Sucrose Utilization for Improved Crop Yields: A Review Article

Foliar application of ferroferric oxide nanomaterials enhance source-sink communication and growth in soybean

Innovative technology to address iron deficiency in agriculture while reducing environmental burden is needed because of increasing food demand for the rapidly rising global population. The impact of foliar application of ferroferric oxide nanomaterials (Fe3O4 NMs) at different concentrations (1-50 mg/L) on soybean growth were investigated in the whole life cycle. The beneficial effects of Fe3O4 NMs on soybean were concentration-dependent and exhibited nano-effect. Foliar application with 10 mg/L Fe3O4 NMs exhibited the best performance, notably improving fresh shoot biomass by 9.7-36.2 % among three stages, and increasing root/shoot ratio by 39.1-78.2 %, which are higher than commercial iron fertilizer. Transcriptomic and metabolomic analyses revealed that Fe3O4 NMs: (1) increased soybean photosynthesis to supply more sucrose in soybean leaves; (2) upregulated sucrose transporter genes expression, enhanced auxin and abscisic acid content, and augmented stage-specific sucrose-related metabolites (including tricarboxylic acid cycle and amino acids at seedling stage, the antioxidants at flowering and mature stage) in leaves, thereby enhancing the ability of sucrose transport from source to sink, and finally improving the developments of soybean different sinks among different stages. Our findings highlight the considerable potential of Fe3O4 NMs as a sustainable and high-efficiency crop fertilizer strategy.

Transcriptomic Analysis Identifies Molecular Response of the Tolerant Alfalfa (Medicago sativa) Cultivar Nongjing 1 to Saline-Alkali Stress

Alfalfa (Medicago sativa) is a perennial forage crop with significant economic and ecological significance. If alfalfa can be planted in saline-alkali land, it will not only improve the utilization rate of marginal land and alleviate the competition between forage and cereal crops for arable land but will also increase the yield of high-quality domestic forage. In this study, we conducted transcriptomic analysis on the saline-alkali-tolerant alfalfa cultivar NQ-1 and compared its metabolite accumulation levels with saline-alkali-sensitive cultivars. The results showed that under saline-alkali stress, the photosynthesis and some secondary metabolic pathways in NQ-1 were activated, such as α-Linolenic acid metabolism, Phenylpropanoid and Flavonoid biosynthesis, and Photosynthesis-related pathways, providing substances and energy for enhancing NQ-1 stress tolerance. Furthermore, some specific flavonoids were detected that may contribute to the saline-alkali tolerance of NQ-1. In addition, transcription factors that may regulate flavonoid biosynthesis in NQ-1 under saline-alkali stress were also identified. This study deepens the understanding of the resistance mechanism of saline-alkali-tolerant cultivars of alfalfa and provides valuable information for molecular design breeding strategies for stress-resistant alfalfa.

Exploring Plant Resilience Through Secondary Metabolite Profiling: Advances in Stress Response and Crop Improvement

The metabolome, encompassing small molecules within organisms, provides critical insights into physiology, environmental influences, and stress responses. Metabolomics enables comprehensive analysis of plant metabolites, uncovering biomarkers and mechanisms underlying stress adaptation. Regulatory genes such as MYB and WRKY are central to secondary metabolite synthesis and environmental resilience. By integrating metabolomics with genomics, researchers can explore stress-related pathways and advance crop improvement efforts. This review examines metabolomic profiling under stress conditions, emphasizing drought tolerance mechanisms mediated by amino acids and organic acids. Additionally, it highlights the shikimate pathway's pivotal role in synthesizing amino acids and secondary metabolites essential for plant defense. These insights contribute to understanding metabolic networks that drive plant resilience, informing strategies for agricultural sustainability.

QTL mapping and whole-genome sequencing analysis for novel genetic resources associated with sucrose content in soybean [Glycine max (L.) Merr.]

