitigate the hazards of salinity stress.

The leaf chlorophyll content (LCC) of vegetation is closely related to photosynthetic efficiency and biological activity. Jujube (Ziziphus jujuba Mill.) is a traditional economic forest tree species. Non-destructive monitoring of LCC of jujube is of great significance for guiding agroforestry production and promoting ecological environment protection in arid and semi-arid lands. Hyperspectral data is an important data source for LCC detection. However, hyperspectral data consists of a multitude of bands and contains extensive information. As a result, certain bands may exhibit high correlation, leading to redundant spectral information. This redundancy can distort LCC prediction results and reduce accuracy. Therefore, it is crucial to select appropriate preprocessing methods and employ effective data mining techniques when analyzing hyperspectral data. This study aims to evaluate the performance of hyperspectral data for estimating LCC of jujube trees by integrating different derivative processing techniques with different dimensionality reduction algorithms. Hyperspectral reflectance data were obtained through simulations using an invertible forest reflectance model (INFORM) and measurements from jujube tree canopies. The least absolute shrinkage and selection operator (LASSO) and elastic net (EN) were employed to identify the important bands in the original spectra (OS), first derivative spectra (FD), and second derivative spectra (SD). Support vector regression (SVR) was used to establish the estimation model. The results show that compared with full-spectrum modeling, LASSO and EN algorithms are effective methods for preventing overfitting in LCC machine learning estimation models for different spectral derivatives. The LASSO/EN-based estimation models constructed using FD and SD exhibited superior R2 compared to the OS. The important band of SD can best reveal the relevant information of jujube LCC, and SD-EN-SVR is the most ideal model in both the simulated dataset (R2 = 0.99, RMSE=0.61) and measured dataset (R2 = 0.89, RMSE=0.91). Our results provided a reference for rapid and non-destructive estimation of the LCC of agroforestry vegetation using canopy hyperspectral data.

The ecological restoration of saline land in the Yellow River Delta is essential for the sustainability of this region. Halophytic species, like Suaeda salsa, are critical for the restoration process. However, potential differences in traits of heteromorphic seeds collected from the intertidal zone and inland condition have been largely overlooked. The seeds were analyzed for hardness, nutrient elements, and secretions, while structural differences were observed under a stereomicroscope. Germination percentages of the different seed types and subsequent seedling growth were also recorded. Our study found that the black seeds from intertidal zone had the highest hardness when compared to the three other types of seeds. Nutrient analysis revealed that brown seeds had a higher iron (Fe) content than black seeds. Accordingly, brown seed embryos were greener compared to their black seed counterparts due to the iron’s role in chlorophyll synthesis. Our results also revealed that brown seeds secreted greater amounts of exudates than black seeds. Finally, both the intertidal brown seeds and the inland-grown brown seeds had higher germination percentages and better early seedling growth than the corresponding black seeds. The differential characteristics between dimorphic seeds and seedlings may influence their environmental adaptation in different saline environments.

IntroductionThe evolution and maintenance of plant polymorphism have always received much attention. Gender diphasy is a rare sexual system. Plant individuals with gender diphasy can adjust the resource allocation of different functional organs according to the changes of environmental conditions to regulate the sex expression of individuals, and the sex expression can be converted between years. However, our understanding of sex expression in plants is still very insufficient. In this study, we explored whether the perennial plant Lilium concolor var. megalanthum has a gender diphasy system and whether environmental resource availability affects its resource allocation and sex expression.MethodBy collecting the bulbs of two sexual phenotypes (male and hermaphrodite) in the field and simulating the application of different levels of nutrients under the same habitat conditions, the growth and reproduction indexes and sex expression of plants in two years (2021 and 2022) were measured to evaluate the resource allocation strategy and sex expression pattern of Lilium concolor var. megalanthum.ResultsWe found that the sex expression of Lilium concolor var. megalanthum was variable in continuous years. Under limited resources, Lilium concolor var. megalanthum increases the biomass resources of the leaves and has a longer flowering period. Resource availability regulates the growth, reproduction and sex expression of Lilium concolor var. megalanthum. Bulb size is the main factor affecting its growth, reproduction and sex expression after accumulating sufficient resources.DiscussionThis study confirms that Lilium concolor var. megalanthum has gender diphasy system. There is a strong trade-off between growth and reproduction under limited resources. Nutrient levels can regulate the reproduction and sex expression process of Lilium concolor var. megalanthum. With the growth of Lilium concolor var. megalanthum in consecutive years, the size dependence of bulbs may be the decisive factor in its sex expression.

