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Crop models are instrumental in simulating resource utilization in agriculture, yet their complexity necessitates extensive calibration, which can impact the accuracy of yield predictions. Machine learning shows promise for enhancing yield estimations but relies on vast amounts of training data. This study aims to improve the pakchoi yield prediction accuracy of simulation models. We developed a stacking ensemble learning model that integrates three base models—EU-Rotate_N, Random Forest Regression and Support Vector Regression—with a Multi-layer Perceptron as the meta-model for the pakchoi dry matter yield prediction. To enhance the training dataset and bolster machine learning performance, we employed the EU-Rotate_N model to simulate daily dry matter yields for unsampled data. The test results revealed that the stacking model outperformed each base model. The stacking model achieved an R² value of 0.834, which was approximately 0.1 higher than that of the EU-Rotate_N model. The RMSE and MAE were 0.283 t/ha and 0.196 t/ha, respectively, both approximately 0.6 t/ha lower than those of the EU-Rotate_N model. The performance of the stacking model, developed with the expanded dataset, showed a significant improvement over the model based on the original dataset. [ABSTRACT FROM AUTHOR]

Pumpkin (Cucurbita maxima) is an important vegetable crop of the Cucurbitaceae plant family. The fruits of pumpkin are often used as directly edible food or raw material for a number of processed foods. In nature, mature pumpkin fruits differ in size, shape, and color. The Atlantic Giant (AG) cultivar has the world's largest fruits and is described as the giant pumpkin. AG is well-known for its large and bright-colored fruits with high ornamental and economic value. At present, there are insufficient studies that have focused on the formation factors of the AG cultivar. To address these knowledge gaps, we performed comparative transcriptome, proteome, and metabolome analysis of fruits from the AG cultivar and a pumpkin with relatively small fruit (Hubbard). The results indicate that up-regulation of gene-encoded expansins contributed to fruit cell expansion, and the increased presence of photoassimilates (stachyose and D-glucose) and jasmonic acid (JA) accumulation worked together in terms of the formation of large fruit in the AG cultivar. Notably, perhaps due to the rapid transport of photoassimilates, abundant stachyose that was not converted into glucose in time was detected in giant pumpkin fruits, implying that a unique mode of assimilate unloading is in existence in the AG cultivar. The potential molecular regulatory network of photoassimilate metabolism closely related to pumpkin fruit expansion was also investigated, finding that three MYB transcription factors, namely CmaCh02G015900, CmaCh01G018100, and CmaCh06G011110, may be involved in metabolic regulation. In addition, neoxanthin (a type of carotenoid) exhibited decreased accumulation that was attributed to the down-regulation of carotenoid biosynthesis genes in AG fruits, which may lead to pigmentation differences between the two pumpkin cultivars. Our current work will provide new insights into the potential formation factors of giant pumpkins for further systematic elucidation. [ABSTRACT FROM AUTHOR]

The optimization of the sink-source relationship is of great importance for crop yield regulation. Cucumber is a typical raffinose family oligosaccharide (RFO)-transporting crop. DNA methylation is a common epigenetic modification in plants, but its role in sink-source regulation has not been demonstrated in RFO-translocating species. Here, whole-genome bisulfite sequencing (WGBS-seq) was conducted to compare the nonfruiting-node leaves (NFNLs) and leaves of fruit setting (FNLs) at the 12th node by removing all female flowers in other nodes of the two treatments. We found considerable differentially methylated genes enriched in photosynthesis and carbohydrate metabolic processes. Comparative transcriptome analysis between FNLs and NFNLs indicated that many differentially expressed genes (DEGs) with differentially methylated regions were involved in auxin, ethylene and brassinolide metabolism; sucrose metabolism; and RFO synthesis pathways related to sink-source regulation. Moreover, DNA methylation levels of six sink-source-related genes in the pathways mentioned above decreased in leaves after 5-aza-dC-2′-deoxycytidine (5-Aza-dC, a DNA methyltransferase inhibitor) treatment on FNLs, and stachyose synthase (CsSTS) gene expression, enzyme activity and stachyose content in RFO synthesis pathway were upregulated, thereby increasing fruit length and dry weight. Taken together, our findings proposed an up-to-date inference for the potential role of DNA methylation in the sink-source relationship, which will provide important references for further exploring the molecular mechanism of DNA methylation in improving the yield of RFO transport plants. [ABSTRACT FROM AUTHOR]