KEY MESSAGE

A major QTL for sucrose content was mapped on chromosome 8 in PI 506593. The novel genetic variants and candidate genes were further identified within the major QTL. Sucrose in soybean [Glycine max (L.) Merr.] contribute to animal feed efficiency and natural sweetness of soy products. Thus, identifying novel genetic resources, such as quantitative trait loci (QTL), associated with sucrose content in soybean is essential for enhancing seed values. In this study, two recombinant inbred line populations derived from the same high sucrose donor parent, PI 506593, were used to identify significant QTLs. A total of 11 sucrose-related regions on chromosomes (Chrs.) 4, 5, 6, 8, 10, and 13 were identified using QTL analysis. Among them, four QTLs (qSUC_08.1, qSUC_08.2, qSUC_08.3, and qSUC_08.4) were clustered in the interval of 40,597,410-42,861,364 bp on Chr. 8, which was considered major QTL region. A desirable marker at 41,834,095 bp was tested in two populations, showing that two phenotypically extreme groups were efficiently differentiated. We further identified 44 and 54 candidate genes with non-synonymous mutations in the major QTL region based on the annotations of Wm82.a2.v1 and Wm82.a5.v1 assemblies, respectively. Among 54 candidate genes from Wm82.a5.v1, Protein Variation Effect Analyzer (PROVEAN) revealed that 18 genes contained 34 variants that had deleterious impacts on biological functions. RNA-seq analysis highlighted five candidate genes that were highly expressed in pod and seed tissues during reproductive stages and other plant parts. A gene, Gm_Wm82_23219 (Glyma.08G293800, Wm82.a2.v1) encoding proline-rich protein 4-like, was highlighted in both PROVEAN and RNA-seq analyses. Novel findings in this study will be valuable genetic resources in soybean breeding programs that aim to improve efficiency in animal feed and human food.

Divergence in the effects of sugar feedback regulation on the major gene regulatory network and metabolism of photosynthesis in leaves between the two founding Saccharum species

Sugarcane is a crop that accumulates sucrose with high photosynthesis efficiency. Therefore, the feedback regulation of sucrose on photosynthesis is crucial for improving sugarcane yield. Saccharum spontaneum and Saccharum officinarum are the two founding Saccharum species for modern sugarcane hybrids. S. spontaneum exhibits a higher net photosynthetic rate but lower sucrose content than S. officinarum. However, the mechanism underlying the negative feedback regulation of photosynthesis by sucrose remains poorly understood. This study investigates the effects of exogenous sucrose treatment on S. spontaneum and S. officinarum. Exogenous sucrose treatment increases sucrose content in the leaf base but inhibits photosynthetic efficiency and the expression of photosynthesis-related pathway genes (including RBCS and PEPC) in both species. However, gene expression patterns differed significantly, with few differentially expressed genes (DEGs) shared between the two species, indicating a differential response to exogenous sucrose. The expression networks of key genes involved in sugar metabolism, sugar transport, and PEPC and RBCS showed divergence between two species. Additionally, DEGs involved in the pentose phosphate pathway and the metabolism of alanine, aspartate, and glutamate metabolism were uniquely enriched in S. spontaneum, potentially contributing to the differential changes in sucrose content in the tip between the two species. We propose a model of the mechanisms underlying the negative feedback regulation of photosynthesis by sucrose in the leaves of S. spontaneum and S. officinarum. Our findings enhance the understanding of sucrose feedback regulation on photosynthesis and provide insights into the divergent molecular mechanisms of sugar accumulation in Saccharum.

Characterization of Main Responsive Genes Reveals Their Regulatory Network Attended by Multi-Biological Metabolic Pathways in Paclobutrazol (PAC)-Modulated Grape Seed Development (GSD) at the Stone-Hardening Stage