Long-term application of nitrogen (N) fertilizer adversely degrades soil and decreases crop yield. Biochar amendment with N fertilizer not only can increase yield but also can improve the soil. A 3-year field experiment was conducted to determine the effect of biochar doses with N fertilizer on maize yield and soil N and water dynamics under border irrigation (BI) and drip irrigation (DI) methods. Treatments were 260 kg N ha−1 without biochar addition and combined with low, medium, and high doses of biochar, namely, 15.5 t ha−1, 30.7 t ha−1, and 45.3 t ha−1 (NB0, NB1, NB2, and NB3), respectively. The biochar doses and irrigation methods significantly (p < 0.05) increased maize growth and yield characteristics, irrigation water use efficiency (IWUE), and fertilizer N use efficiency (FNUE) and enhanced the soil properties. In the BI and DI method, the NB1, NB2, and NB3 treatments increased yield by 4.96%–6.10%, 8.36%–9.85%, and 9.65%–11.41%, respectively, compared to NB0. In terms of IWUE and FNUE, the non-biochar treatment had lower IWUE and FNUE compared to biochar combined with N fertilizer treatments under both BI and DI methods. In the BI method, the IWUE in NB2 and NB3 ranged from 3.36 to 3.43 kg kg−1, and in DI, it was maximum, ranging from 5.70 to 5.94 kg kg−1. Similarly, these medium and high doses of biochar increased the FNUE of maize. The FNUEs in NB2 and NB3 under BI ranged from 38.72 to 38.95 kg kg−1 and from 38.89 to 39.58 kg kg−1, while FNUEs of these same treatments under DI ranged from 48.26 to 49.58 kg kg−1 and from 48.92 to 50.28 kg kg−1. The effect of biochar was more obvious in DI as compared to the BI method because soil water content (SWC) and soil N concentrations (SNCs) were higher at rhizosphere soil layers under DI. Biochar improved SWC and SNC at 0–20 cm and 20–40 cm soil layers and decreased below 60-cm soil layers. In contrast, despite biochar-controlled SWC and SNCs, still, values of these parameters were higher in deeper soil layers. In the BI method, the SNCs were higher at 60–80 cm and 80–100 cm compared to the top and middle soil layers. Depth-wise results of SNC demonstrated that the biochar’s ability to store SNC was further enhanced in the DI method. Moreover, biochar increased soil organic matter (OM) and soil aggregate stability and maintained pH. The NB0 treatment increased soil OM by 11.11%–14.60%, NB2 by 14.29%–19.42%, and NB3 by 21.98%–23.78% in both irrigation methods. This increased OM resulted in improved average soil aggregates stability by 2.45%–11.71% and 4.52%–14.66% in the BI and DI method, respectively. The results of our study revealed that combined application of N fertilizer with a medium dose of biochar under the DI method would be the best management practice, which will significantly increase crop yield, improve SWC, enrich SNC and OM, improve soil structure, and maintain pH.

Secondary soil salinization in arid and semi-arid regions is a serious problem that severely hampers local agricultural productivity and poses a threat to the long-term sustainability of food production. the utilization of organic soil amendments presents a promising approach to mitigate yield losses and promote sustainable agricultural production in saline-alkali soil. In this study, we established four distinct treatments, chemical fertilizer (CK), humic acid with chemical fertilizer (HA), carboxymethyl cellulose with chemical fertilizer (CMC), and amino acid with chemical fertilizer (AA), to elucidate their respective impacts on the reclamation of saline soil and the growth of maize. The findings of our study reveal notable variations in desalination rates within the 0-40 cm soil layer due to the application of distinct soil amendments, ranging from 11.66% to 37.17%. Moreover, application of amendments significantly increased the percentage of soil macro-aggregates as compared to the CK treatment. Furthermore, HA and AA treatments significantly augmented soil nutrient content (HA: 48.07%; AA: 39.50%), net photosynthetic rate (HA: 12.68%; AA: 13.94%), intercellular CO2 concentration (HA: 57.20%; AA: 35.93%) and maize yield (HA:18.32%; AA:16.81%). Correlation analysis and structural equation modeling unveiled diverse mechanisms of yield enhancement for HA, CMC, and AA treatments. HA enhanced yield by increasing organic matter and promoting soil aggregate formation, CMC improved soil water content and facilitated salt leaching due to its excellent water-holding properties, while AA increased yield by elevating soil organic matter and effective nitrogen content. Among the array of soil amendment materials scrutinized, HA treatment emerged as the most promising agent for enhancing soil conditions and is thus recommended as the preferred choice for treating local saline soils.

The great success of deep learning in the field of computer vision provides a development opportunity for intelligent information extraction of remote sensing images. In the field of agriculture, a large number of deep convolutional neural networks have been applied to crop spatial distribution recognition. In this paper, crop mapping is defined as a semantic segmentation problem, and a multi-scale feature fusion semantic segmentation model MSSNet is proposed for crop recognition, aiming at the key problem that multi-scale neural networks can learn multiple features under different sensitivity fields to improve classification accuracy and fine-grained image classification. Firstly, the network uses multi-branch asymmetric convolution and dilated convolution. Each branch concatenates conventional convolution with convolution nuclei of different sizes with dilated convolution with different expansion coefficients. Then, the features extracted from each branch are spliced to achieve multi-scale feature fusion. Finally, a skip connection is used to combine low-level features from the shallow network with abstract features from the deep network to further enrich the semantic information. In the experiment of crop classification using Sentinel-2 remote sensing image, it was found that the method made full use of spectral and spatial characteristics of crop, achieved good recognition effect. The output crop classification mapping was better in plot segmentation and edge characterization of ground objects. This study can provide a good reference for high-precision crop mapping and field plot extraction, and at the same time, avoid excessive data acquisition and processing.