Straw mulching on wet beds is an effective method to alleviate continuous cropping obstacles in greenhouses. However, this technique cannot be applied in the production of leafy vegetables with high planting density. Straw mulching in furrows is an alternative method in this circumstance. In this study, celery (Apium graveolens L.), a vegetable that prefers a high planting density and wet soil, was used to test furrow straw mulching technology, and the effect of different straw amounts and straw decomposers on soil improvement and celery production was investigated. The results showed that straw mulching in furrows significantly reduced soil conductivity and nitrate nitrogen levels, increased the contents of soil organic carbon as well as phosphorus and potassium nutrients in the bed, and improved celery yield and quality, indicating the significant lateral movement of released nutrients between the furrow and bed. The positive effects of 15,000 kg/ha straw application were more pronounced than those of 7500 kg/ha and 11,250 kg/ha. In addition, straw decomposers accelerated nutrient release and improved celery yield and quality. A decomposer named "ZhuBang" containing Bacillus licheniformis was the most effective. We concluded that furrow straw mulching combined with straw decomposer application is an effective measure for the sustainable production of leafy vegetables in intensive vegetable production facilities. [ABSTRACT FROM AUTHOR]

The bZIP (basic leucine zipper) proteins play crucial roles in various biological functions. Nitrogen (N) is an essential element for plant growth, especially in cucumber (Cucumis sativus) due to its shallow roots. However, the regulation of bZIP genes in cucumber nitrogen metabolism has not been studied yet. In this study, we identified a total of 72 bZIP genes (CsbZIPs) in the cucumber genome that could be classified into 13 groups. These genes were unevenly distributed on seven chromosomes, and synteny analysis showed that the CsbZIP genes were expanded in a segmentally duplicating manner. Furthermore, our genome-wide expression analysis suggested that CsbZIP genes had different patterns and that five CsbZIP genes were regulated by nitrogen treatment in both leaves and roots. Consistent with CsNPF, CsbZIP55 and CsbZIP65 were regulated by nitrogen treatment in leaves and roots. Moreover, the subcellular localization showed that CsbZIP55 and CsbZIP65 were specifically located in the nucleus, and the transcriptional activation assay showed that CsbZIP55 and CsbZIP65 have transcriptional activation activity. Additionally, in the CsbZIP55 and CsbZIP65 overexpression plants, most nitrogen-regulated CsNPF genes were downregulated. Taken together, our comprehensive analysis of the bZIP gene family lays a foundation for understanding the molecular and physiological functions of CsbZIPs. [ABSTRACT FROM AUTHOR]

Invertases and their inhibitors play important roles in sucrose metabolism, growth and development, signal transduction, and biotic and abiotic stress tolerance in many plant species. However, in cucumber, both the gene members and functions of invertase and its inhibitor families remain largely unclear. In this study, in comparison with the orthologues of Citrullus lanatus (watermelon), Cucumis melo (melon), and Arabidopsis thaliana (Arabidopsis), 12 invertase genes and 12 invertase inhibitor genes were identified from the genome of Cucumis sativus (cucumber). Among them, the 12 invertase genes were classified as 4 cell wall invertases, 6 cytoplasmic invertases, and 2 vacuolar invertases. Most invertase genes were conserved in cucumber, melon, and watermelon, with several duplicate genes in melon and watermelon. Transcriptome analysis distinguished these genes into various expression patterns, which included genes CsaV3_2G025540 and CsaV3_2G007220, which were significantly expressed in different tissues, organs, and development stages, and genes CsaV3_7G034730 and CsaV3_5G005910, which might be involved in biotic and abiotic stress. Six genes were further validated in cucumber based on quantitative real-time PCR (qRT–PCR), and three of them showed consistent expression patterns as revealed in the transcriptome. These results provide important information for further studies on the physiological functions of cucumber invertases (CSINVs) and their inhibitors (CSINHs). [ABSTRACT FROM AUTHOR]