Paclobutrazol (PAC) is a significant inhibitor of gibberellin biosynthesis that profoundly influences grape seed development (GSD) through the modulation of key molecular pathways. Here, we identified 6659 differentially expressed genes (DEGs) in GSD under PAC treatment, with 3601 up-regulated and 3058 down-regulated. An analysis of hormone-associated DEGs revealed that auxin-related genes (16) were the most up-regulated, followed by genes associated with brassinosteroid and ABA. In contrast, cytokinin- and gibberellin-related genes exhibited a suppressive response. PAC treatment also triggered extensive reprogramming of metabolic pathways, including 44 genes involved in starch and sucrose metabolism (24 up-regulated, 20 down-regulated), 101 cell wall-related genes (53 up-regulated, 48 down-regulated), and 110 transcription factors (77 up-regulated, 33 down-regulated). A cis-element analysis of the promoters of 76 hormone-responsive genes identified 14 types of hormone-responsive cis-elements, with ABRE being the most prevalent. Genes responsible for inactivating active hormones, such as ABA-VvPP2CA, IAA-VvGH3.1, and CK-VvARR9-1, were also identified. Concurrently, PAC negatively regulated hormone-active genes, including BR-VvXTH25, SA-VvTGA21-3, and JA-VvTIFY3B, leading to reduced levels of these hormones. PAC modulates GSD by mediating the dynamic balance of multi-hormone accumulations. Furthermore, development-related cis-elements such as the AACA-motif, AAGAA-motif, AC-I, AC-II, O2-site, as-1, CAT-box, CCAAT-box, circadian, GCN4-motif, RY-element, HD-Zip 1, HD-Zip 3, MSA-like, MYB-like sequence, MYB-binding site, and MYB recognition site, were found in key DEGs involved in starch and sucrose metabolism, cell wall remodeling, and epigenetic regulation. This indicates that these pathways are responsive to PAC modulation during GSD. Finally, we developed a comprehensive regulatory network to illustrate the PAC-mediated pathways involved in GSD. This network integrates multi-hormonal signaling, cell wall remodeling, epigenetic regulation, and transcription factors, highlighting PAC's pivotal role in GSD. Our findings provide new insights into the complex mechanisms underlying PAC's effects on grapevine development.

Engineering source-sink relations by prime editing confers heat-stress resilience in tomato and rice

A 2°C climate-warming scenario is expected to further exacerbate average crop losses by 3%-13%, yet few heat-tolerant staple-crop varieties are available toward meeting future food demands. Here, we develop high-efficiency prime-editing tools to precisely knockin a 10-bp heat-shock element (HSE) into promoters of cell-wall-invertase genes (CWINs) in elite rice and tomato cultivars. HSE insertion endows CWINs with heat-responsive upregulation in both controlled and field environments to enhance carbon partitioning to grain and fruits, resulting in per-plot yield increases of 25% in rice cultivar Zhonghua11 and 33% in tomato cultivar Ailsa Craig over heat-stressed controls, without fruit quality penalties. Up to 41% of heat-induced grain losses were rescued in rice. Beyond a prime-editing system for tweaking gene expression by efficiently delivering bespoke changes into crop genomes, we demonstrate broad and robust utility for targeted knockin of cis-regulatory elements to optimize source-sink relations and boost crop climate resilience.

BX517, an inhibitor of the mammalian phospholipid-dependent kinase 1 (PDK1), antagonizes sucrose-induced plant growth and represses the target of rapamycin (TOR) signaling and the cell cycle through WEE1 kinase in Arabidopsis thaliana

The target of rapamycin (TOR) signaling pathway is critical for plant growth and stress adaptation through maintaining the proper balance between cell proliferation and differentiation. Here, by using BX517, an inhibitor of the mammalian phosphoinositide-dependent protein kinase 1 (PDK1), we tested the hypothesis that a plant ortholog of PDK1 could influence the TOR complex activity and its target, the S6 ribosomal protein kinase (S6K) in Arabidopsis seedlings. Through locally applying sucrose to leaves, which promotes root growth and plant biomass production via TOR signaling, we could demonstrate the opposite trend upon BX517 treatment, which antagonized sucrose-induced plant growth and overly decreased root development through inhibiting the expression of mitotic cyclins CYCB1 and CYCA3 in root meristems. Evidence was gathered that the WEE1 kinase, a master regulator of the DNA damage rescue system in meristems, operates downstream of a plant BX517 target(s). TOR protein activity and WEE1 expression were analyzed through protein blots and reporter gene activity, respectively, and their relationship with meristematic cell cycle progression was tested through genetic analyses. BX517 reduced TOR kinase activity, activated WEE1 expression in shoot, root, and lateral root meristems, and inhibited meristematic cell cycle progression in roots, suggesting that PDK1 is a critical element for plant responses to mitogenic factors through modulating TOR activity. Our data uncover a relation between a PDK1 ortholog with TOR activity and the expression of WEE1 kinase for growth and stress responses in plants.