In response to salt stress, plants alter the expression of manifold gene networks, enabling them to survive and thrive in the face of adversity. As a result, the growth and development of plant roots could be drastically altered, with significant inhibition of the growth of root meristematic zones. Although it is known that root growth is primarily regulated by auxins and cytokinins, the molecular regulatory mechanism by which salt stress stunts root meristems remains obscure. In this study, we found that the ZmmiR169q/ZmNF-YA8 module regulates the growth of maize taproots in response to salt stress. Salt stress downregulates ZmmiR169q expression, allowing for significant upregulation of ZmNF-YA8, which, in turn, activates ZmERF1B, triggering the upregulation of ASA1 and ASA2, two rate-limiting enzymes in the biosynthesis of tryptophan (Trp), leading to the accumulation of auxin in the root tip, thereby inhibiting root growth. The development of the maize root is stymied as meristem cell division and meristematic zone expansion are both stifled. This study reveals the ZmmiR169q/ZmNF-YA8 module’s involvement in maintaining an equilibrium in bestowing plant salt tolerance and root growth and development under salt stress, providing new insights into the molecular mechanism underlying the homeostatic regulation of plant development in response to salt stress.

This study presents a chromosome-level, near-complete genome assembly of Thalia dealbata (Marantaceae), a typical emergent wetland plant with high ornamental and environmental value. Based on 36.99 Gb PacBio HiFi reads and 39.44 Gb Hi-C reads, we obtained a 255.05 Mb assembly, of which 251.92 Mb (98.77%) were anchored into eight pseudo-chromosomes. Five pseudo-chromosomes were completely assembled, and the other three had one to two gaps. The final assembly had a high contig N50 value (29.80 Mb) and benchmarking universal single-copy orthologs (BUSCO) recovery score (97.52%). The T. dealbata genome had 100.35 Mb repeat sequences, 24,780 protein-coding genes, and 13,679 non-coding RNAs. Phylogenetic analysis revealed that T. dealbata was closest to Zingiber officinale, whose divergence time was approximately 55.41 million years ago. In addition, 48 and 52 significantly expanded and contracted gene families were identified within the T. dealbata genome. Moreover, 309 gene families were specific to T. dealbata, and 1,017 genes were positively selected. The T. dealbata genome reported in this study provides a valuable genomic resource for further research on wetland plant adaptation and the genome evolution dynamics. This genome is also beneficial for the comparative genomics of Zingiberales species and flowering plants.

Volatile compounds including terpenes, aldehyde, phenol, and alcohol are significantly contributed floral and fruity aromas to the Muscat variety. ‘Ruidu Hongyu’ grapevine is one of the newly developed grape varieties, and cultivation of this variety has been extended across China due to unique quality traits and taste. In this study, HS-SPME/GC−MS and transcriptome sequencing analysis were performed to evaluate the impact of exogenous 2,4-epibrassinolide (EBR), jasmonic acid (JA), and their signaling inhibitors brassinazole (Brz)/sodium diethyldithiocarbamate (DIECA) on the biosynthesis of aroma substances in ‘Ruidu Hongyu’ grapevine. According to the results, exogenous BR and JA promoted the accumulation of various aroma substances, including hexenal, 2-hexenal, nerol oxide, vanillin, hotrienol, terpineol, neral, nerol, geraniol, and geranic acid. After EBR and JA treatments, most of the genes responsible for terpene, aldehyde, and alcohol biosynthesis expressed at a higher level than the CK group. Relatively, EBR treatment could not only promote endogenous BR biosynthesis and metabolism but also elevate BR signaling transduction. JA treatment contributed to endogenous JA and MeJA accumulation, as well. Through transcriptome sequencing, a total of 3043, 903, 1470, and 607 DEGs were identified in JA vs. JD, JA vs. CK, BR vs. CK, and BR vs. Brz, respectively. There were more DEGs under both EBR and JA treatments at late fruit ripening stages. The findings of this study increase our understanding regarding aroma substances biosynthesis and endogenous BR/JA metabolism in response to exogenous EBR and JA signals.

IntroductionHumic substances (HSs), components of plant biostimulants, are known to influence plant physiological processes, nutrient uptake and plant growth, thereby increasing crop yield. However, few studies have focused on the impact of HS on overall plant metabolism, and there is still debate over the connection between HS’ structural characteristics and their stimulatory actions.MethodsIn this study, two different HSs (AHA, Aojia humic acid and SHA, Shandong humic acid) screened in a previous experiment were chosen for foliar spraying, and plant samples were collected on the tenth day after spraying (62 days after germination) to investigate the effects of different HSs on photosynthesis, dry matter accumulation, carbon and nitrogen metabolism and overall metabolism in maize leaf.Results and discussionThe results showed different molecular compositions for AHA and SHA and a total of 510 small molecules with significant differences were screened using an ESI-OPLC-MS techno. AHA and SHA exerted different effects on maize growth, with the AHA inducing more effective stimulation than the SHA doing. Untargeted metabolomic analysis revealed that the phospholipid components of maize leaves treated by SHA generally increased significantly than that in the AHA and control treatments. Additionally, both HS-treated maize leaves exhibited different levels of accumulation of trans-zeatin, but SHA treatment significantly decreased the accumulation of zeatin riboside. Compared to CK treatment, AHA treatment resulted in the reorganization of four metabolic pathways: starch and sucrose metabolism, TCA cycle, stilbenes, diarylheptanes, and curcumin biosynthesis, and ABC transport, SHA treatment modified starch and sucrose metabolism and unsaturated fatty acid biosynthesis. These results demonstrate that HSs exert their function through a multifaceted mechanism of action, partially connected to their hormone-like activity but also involving hormoneindependent signaling pathways.

IntroductionMaize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation.MethodsIn order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions.Results and discussionThe results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.

We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.