Soil is the base for conventional plant growth. The rhizosphere pressure generated from soil compaction shows a dual effect on plant growth in agricultural production. Compacted soil leads to root growth stagnation and causes bending or thickening, thus affecting the growth of aboveground parts of plants. In arrowhead (Sagittaria trifolia L.), the corms derived from the expanded tips of underground stolons are its storage organ. We found that the formation of corms was significantly delayed under hydroponic conditions without rhizosphere pressure originating from soil/sand. In the initial stage of corm expansion, the anatomic structure of arrowhead corm-forming parts harvested from hydroponics and sand culture was observed, and we found that the corm expansion was derived from cell enlargement and starch accumulation. Comparative transcriptome analysis indicated that the corm expansion was closely related to the change in endogenous hormone levels. Endogenous abscisic acid and salicylic acid concentrations were significantly increased in sand-cultured corms. Higher ethylene and jasmonic acid contents were also detected in all arrowhead samples, demonstrating that these hormones may play potential roles in the rhizosphere pressure response and corm expansion. The expression of genes participating in hormone signaling could explain the rising accumulation of certain hormones. Our current results draw an extensive model to reveal the potential regulation mechanism of arrowhead corm expansion promoted by rhizosphere pressure, which will provide important references for further studying the molecular mechanism of rhizosphere pressure modulating the development of underground storage organs in other plants. [ABSTRACT FROM AUTHOR]

To pursue high yields, the excessive application of nitrogen (N) fertilizer has been reported in high-residual soil nitrate levels, excessive nitrate leaching, and nitrate contamination of groundwater. In this study, tomato crops (Lycopersicon esculentum Mill.) were subjected to various nitrogen treatments, and the nitrate nitrogen content, soil water content at different soil layers, dry matter, and yield were measured. A mechanistic model, EU-Rotate_N, was used to simulate the aforementioned indexes in a region of Jiangsu province with a relatively higher water table. The predicted values of soil moisture and soil nitrate content at various soil depths agree well with the measured values during tomato growth. The statistical index of soil water content ranged from 0.367 to 0.749, 0.856 to 0.947, and the statistical index of soil nitrate nitrogen content ranged from 0.365 to 0.698, and 0.869 to 0.932, for Autumn-Winter (AW) and Spring-Summer (SS) crops, respectively. Moreover, the dry weight and yield simulation effects of the tomato are also in good agreement with the actual measured values. The results show that the EU-Rotate_N model is effective in simulating soil water content, nitrate nitrogen content, dry matter quality, and yield in Jiangsu province, with little underestimation in soil water content at a soil depth of 20–30 cm during SS, which might be improved further considering the high water table of the region. [ABSTRACT FROM AUTHOR]

Real-time quantitative PCR (RT-qPCR) is a method with high sensitivity and convenience that has been extensively used to analyze the expression level of target genes. A reference gene with a highly stable expression is required to ensure the accuracy of experimental results. However, the report on appropriate reference genes in arrowheads (Sagittaria trifolia) is still limited. In this study, eight candidate reference genes (ACT5, UBQ, GAPDH, CYP, NAC, IDH, SLEEPER and PLA) were selected. The candidate genes were employed in a RT-qPCR assay in different tissues at different developmental stages of the same tissue (including corm, leaf and leafstalk) in arrowheads. Five statistical algorithms, GeNorm, NormFinder, BestKeeper, delta cycle threshold (ΔCt) and RefFinder, were used to evaluate the stability of these genes' expressions in order to identify the appropriate reference genes. The results showed that UBQ was the optimum reference gene in leaf, leafstalk, root, stolon and corm, IDH exhibited the most stable expression during the expansion of corm, UBQ and PLA were the most stable reference genes in developmental stages of leaf and leafstalk, respectively. Finally, the reliability of reference genes was further confirmed by the normalization of PDS and EXP1 genes under different arrowhead tissues and developmental stages of corm, respectively. This study constitutes important guidance for the selection of reliable reference genes for analyzing the tissue- and developmental-stage-specific expression of genes in arrowheads. [ABSTRACT FROM AUTHOR]