The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus

One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.

Identifying candidate genes for sugar accumulation in sugarcane: an integrative approach

BACKGROUND

Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high degree of polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation. One successful strategy for identifying candidate genes linked to agronomic traits, particularly those associated with sugar accumulation, leverages synteny and potential collinearity with related species.

RESULTS

In this study, we explored synteny between sorghum and sugarcane. Genes from a sorghum Brix QTL were used to screen bacterial artificial chromosome (BAC) libraries from two Brazilian sugarcane varieties (IACSP93-3046 and SP80-3280). The entire region was successfully recovered, confirming synteny and collinearity between the species. Manual annotation identified 51 genes in the hybrid varieties that were subsequently confirmed to be present in Saccharum spontaneum. This study employed a multifaceted approach to identify candidate genes for sugar accumulation, including retrieving the genomic region of interest, performing a gene-by-gene analysis, analyzing RNA-seq data for internodes from Saccharum officinarum and S. spontaneum accessions, constructing a coexpression network to examine the expression patterns of genes within the studied region and their neighbors, and finally identifying differentially expressed genes (DEGs).

CONCLUSIONS

This comprehensive approach led to the discovery of three candidate genes potentially involved in sugar accumulation: an ethylene-responsive transcription factor (ERF), an ABA 8'-hydroxylase, and a prolyl oligopeptidase (POP). These findings could be valuable for identifying additional candidate genes for other important agricultural traits and directly targeting candidate genes for further work in molecular breeding.

Precise application of water and fertilizer to crops: challenges and opportunities

Precision water and fertilizer application technologies have emerged as crucial innovations in sustainable agriculture, addressing the pressing need to enhance crop yield and quality while optimizing resource use and minimizing environmental impacts. This review systematically explores the latest advancements in precision water and fertilizer application technologies. It examines the integration of advanced sensors, remote sensing, and machine learning algorithms in precision agriculture, assessing their roles in optimizing irrigation and nutrient management. The study evaluates various precision techniques, including micro-irrigation systems, variable rate technology (VRT), and predictive modeling, along with their implementation in diverse agricultural settings. Furthermore, the review addresses the challenges posed by soil environmental heterogeneity and emphasizes the necessity for a scientific index system to guide precise applications. Advanced irrigation methods, such as subsurface drip irrigation and micro-sprinkling, improve water-use efficiency and reduce salinity levels, while precision fertilization techniques optimize nutrient uptake and minimize leaching. The integration of machine learning and remote sensing facilitates real-time monitoring and adaptive management, resulting in increased resource use efficiency and reduced environmental pollution. However, the effectiveness of these technologies is contingent upon addressing soil heterogeneity and developing standardized application indices. This review highlights the novel combination of advanced sensing technologies and data analytics in precision agriculture, enabling targeted interventions tailored to specific field conditions. It underscores the importance of integrating soil microbial community dynamics and biochemical indicators with precision management practices to enhance soil fertility and crop performance. Furthermore, the development of predictive models and time series analysis tools represents a significant advancement in anticipating and responding to changing environmental conditions. Precision water and fertilizer application technologies offer substantial benefits for sustainable agricultural practices by improving crop yields, enhancing resource efficiency, and mitigating environmental impacts. The strategic integration of these technologies with tailored agricultural practices and robust monitoring systems is essential for optimizing nutrient cycling and maintaining soil health. Addressing existing challenges through interdisciplinary research and collaborative efforts will further advance the implementation of precision agriculture, contributing to long-term soil sustainability and global food security.