IntroductionOat (Avena sativa L.) is an important cereal crop grown worldwide for grain and forage, owing to its high adaptability to diverse environments. However, the genetic and genomics research of oat is lagging behind that of other staple cereal crops. MethodsIn this study, a collection of 288 oat lines originating worldwide was evaluated using 2,213 single nucleotide polymorphism (SNP) markers obtained from an oat iSelect 6K-beadchip array to study its genetic diversity, population structure, and linkage disequilibrium (LD) as well as the genotype–phenotype association for hullessness and lemma color.ResultsThe average gene diversity and polymorphic information content (PIC) were 0.324 and 0.262, respectively. The first three principal components (PCs) accounted for 30.33% of the genetic variation, indicating that the population structure of this panel of oat lines was stronger than that reported in most previous studies. In addition, accessions could be classified into two subpopulations using a Bayesian clustering approach, and the clustering pattern of accessions was closely associated with their region of origin. Additionally, evaluation of LD decay using 2,143 mapped markers revealed that the intrachromosomal whole-genome LD decayed rapidly to a critical r2 value of 0.156 for marker pairs separated by a genetic distance of 1.41 cM. Genome-wide association study (GWAS) detected six significant associations with the hullessness trait. Four of these six markers were located on the Mrg21 linkage group between 194.0 and 205.7 cM, while the other two significant markers mapped to Mrg05 and Mrg09. Three significant SNPs, showing strong association with lemma color, were located on linkage groups Mrg17, Mrg18, and Mrg20.DiscussionOur results discerned relevant patterns of genetic diversity, population structure, and LD among members of a worldwide collection of oat landraces and cultivars proposed to be ‘typical’ of the Qinghai-Tibetan Plateau. These results have important implications for further studies on association mapping and practical breeding in high-altitude oat.

Groundnut or peanut (Arachis hypogaea) is a legume crop. Its seeds are rich in protein and oil. Aldehyde dehydrogenase (ALDH, EC: 1.2.1.3) is an important enzyme involved in detoxification of aldehyde and cellular reactive oxygen species, as well as in attenuation of lipid peroxidation-meditated cellular toxicity under stress conditions. However, few studies have been identified and analyzed about ALDH members in Arachis hypogaea. In the present study, 71 members of the ALDH superfamily (AhALDH) were identified using the reference genome obtained from the Phytozome database. A systematic analysis of the evolutionary relationship, motif, gene structure, cis-acting elements, collinearity, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and expression patterns was conducted to understand the structure and function of AhALDHs. AhALDHs exhibited tissue-specific expression, and quantitative real-time PCR identified significant differences in the expression levels of AhALDH members under saline-alkali stress. The results revealed that some AhALDHs members could be involved in response to abiotic stress. Our findings on AhALDHs provide insights for further study.

High-affinity K+ transporters (HKTs) are known as transmembrane cation transporters and are involved in Na+ or Na+-K+ transport in plants. In this study, a novel HKT gene SeHKT1;2 was isolated and characterized from the halophyte, Salicornia europaea. It belongs to subfamily I of HKT and shows high homology with other halophyte HKT proteins. Functional characterization of SeHKT1;2 indicated that it contributes to facilitating Na+ uptake in Na+-sensitive yeast strains G19, however, cannot rescue the K+ uptake-defective phenotype of yeast strain CY162, demonstrating SeHKT1;2 selectively transports Na+ rather than K+. The addition of K+ along with NaCl relieved the Na+ sensitivity. Furthermore, heterologous expression of SeHKT1;2 in sos1 mutant of Arabidopsis thaliana increased salt sensitivity and could not rescued the transgenic plants. This study will provide valuable gene resources for improving the salt tolerance in other crops by genetic engineering.

Stem growth and development has considerable effects on plant architecture and yield performance. Strigolactones (SLs) modulate shoot branching and root architecture in plants. However, the molecular mechanisms underlying SLs regulate cherry rootstocks stem growth and development remain unclear. Our studies showed that the synthetic SL analog rac-GR24 and the biosynthetic inhibitor TIS108 affected stem length and diameter, aboveground weight, and chlorophyll content. The stem length of cherry rootstocks following TIS108 treatment reached a maximum value of 6.97 cm, which was much higher than that following rac-GR24 treatments at 30 days after treatment. Stem paraffin section showed that SLs affected cell size. A total of 1936, 743, and 1656 differentially expressed genes (DEGs) were observed in stems treated with 10 μM rac-GR24, 0.1 μM rac-GR24, and 10 μM TIS108, respectively. RNA-seq results highlighted several DEGs, including CKX, LOG, YUCCA, AUX, and EXP, which play vital roles in stem growth and development. UPLC-3Q-MS analysis revealed that SL analogs and inhibitors affected the levels of several hormones in the stems. The endogenous GA3 content of stems increased significantly with 0.1 μM rac-GR24 or 10 μM TIS108 treatment, which is consistent with changes in the stem length following the same treatments. This study demonstrated that SLs affected stem growth of cherry rootstocks by changing other endogenous hormone levels. These results provide a solid theoretical basis for using SLs to modulate plant height and achieve sweet cherry dwarfing and high-density cultivation.