MADS-box genes are important transcription factors in eukaryotes that are involved in regulating the growth and development of many plants. Jiaobai is a special aquatic vegetable formed through the stem expansion of Zizania latifolia infected by Ustilago esculenta and is wildly cultivated in Southeast Asia. To date, the biological function of MADS-box genes in Z. latifolia remains largely unknown. In this study, a genome-wide search for MADS-box genes in Z. latifolia was performed, and 87 MADS-box genes were identified. According to the phylogenetic analysis, there were 27 type I genes and 60 type II genes. The type I genes were mainly distributed in the Mα, Mβ and Mγ subfamilies, and the type II genes were divided into 14 subfamilies and unevenly distributed across 17 chromosomes. The encoded protein sequences ranged from 91 to 433 amino acids, the number of exons was 1~14, and most type I genes did not contain introns. The promoter region contained a large number of functional domains related to light response, plant hormones, stress and the meristem. An analysis of the expression patterns showed that there were massive differences in the expression of the MADS-box genes in different tissues, with six genes highly expressed in leaves and eight genes highly expressed in the stem apical meristem. Photoperiod and temperature were found to regulate the formation of the stem gall (SG) of Z. latifolia, and short-day (SD) conditions had an obvious promoting effect. ZlMADS57 and ZlMADS85 were significantly increased in SG under SD. Further analysis of the expression levels of MADS-box genes during the developmental stages of Z. latifolia found that the ZlMADS45, ZlMADS57, ZlMADS81 and ZlMADS85 were highly expressed 10 days before the SG formation, and ZlMADS66 reached its highest value on the day when the SG began forming. ZlMADS14, ZlMADS15, ZlMADS32, ZlMADS36, ZlMADS59 and ZlMADS71 were highly expressed after SG expansion, indicating that the MADS-box gene may play an important role in regulating SG formation and the subsequent expansion of Jiaobai. This study provides a reference for the functional identification of the MADS-box gene family and establishes a foundation for regulating the maturity of Z. latifolia. [ABSTRACT FROM AUTHOR]

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins perform an essential role in regulating plant nitrate absorption and distribution and in improving plant nitrogen use efficiency. In this study, cucumber (Cucumis sativus L.) NPF genes were comprehensively analyzed at the whole genome level, and 54 NPF genes were found to be unevenly distributed on seven chromosomes in the cucumber genome. The phylogenetic analysis showed that these genes could be divided into eight subfamilies. We renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes. By surveying the expression profiles of CsNPF genes in various tissues, we found that CsNPF6.4 was specifically expressed in roots, indicating that CsNPF6.4 may play a role in N absorption; CsNPF6.3 was highly expressed in petioles, which may be related to NO3− storage in petioles; and CsNPF2.8 was highly expressed in fruits, which may promote NO3− transport to the embryos. We further examined their expression patterns under different abiotic stress and nitrogen conditions, and found that CsNPF7.2 and CsNPF7.3 responded to salt, cold, and low nitrogen stress. Taken together, our study lays a foundation for further exploration of the molecular and physiological functions of cucumber nitrate transporters. [ABSTRACT FROM AUTHOR]

WD40 proteins, a super gene family in eukaryotes, are involved in multiple biological processes. Members of this family have been identified in several plants and shown to play key roles in various development processes, including acting as scaffolding molecules with other proteins. However, WD40 proteins have not yet been systematically analyzed and identified in Cucurbita maxima. In this study, 231 WD40 proteins (CmWD40s) were identified in C. maxima and classified into five clusters. Eleven subfamilies were identified based on different conserved motifs and gene structures. The CmWD40 genes were distributed in 20 chromosomes; 5 and 33 pairs of CmWD40s were distinguished as tandem and segmental duplications, respectively. Overall, 58 pairs of orthologous WD40 genes in C. maxima and Arabidopsis thaliana, and 56 pairs of orthologous WD40 genes in C. maxima and Cucumis sativus were matched. Numerous CmWD40s had diverse expression patterns in fruits, leaf, stem, and root. Several genes were involved in responses to NaCl. The expression pattern of CmWD40s suggested their key role in fruit development and abiotic stress response. Finally, we identified 14 genes which might be involved in fruit development. Our results provide valuable basis for further functional verification of CmWD40s in C. maxima. [ABSTRACT FROM AUTHOR]