Enhancing Photosynthetic Carbon Transport in Rice Plant Optimizes Rhizosphere Bacterial Community in Saline Soil

Saline soils exert persistent salt stress on plants that inhibits their ability to carry out photosynthesis and leads to photosynthetic carbon (C) scarcity in plant roots and the rhizosphere. However, it remains unclear how a rhizosphere environment is shaped by photosynthetic C partitioning under saline conditions. Given that sucrose is the primary form of photosynthetic C transport, we, respectively, created sucrose transport distorted (STD) and enhanced (STE) rice lines through targeted mutation and overexpression of the sucrose transporter gene OsSUT5. This approach allowed us to investigate different scenarios of photosynthate partitioning to the rhizosphere. Compared to the non-saline soil, we found a significant decrease in soil dissolved organic carbon (DOC) in the rhizosphere, associated with a reduction in bacterial diversity when rice plants were grown under moderate saline conditions. These phenomena were sharpened with STD plants but were largely alleviated in the rhizosphere of STE plants, in which the rhizosphere DOC, and the diversity and abundances of dominant bacterial phyla were measured at comparable levels to the wildtype plants under non-saline conditions. The complexity of bacteria showed a greater level in the rhizosphere of STE plants grown under saline conditions. Several salt-tolerant genera, such as Halobacteroidaceae and Zixibacteria, were found to colonize the rhizosphere of STE plants that could contribute to improved rice growth under persistent saline stresses, due to an increase in C deposition.

Combined transcriptome and physiological analysis reveals exogenous sucrose enhances photosynthesis and source capacity in foxtail millet

Foxtail millet (Setaria italica (L.) P. Beauv.) is an environmentally friendly crop that meets the current requirements of international food security and is widely accepted as a photosynthesis research model. However, whether exogenous sucrose treatment has a positive effect on foxtail millet growth remains unknown. Here, we employed physiological and molecular approaches to identify photosynthesis and source capacity associated with exogenous sucrose during the growth of Jingu 21 seedlings. RNA-seq analysis showed that some differentially expressed genes (DEGs) related to photosynthesis and carotenoid biosynthesis were induced by exogenous sucrose and that most of these genes were up-regulated. An increase in gas exchange parameters, chlorophyll content, and chlorophyll fluorescence of Jingu 21 was noted after exogenous sucrose addition. Furthermore, exogenous sucrose up-regulated genes encoding sucrose and hexose transporters and enhanced starch and sucrose metabolism. More DEGs were up-regulated by sucrose, the nonstructural carbohydrate (NSC) content in the leaves increased and energy metabolism and sucrose loading subsequently improved, ultimately enhancing photosynthesis under normal and dark conditions. Further analysis revealed that WRKYs, ERFs, HY5, RAP2, and ABI5 could be key transcription factors involved in growth regulation. These results indicate that exogenous sucrose affects the normal photosynthetic performance of foxtail millet by increasing NSC transport and loading. They improve our understanding of the molecular mechanisms of the effects of exogenous sucrose on photosynthesis in foxtail millet, providing an effective measure to enhance source-sink relationships and improve yield.

Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa

Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1' was treated with 50 mM NaHCO3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties.

Comparative analysis of the nutritional, physicochemical, and bioactive characteristics of Artemisia abyssinica and Artemisia arborescens for the evaluation of their potential as ingredients in functional foods

Artemisia abyssinica and Artemisia arborescens are unique plants that show significant bioactive properties and are used for the treatment of a variety of diseases. This study assessed the nutritional values, functional properties, chemical composition, and bioactive attributes of these plants as functional nutritional supplements. Compared to A. arborescens, A. abyssinica had higher fat (4.76%), fiber (16.07%), total carbohydrates (55.87%), and energy (302.15 kcal/100 g DW), along with superior functional properties, including higher water and oil absorption capacities (638.81% and 425.85%, respectively) and foaming capacity and stability (25.67% and 58.48%). The investigation of volatile compounds found that A. abyssinica had higher amounts of hotrienol (4.53%), yomogi alcohol (3.92%), caryophyllene (3.67%), and carvotanacetone (3.64%), which possess anti-inflammatory, antimicrobial, and antioxidant properties. Artemisia abyssinica contributed over 30% of the recommended dietary intake (RDI) of amino acids. It displayed superior levels of sodium (31.46 mg/100 g DW) and calcium (238.07 mg/100 g DW). It also exhibited higher levels of organic acids, particularly malic acid, butyric acid, and succinic acid, compared to A. arborescens. Fatty acid analysis revealed palmitic and linoleic acids as primary components in both plants, with A. abyssinica having a higher palmitic acid content. Artemisia abyssinica also had higher vitamin C and thiamine levels. Although A. arborescens showed the highest total phenolic content (TPC), antioxidant activity, and capacity, A. abyssinica demonstrated acceptable efficiency in TPC and antioxidant content. These findings highlight the potential of both Artemisia species, particularly A. abyssinica, as valuable sources of nutrients and bioactive compounds for various applications.