Grape berries contain a variety of metabolites, such as anthocyanins, sugars, fatty acids, and antioxidants. Endogenous phytohormones strongly influence these metabolites, which regulate berry quality improvement. In this study, we evaluated the effects of 2,4-epibrassinolide (EBR, brassinolide (BR)-like growth regulator), jasmonic acid (JA), and their signaling inhibitors brassinazole (Brz), and sodium diethyldithiocarbamate (DIECA) on berry quality and antioxidant ability. Overall, the pre-harvest application of 0.5 mg L-1 EBR and 100 μmol L-1 JA significantly influences the quality of the grape berry. Results showed that EBR was superior to other treatments at enhancing the content of different metabolites, including anthocyanins, fructose, glucose, and a variety of fatty acids, in grapes. EBR and JA also enhanced the synthesis of gibberellin3 (GA3), cytokinin (CTK), salicylic acid (SA), JA, methyl jasmonate (MeJA), BR, and abscisic acid (ABA), while inhibiting the synthesis of auxin (IAA). Most genes related to BR/JA and anthocyanins/sugars/fatty acids biosynthesis were up-regulated. The effects of Brz and DIECA on the grape berry quality were totally reversed throughout the study, as shown by EBR and JA. According to correlation analysis, EBR and JA have a beneficial positive interaction that promotes the formation of strong coherences in grape berries between ABA/IAA/ZT-fruit expansion, BR/JA/MeJA/GA3/ZR-biochemical characteristics development, JA/MeJA/ABA/GA3/SA/ZR-antioxidant capacity enhancement, and JA/MeJA/IAA/GA3/ZT/ZR-fatty acids accumulation. In this regard, we concluded that preharvest exogenous 0.5 mg L-1 EBR and 100 μmol L-1 JA is a successful way to improve grape berry quality.

Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were applied to analyze metabolites in perilla leaves (PLs) during its developmental process. In total, 118 metabolites were identified, including volatile and non-volatile compounds, such as terpenoids, sugars, amino acids, organic acids, fatty acids, phenolic acids, flavonoids, and others. Principal component analysis (PCA) indicated great variations of metabolites during PLs development. Clustering analysis (CA) clarified the dynamic patterns of the metabolites. The heatmap of CA showed that most of the detected metabolites were significantly accumulated at stage 4 which is the pre anthesis period, and declined afterwards. The results of the present study provide a comprehensive overview of the metabolic dynamics of developing PLs which suggested that pre anthesis period is the best harvest time for PLs.

Effects of wind erosion on growth and adaptability have been widely reported in many plants, but little attention has been paid to dioecious plants. Recent studies have shown that sex-specific responses to environmental changes in many plants exist. To explore sexual differences in response to wind erosion, female and male Salix gordejevii saplings growing on inter-dune land (no erosion) and on the windward slope of the dune (20cm wind erosion) in Hunshandake Sandy Land were chosen and their morphology, biomass and physiological traits were investigated, respectively. Wind erosion significantly reduced plant growth, biomass accumulation, gas exchange and chlorophyll fluorescence, and obviously disrupted osmotic regulation function and antioxidant enzyme system in both sexes, especially in males. Under wind erosion condition, females exhibited higher sapling height (SH), basal diameter (BD), leaf dry mass (LDM), root dry mass (RDM), total dry mass (TDM), root percentage in total dry mass, net photosynthesis rate (Pn), maximum efficiency of photosystem II (Fv/Fm), effective quantum yield of PSII (ΦPSII), relative water content (RWC) of leaves, superoxide dismutase (SOD) and peroxidase (POD) activities, but lower malondialdehyde (MDA), proline as well as soluble sugar content than did males. However, no significant sexual differences in most of these traits were observed under no erosion condition. Our results demonstrated that females possess a greater resistance to wind erosion than do males, with females having a better photosynthetic capacity, stronger water retention capacity and more efficient antioxidant system to alleviate negative effects caused by aeolian environment.

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

Plant growth and its changes over space and time are effective indicators for signifying ecosystem health. However, large uncertainties remain in characterizing and attributing vegetation changes in the ecologically fragile South China Karst region, since most existing studies were conducted at a coarse spatial resolution or covered limited time spans. Considering the highly fragmented landscapes in the region, this hinders their capability in detecting fine information of vegetation dynamics taking place at local scales and comprehending the influence of climate change usually over relatively long temporal ranges. Here, we explored the spatiotemporal variations in vegetation greenness for the entire South China Karst region (1.9 million km2) at a resolution of 30m for the notably increased time span (1987-2018) using three decadal Landsat images and the cloud-based Google Earth Engine. Moreover, we spatially attributed the vegetation changes and quantified the relative contribution of driving factors. Our results revealed a widespread vegetation recovery in the South China Karst (74.80%) during the past three decades. Notably, the area of vegetation recovery tripled following the implementation of ecological engineering compared with the reference period (1987-1999). Meanwhile, the vegetation restoration trend was strongly sustainable beyond 2018 as demonstrated by the Hurst exponent. Furthermore, climate change contributed only one-fifth to vegetation restoration, whereas major vegetation recovery was highly attributable to afforestation projects, implying that anthropogenic influences accelerated vegetation greenness gains in karst areas since the start of the new millennium during which ecological engineering was continually established. Our study provides additional insights into ecological restoration and conservation in the highly heterogeneous karst landscapes and other similar ecologically fragile areas worldwide.