The rational use of a large amount of straw produced from grain fields is an important issue in major grain-producing areas. On the other hand, due to the long-term preferential applications of chemical fertilizers, soil organic carbon (SOC) content, soil fertility and organic matter levels have decreased, and the soil physical-chemical properties have deteriorated in protected agricultural facilities. In this study, a wet crop, taro (Colocasia esculenta (L.) Schott) and the straw of two main crops [wheat (Triticum aestivum L.) and rice (Oryza sativa L.)] were selected to investigate the effect of row-surface straw mulching on taro yields and soil chemical properties. The results showed that nearly all wheat straw and 74% of rice straw decomposed in one season under wet conditions. Straw mulching significantly increased the taro yield, increased the levels of SOC, soil rapid available nitrogen, phosphorus and potassium, and improved the activities of sucrase and phosphatase in the soil. We conclude that row-surface straw mulching t of wet crops could not only improve the soil properties and crop yields in the protected facility but could also consume considerable straw (wheat: 14,250 kg/ha, rice: 111,00 kg/ha), and the method applied in other areas with similar conditions. [ABSTRACT FROM AUTHOR]

The controlling of robotic arms based on brain–computer interface (BCI) can revolutionize the quality of life and living conditions for individuals with physical disabilities. Invasive electroencephalography (EEG)-based BCI has been able to control multiple degrees of freedom (DOFs) robotic arms in three dimensions. However, it is still hard to control a multi-DOF robotic arm to reach and grasp the desired target accurately in complex three-dimensional (3D) space by a noninvasive system mainly due to the limitation of EEG decoding performance. In this study, we propose a noninvasive EEG-based BCI for a robotic arm control system that enables users to complete multitarget reach and grasp tasks and avoid obstacles by hybrid control. The results obtained from seven subjects demonstrated that motor imagery (MI) training could modulate brain rhythms, and six of them completed the online tasks using the hybrid-control-based robotic arm system. The proposed system shows effective performance due to the combination of MI-based EEG, computer vision, gaze detection, and partially autonomous guidance, which drastically improve the accuracy of online tasks and reduce the brain burden caused by long-term mental activities. [ABSTRACT FROM AUTHOR]

A Raffinose family oligosaccharides (RFOs) is one of the major translocated sugars in the vascular bundle of cucumber, but little RFOs can be detected in fruits. Alpha-galactosidases (α-Gals) catalyze the first catabolism step of RFOs. Six α-Gal genes exist in a cucumber genome, but their spatial functions in fruits remain unclear. Here, we found that RFOs were highly accumulated in vascular tissues. In phloem sap, the stachyose and raffinose content was gradually decreased, whereas the content of sucrose, glucose and fructose was increased from pedicel to fruit top. Three alkaline forms instead of acid forms of α-Gals were preferentially expressed in fruit vascular tissues and alkaline forms have stronger RFO-hydrolysing activity than acid forms. By inducible gene silencing of three alkaline forms of α-Gals, stachyose was highly accumulated in RNAi-CsAGA2 plants, while raffinose and stachyose were highly accumulated in RNAi-CsAGA1 plants. The content of sucrose, glucose and fructose was decreased in both RNAi-CsAGA1 and RNAi-CsAGA2 plants after β-estradiol treatment. In addition, the fresh- and dry-weight of fruits were significantly decreased in RNAi-CsAGA1 and RNAi-CsAGA2 plants. In cucurbitaceous plants, the non-sweet motif within the promoter of ClAGA2 is widely distributed in the promoter of its homologous genes. Taken together, we found RFOs hydrolysis occurred in the vascular tissues of fruits. CsAGA1 and CsAGA2 played key but partly distinct roles in the hydrolysis of RFOs. [ABSTRACT FROM AUTHOR]