Phosphorus deficiency promotes root:shoot ratio and carbon accumulation via modulating sucrose utilization in maize

Phosphorus deficiency usually promotes root:shoot ratio and sugar accumulation. However, how the allocation and utilization of carbon assimilates are regulated by phosphorus deficiency remains unclear. To understand how phosphorus deficiency affects the allocation and utilization of carbon assimilates, we systematically investigated the fixation and utilization of carbon, along with its diurnal and spatial patterns, in hydroponically grown maize seedlings under low phosphorus treatment. Under low phosphorus, sucrolytic activity was slightly inhibited by 12.0% in the root but dramatically inhibited by 38.8% in the shoot, corresponding to the promoted hexose/sucrose ratio and biomass in the root. Results point to a stable utilization of sucrose in the root facilitating competition for more assimilates, while increasing root:shoot ratio. Moreover, starch and sucrose accumulated in the leaves under low phosphorus. Spatially, starch and sucrose were oppositely distributed, starch mainly in the leaf tip, and sucrose mainly in the leaf base and sheath. Evidence of sucrose getting stuck in leaf base and sheath suggests that carbon accumulation is not attributed to carbon assimilation or export disturbance, but may be due to poor carbon utilization in the sinks. These findings improve the understanding of how low phosphorus regulates carbon allocation between shoot and root for acclimation to stress, and highlight the importance of improving carbon utilization in sinks to deal with phosphorus deficiency.

Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.)

Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.

Engineering the Rhizosphere Microbiome with Plant Growth Promoting Bacteria for Modulation of the Plant Metabolome

Plant-growth-promoting bacteria (PGPB) have beneficial effects on plants. They can promote growth and enhance plant defense against abiotic stress and disease, and these effects are associated with changes in the plant metabolite profile. The research problem addressed in this study was the impact of inoculation with PGPB on the metabolite profile of Salicornia europaea L. across controlled and field conditions. Salicornia europaea seeds, inoculated with Brevibacterium casei EB3 and Pseudomonas oryzihabitans RL18, were grown in controlled laboratory experiments and in a natural field setting. The metabolite composition of the aboveground tissues was analyzed using GC-MS and UHPLC-MS. PGPB inoculation promoted a reconfiguration in plant metabolism in both environments. Under controlled laboratory conditions, inoculation contributed to increased biomass production and the reinforcement of immune responses by significantly increasing the levels of unsaturated fatty acids, sugars, citric acid, acetic acid, chlorogenic acids, and quercetin. In field conditions, the inoculated plants exhibited a distinct phytochemical profile, with increased glucose, fructose, and phenolic compounds, especially hydroxybenzoic acid, quercetin, and apigenin, alongside decreased unsaturated fatty acids, suggesting higher stress levels. The metabolic response shifted from growth enhancement to stress resistance in the latter context. As a common pattern to both laboratory and field conditions, biopriming induced metabolic reprogramming towards the expression of apigenin, quercetin, formononetin, caffeic acid, and caffeoylquinic acid, metabolites that enhance the plant's tolerance to abiotic and biotic stress. This study unveils the intricate metabolic adaptations of Salicornia europaea under controlled and field conditions, highlighting PGPB's potential to redesign the metabolite profile of the plant. Elevated-stress-related metabolites may fortify plant defense mechanisms, laying the groundwork for stress-resistant crop development through PGPB-based inoculants, especially in saline agriculture.