The root system is essential for the stable growth of plants. Roots help anchor plants in the soil and play a crucial role in water uptake, mineral nutrient absorption and endogenous phytohormone formation. Root-restriction (RR) cultivation, a powerful technique, confines plant roots to a specific soil space. In the present study, roots of one-year-old “Muscat Hamburg” grapevine under RR and control (nR) treatments harvested at 70 and 125 days after planting were used for transcriptome sequencing, and in total, 2031 (nR7 vs. nR12), 1445 (RR7 vs. RR12), 1532 (nR7 vs. RR7), and 2799 (nR12 vs. RR12) differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment analysis demonstrated that there were several genes involved in the response to different phytohormones, including abscisic acid (ABA), auxin (IAA), ethylene (ETH), gibberellins (GAs), and cytokinins (CTKs). Among them, multiple genes, such as PIN2 and ERF113, are involved in regulating vital plant movements by various phytohormone pathways. Moreover, following RR cultivation, DEGs were enriched in the biological processes of plant-type secondary cell wall biosynthesis, the defense response, programmed cell death involved in cell development, and the oxalate metabolic process. Furthermore, through a combined analysis of the transcriptome and previously published microRNA (miRNA) sequencing results, we found that multiple differentially expressed miRNAs (DEMs) and DEG combinations in different comparison groups exhibited opposite trends, indicating that the expression levels of miRNAs and their target genes were negatively correlated. Furthermore, RR treatment indeed significantly increased the ABA content at 125 days after planting and significantly decreased the IAA content at 70 days after planting. Under RR cultivation, most ABA biosynthesis-related genes were upregulated, while most IAA biosynthesis-related genes were downregulated. These findings lay a solid foundation for further establishing the network through which miRNAs regulate grapevine root development through target genes and for further exploring the molecular mechanism through which endogenous ABA and IAA regulate root architecture development in grapevine.

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 qTSE8 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.

Arbuscular mycorrhizal (AM) symbiosis in soil may be directly or indirectly involved in the reproductive process of sexually reproducing plants (seed plants), and affect their reproductive fitness. However, it is not clear how underground AM symbiosis affects plant reproductive function. Here, we reviewed the studies on the effects of AM symbiosis on plant reproductive fitness including both male function (pollen) and female function (seed). AM symbiosis regulates the development and function of plant sexual organs by affecting the nutrient using strategy and participating in the formation of hormone networks and secondary compounds in host plants. The nutrient supply (especially phosphorus supply) of AM symbiosis may be the main factor affecting plant's reproductive function. Moreover, the changes in hormone levels and secondary metabolite content induced by AM symbiosis can also affect host plants reproductive fitness. These effects can occur in pollen formation and transport, pollen tube growth and seed production, and seedling performance. Finally, we discuss other possible effects of AM symbiosis on the male and female functional fitness, and suggest several additional factors that may be involved in the influence of AM symbiosis on the reproductive fitness of host plants. We believe that it is necessary to accurately identify and verify the mechanisms driving the changes of reproductive fitness of host plant in symbiotic networks in the future. A more thorough understanding of the mechanism of AM symbiosis on reproductive function will help to improve our understanding of AM fungus ecological roles and may provide references for improving the productivity of natural and agricultural ecosystems.

Four P4-ATPase flippase genes, VdDrs2, VdNeo1, VdP4-4, and VdDnf1 were identified in Verticillium dahliae, one of the most devastating phytopathogenic fungi in the world. Knock out of VdDrs2, VdNeo1, and VdP4-4, or knock down of VdDnf1 significantly decreased the pathogenicity of the mutants in cotton. Among the mutants, the greatest decrease in pathogenicity was observed in ΔVdDrs2. VdDrs2 was localized to plasma membrane, vacuoles, and trans-Golgi network (TGN). In vivo observation showed that the infection of the cotton by ΔVdDrs2 was significantly delayed. The amount of two known Verticillium toxins, sulfacetamide, and fumonisin B1 in the fermentation broth produced by the ΔVdDrs2 strain was significantly reduced, and the toxicity of the crude Verticillium wilt toxins to cotton cells was attenuated. In addition, the defect of VdDrs2 impaired the synthesis of melanin and the formation of microsclerotia, and decreased the sporulation of V. dahliae. Our data indicate a key role of P4 ATPases-associated vesicle transport in toxin secretion of disease fungi and support the importance of mycotoxins in the pathogenicity of V. dahliae.

Cistanche salsa (C. A. Mey.) G. Beck, a holoparasitic desert medicine plant with multiple hosts, is regarded as a potential future desert economic plant. However, as a result of excessive exploitation and poaching, its wild resources have become scarce. Thus, before developing its desert economic value, this plant has to be protected, and the identification of its natural reserve is currently the top priority. However, in previous nature reserve prediction studies, the influence of host plants has been overlooked, particularly in holoparasitic plants with multiple hosts. In this study, we sought to identify the conservation areas of wild C. salsa by considering multiple host–plant interactions and climate change conditions using the MaxEnt model. Additionally, a Principal Component Analysis (PCA) was used to reduce the autocorrelation between environmental variables. The effects of the natural distribution of the host plants in terms of natural distribution from the perspective of niche similarities and extrapolation detection were considered by filtering the most influential hosts: Krascheninnikovia ceratoides (Linnaeus), Gueldenstaedt, and Nitraria sibirica Pall. Additionally, the change trends in these hosts based on climate change conditions combined with the change trends in C. salsa were used to identify a core protection area of 126483.5 km2. In this article, we corrected and tried to avoid some of the common mistakes found in species distribution models based on the findings of previous research and fully considered the effects of host plants for multiple-host holoparasitic plants to provide a new perspective on the prediction of holoparasitic plants and to provide scientific zoning for biodiversity conservation in desert ecosystems. This research will hopefully serve as a significant reference for decision-makers.

Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.

Northeast China is a major soybean production region in China. A representative sample of the Northeast China soybean germplasm population (NECSGP) composed of 361 accessions was evaluated for their seed protein content (SPC) in Tieling, Northeast China. This SPC varied greatly, with a mean SPC of 40.77%, ranging from 36.60 to 46.07%, but it was lower than that of the Chinese soybean landrace population (43.10%, ranging from 37.51 to 50.46%). The SPC increased slightly from 40.32–40.97% in the old maturity groups (MG, MGIII + II + I) to 40.93–41.58% in the new MGs (MG0 + 00 + 000). The restricted two-stage multi-locus genome-wide association study (RTM-GWAS) with 15,501 SNP linkage-disequilibrium block (SNPLDB) markers identified 73 SPC quantitative trait loci (QTLs) with 273 alleles, explaining 71.70% of the phenotypic variation, wherein 28 QTLs were new ones. The evolutionary changes of QTL-allele structures from old MGs to new MGs were analyzed, and 97.79% of the alleles in new MGs were inherited from the old MGs and 2.21% were new. The small amount of new positive allele emergence and possible recombination between alleles might explain the slight SPC increase in the new MGs. The prediction of recombination potentials in the SPC of all the possible crosses indicated that the mean of SPC overall crosses was 43.29% (+2.52%) and the maximum was 50.00% (+9.23%) in the SPC, and the maximum transgressive potential was 3.93%, suggesting that SPC breeding potentials do exist in the NECSGP. A total of 120 candidate genes were annotated and functionally classified into 13 categories, indicating that SPC is a complex trait conferred by a gene network.

Citrus is one of the most important fruits in China. Miyagawa Satsuma, one kind of citrus, is a nutritious agricultural product with regional characteristics of Chongming Island. Near-infrared Spectroscopy (NIR) is a proper method for studying the quality of fruits, because it is low-cost, efficient, non-destructive, and repeatable. Therefore, the NIR technique is used to detect citrus's soluble solid content (SSC) in this study. After obtaining the original spectral data, the first 70% of them are divided into the training set and 30% into the test set. Then, the Random Frog algorithm is chosen to select characteristic wavelengths, which reduces the dimension of the data and the complexity of the model, and accordingly makes the generalization of the classification model better. After comparing the performance of various classifiers (AdaBoost, KNN, LS-SVM, and Bayes) under different characteristic wavelength numbers, the AdaBoost classifier outperforms using 275 characteristic wavelengths for modeling eventually. The accuracy, precision, recall, and F1-score are 78.3%, 80.5%, 78.3%, and 0.780, respectively and the ROC (Receiver Operating Characteristic Curve, ROC curve) is close to the upper left corner, suggesting that the classification model is acceptable. The results demonstrate that it is feasible to use the NIR technique to estimate whether the citrus is sweet or not. Furthermore, it is beneficial for us to apply the obtained models for identifying the quality of citrus correctly. For fruit traders, the model helps them to determine the growth cycle of citrus more scientifically, improve the level of citrus cultivation and management and the final fruit quality, and thus increase the economic income of fruit traders.

Vaccinium berries are regarded as “superfoods” owing to their high concentrations of anthocyanins, flavonoid metabolites that provide pigmentation and positively affect human health. Anthocyanin localization differs between the fruit of cultivated highbush blueberry (V. corymbosum) and wild bilberry (V. myrtillus), with the latter having deep red flesh coloration. Analysis of comparative transcriptomics across a developmental series of blueberry and bilberry fruit skin and flesh identified candidate anthocyanin regulators responsible for this distinction. This included multiple activator and repressor transcription factors (TFs) that correlated strongly with anthocyanin production and had minimal expression in blueberry (non-pigmented) flesh. R2R3 MYB TFs appeared key to the presence and absence of anthocyanin-based pigmentation; MYBA1 and MYBPA1.1 co-activated the pathway while MYBC2.1 repressed it. Transient overexpression of MYBA1 in Nicotiana benthamiana strongly induced anthocyanins, but this was substantially reduced when co-infiltrated with MYBC2.1. Co-infiltration of MYBC2.1 with MYBA1 also reduced activation of DFR and UFGT, key anthocyanin biosynthesis genes, in promoter activation studies. We demonstrated that these TFs operate within a regulatory hierarchy where MYBA1 activated the promoters of MYBC2.1 and bHLH2. Stable overexpression of VcMYBA1 in blueberry elevated anthocyanin content in transgenic plants, indicating that MYBA1 is sufficient to upregulate the TF module and activate the pathway. Our findings identify TF activators and repressors that are hierarchically regulated by SG6 MYBA1, and fine-tune anthocyanin production in Vaccinium. The lack of this TF module in blueberry flesh results in an absence of anthocyanins.