Enhancing Photosynthesis and Plant Productivity through Genetic Modification

Enhancing crop photosynthesis through genetic engineering technologies offers numerous opportunities to increase plant productivity. Key approaches include optimizing light utilization, increasing cytochrome b6f complex levels, and improving carbon fixation. Modifications to Rubisco and the photosynthetic electron transport chain are central to these strategies. Introducing alternative photorespiratory pathways and enhancing carbonic anhydrase activity can further increase the internal CO2 concentration, thereby improving photosynthetic efficiency. The efficient translocation of photosynthetically produced sugars, which are managed by sucrose transporters, is also critical for plant growth. Additionally, incorporating genes from C4 plants, such as phosphoenolpyruvate carboxylase and NADP-malic enzymes, enhances the CO2 concentration around Rubisco, reducing photorespiration. Targeting microRNAs and transcription factors is vital for increasing photosynthesis and plant productivity, especially under stress conditions. This review highlights potential biological targets, the genetic modifications of which are aimed at improving photosynthesis and increasing plant productivity, thereby determining key areas for future research and development.

Photosynthetic Performance, Carbohydrate Partitioning, Growth, and Yield among Cassava Genotypes under Full Irrigation and Early Drought Treatment in a Tropical Savanna Climate

In a tropical savanna climate like Thailand, cassava can be planted all year round and harvested at 8 to 12 months after planting (MAP). However, it is not clear how water limitation during the dry season without rain affects carbon assimilation, partitioning, and yield. In this field investigation, six cassava genotypes were planted in the rainy season (August 2021) under continuous irrigation (control) or subjected to drought for 60 days from 3MAP to 5MAP during the dry season (November 2021 to January 2022) with no irrigation and rainfall. After that, the plants were rewatered and continued growing until harvest at 12MAP. After 60 days of stress, there were significant reductions in the mean net photosynthesis rate (Pn), petiole, and root dry weight (DW), and slight reductions in leaf, stem, and tuber DW. The mean starch concentrations were reduced by 42% and 16% in leaves and tubers, respectively, but increased by 12% in stems. At 6MAP after 30 days of rewatering, Pn fully recovered, and stem starch was remobilized resulting in a dramatic increase in the DW of all the organs. Although the mean tuber DW of the drought plants at 6MAP was significantly lower than that of the control, it was significantly higher at 12MAP. Moreover, the mean tuber starch concentration at 12MAP of the drought plants (18.81%) was also significantly higher than that of the controls (16.46%). In the drought treatment, the high-yielding varieties, RY9, RY72, KU50, and CMR38-125-77 were similarly productive in terms of tuber DW and starch concentration while the breeding line CM523-7 produced the lowest tuber biomass and significantly lower starch content. Therefore, for cassava planted in the rainy season in the tropical savanna climate, the exposure to drought during the early growth stage was more beneficial than the continuous irrigation.

Transcriptome profiling reveals the impact of various levels of biochar application on the growth of flue-cured tobacco plants

BACKGROUND

Biochar, a carbon-rich source and natural growth stimulant, is usually produced by the pyrolysis of agricultural biomass. It is widely used to enhance plant growth, enzyme activity, and crop productivity. However, there are no conclusive studies on how different levels of biochar application influence these systems.

METHODS AND RESULTS

The present study elucidated the dose-dependent effects of biochar application on the physiological performance, enzyme activity, and dry matter accumulation of tobacco plants via field experiments. In addition, transcriptome analysis was performed on 60-day-old (early growth stage) and 100-day-old (late growth stage) tobacco leaves to determine the changes in transcript levels at the molecular level under various biochar application levels (0, 600, and 1800 kg/ha). The results demonstrated that optimum biochar application enhances plant growth, regulates enzymatic activity, and promotes biomass accumulation in tobacco plants, while higher biochar doses had adverse effects. Furthermore, transcriptome analysis revealed a total of 6561 differentially expressed genes (DEGs) that were up- or down-regulated in the groupwise comparison under different treatments. KEGG pathways analysis demonstrated that carbon fixation in photosynthetic organisms (ko00710), photosynthesis (ko00195), and starch and sucrose metabolism (ko00500) pathways were significantly up-regulated under the optimal biochar dosage (600 kg/ha) and down-regulated under the higher biochar dosage (1800 kg/ha).

CONCLUSION

Collectively, these results indicate that biochar application at an optimal rate (600 kg/ha) could positively affect photosynthesis and carbon fixation, which in turn increased the synthesis and accumulation of sucrose and starch, thus promoting the growth and dry matter accumulation of tobacco plants. However, a higher biochar dosage (1800 kg/ha) disturbs the crucial source-sink balance of organic compounds and inhibits the growth of tobacco plants.