Land degradation caused by soil salinization and wind erosion is the major obstruction to sustainable agriculture in the arid region. Salsola species have the potential to prevent land degradation. However, there is limited information about seed germination requirements and tolerance to salinity and drought for representative Salsola species. This study aimed to assess the effects of the winged perianth (seed structural features) and abiotic factors (light, temperature, salinity, and drought) on the seed germination of these species. These Salsola species varied considerably in seed germination characteristics. Compared with naked seeds, winged seeds had lower germination percentages for S. heptapotamica S. rosacea, and S. nitraria species. Darkness decreased the germination percentage of winged and naked seeds of S. rosacea, however, for S. heptapotamica and S. nitraria, decreased seed germination was only when the winged perianth existed. Germination of S. heptapotamica, S. rosacea, and S. nitraria seeds depended on the perianth and light conditions. The naked seeds of these three species could germinate at a wide range of temperatures, especially in light. The presence of perianth, light, and temperature did not significantly influence the germination of S. ruthenica seeds. When cultivating these species, it is beneficial to remove the winged perianth of seeds and sow it on the soil surface when the temperature is above 5/15°C. In addition, seed germination of Salsola displayed high tolerance to salinity and drought. Compared with winged seeds, naked seeds showed lower recovery germination under high salinity but had a similar recovery of germination under high PEG concentration. Our study provides detailed germination information for the cultivation of these four representative Salsola species in degraded saline soils of the arid zone.

Foliar zinc (Zn) fertilization is an important approach for overcoming crop Zn deficiency, yet little is known regarding the subsequent translocation of this foliar-applied Zn. Using synchrotron-based X-ray fluorescence microscopy (XFM) and transcriptome analysis, the present study examined the translocation of foliar absorbed Zn in sunflower (Helianthus annuus) leaves. Although bulk analyses showed that there had been minimal translocation of the absorbed Zn out of the leaf within 7 days, in situ analyses showed that the distribution of Zn in the leaf had changed with time. Specifically, when Zn was applied to the leaf for 0.5 h and then removed, Zn primarily accumulated within the upper and lower epidermal layers (when examined after 3 h), but when examined after 24 h, the Zn had moved to the vascular tissues. Transcriptome analyses identified a range of genes involved in stress response, cell wall reinforcement, and binding that were initially upregulated following foliar Zn application, whereas they were downregulated after 24 h. These observations suggest that foliar Zn application caused rapid stress to the leaf, with the initial Zn accumulation in the epidermis as a detoxification strategy, but once this stress decreased, Zn was then moved to the vascular tissues. Overall, this study has shown that despite foliar Zn application causing rapid stress to the leaf and that most of the Zn stayed within the leaf over 7 days, the distribution of Zn in the leaf had changed, with Zn mostly located in the vascular tissues 24 h after the Zn had been applied. Not only do the data presented herein provide new insight for improving the efficiency of foliar Zn fertilizers, but our approach of combining XFM with a transcriptome methodological system provides a novel approach for the study of element translocation in plants.

To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size.

Soybean mosaic virus (SMV) is detrimental to soybean (Glycine max) breeding, seed quality, and yield worldwide. Improving the basic resistance of host plants is the most effective and economical method to reduce damage from SMV. Therefore, it is necessary to identify and clone novel SMV resistance genes. Here, we report the characterization of two soybean cultivars, DN50 and XQD, with different levels of resistance to SMV. Compared with XQD, DN50 exhibits enhanced resistance to the SMV strain SC7. By combining bulked-segregant analysis (BSA)-seq and fine-mapping, we identified a novel resistance locus, RSMV-11, spanning an approximately 207-kb region on chromosome 11 and containing 25 annotated genes in the reference Williams 82 genome. Of these genes, we identified eleven with non-synonymous single-nucleotide polymorphisms (SNPs) or insertion-deletion mutations (InDels) in their coding regions between two parents. One gene, GmMATE68 (Glyma.11G028900), harbored a frameshift mutation. GmMATE68 encodes a multidrug and toxic compound extrusion (MATE) transporter that is expressed in all soybean tissues and is induced by SC7. Given that MATE transporter families have been reported to be linked with plant disease resistance, we suggest that GmMATE68 is responsible for SC7 resistance in DN50. Our results reveal a novel SMV-resistance locus, improving understanding of the genetics of soybean disease resistance and providing a potential new tool for marker-assisted selection breeding in soybean.

In most grapevine planting regions, especially in south of China, plenty of rainfall and high water level underground are the characteristic of the area, a series of problem during fruit ripening easily caused poor color quality. Thereby affecting fruit quality, yield and economic benefits. The accumulation of anthocyanin is regulated by transcriptional regulatory factor and a series of cultivation measures, root restriction can make plants in the environment of stress and stress relief, root restriction induced the higher expression of VvMYB15 and VvWRKY40, and consistent with anthocyanin accumulation. Whether and how root restriction-inducible VvMYB15 and VvWRKY40 transcription factor regulate anthocyanin synthesis in grape berry is still unclear. In this study, we identified that the transient overexpression of VvMYB15 and VvWRKY40 alone or both in strawberry fruits and grape berries can promote anthocyanin accumulation and increase the expression level of anthocyanin biosynthetic genes, indicating VvMYB15 and VvWRKY40 play a positive regulator of anthocyanin biosynthesis. Furthermore, we confirmed that both VvMYB15 and VvWRKY40 specifically bind to the promoter region of VvF3′5′H and VvUFGT, and the expression of VvF3′5′H and VvUFGT is further activated through the heterodimer formation between VvMYB15 and VvWRKY40. Finally, we confirmed that VvMYB15 promoted anthocyanin accumulation by interacting with VvWRKY40 in grape berries, our findings provide insights into a mechanism involving the synergistic regulation of root restriction-dependent coloration and biosynthesis via a VvMYB15 and VvWRKY40 alone or both in grape berries.