Characteristics of kopyor coconut (Cocos nucifera L.) using sensory analysis and metabolomics-based approach

Kopyor is a coconut with unique characteristics from Indonesia, one of the largest coconut producers in the world. Kopyor is an edible mature coconut with soft endosperm. Although this fruit is one of the most popular coconuts in the world, there are limited studies on its properties, including its sensory attributes and metabolite profiles. This study investigates the characteristics of kopyor using sensory evaluation, a widely targeted metabolomics approach, and multivariate analysis. The liquid (water) and solid (flesh) endosperms were collected as the samples. The results showed that kopyor has characteristics that distinguish it from normal mature and young coconuts. Kopyor water has a milky, creamy, nutty, bitter, and astringent taste with an oily aftertaste and mouthfeel. Kopyor flesh is soft and moist and gives a sandy mouth feel. This study analyzed the sensory attributes of the kopyor endosperm for the first time and compared it with those of normal mature and young coconuts. A gas chromatography mass spectrometry analysis showed that kopyor contained wider variety of metabolites than normal coconuts of the same age. Based on the differential analysis and orthogonal projections to latent structures-regression, kopyor water was characterized by the accumulation of flavor-related metabolites, such as amino acids and organic acids, which contributed to its sensory complexity. This study solidified the effects of maturation and endosperm type on metabolite accumulation in kopyor endosperm. This pioneering information will lead to the future use of kopyor and other unique coconuts worldwide for food, contributing to the sustainability of the coconut industry.

Physiological and transcriptome analysis of changes in endogenous hormone and sugar content during the formation of tender asparagus stems

Asparagus is a nutritionally dense stem vegetable whose growth and development are correlated with its quality and yield. To investigate the dynamic changes and underlying mechanisms during the elongation and growth process of asparagus stems, we documented the growth pattern of asparagus and selected stem segments from four consecutive elongation stages using physiological and transcriptome analyses. Notably, the growth rate of asparagus accelerated at a length of 25 cm. A significant decrease in the concentration of sucrose, fructose, glucose, and additional sugars was observed in the elongation region of tender stems. Conversely, the levels of auxin and gibberellins(GAs) were elevated along with increased activity of enzymes involved in sucrose degradation. A significant positive correlation existed between auxin, GAs, and enzymes involved in sucrose degradation. The ABA content gradually increased with stem elongation. The tissue section showed that cell elongation is an inherent manifestation of stem elongation. The differential genes screened by transcriptome analysis were enriched in pathways such as starch and sucrose metabolism, phytohormone synthesis metabolism, and signal transduction. The expression levels of genes such as ARF, GA20ox, NCED, PIF4, and otherswere upregulated during stem elongation, while DAO, GA2ox, and other genes were downregulated. The gene expression level was consistent with changes in hormone content and influenced the cell length elongation. Additionally, the expression results of RT-qPCR were consistent with RNA-seq. The observed variations in gene expression levels, endogenous hormones and sugar changes during the elongation and growth of asparagus tender stems offer valuable insights for future investigations into the molecular mechanisms of asparagus stem growth and development and provide a theoretical foundation for cultivation and production practices.

Genetic association analysis in sugarcane (Saccharum spp.) for sucrose accumulation in humid environments in Colombia

BACKGROUND

Sucrose accumulation in sugarcane is affected by several environmental and genetic factors, with plant moisture being of critical importance for its role in the synthesis and transport of sugars within the cane stalks, affecting the sucrose concentration. In general, rainfall and high soil humidity during the ripening stage promote plant growth, increasing the fresh weight and decreasing the sucrose yield in the humid region of Colombia. Therefore, this study aimed to identify markers associated with sucrose accumulation or production in the humid environment of Colombia through a genome-wide association study (GWAS).

RESULTS

Sucrose concentration measurements were taken in 220 genotypes from the Cenicaña's diverse panel at 10 (early maturity) and 13 (normal maturity) months after planting. For early maturity data was collected during plant cane and first ratoon, while at normal maturity it was during plant cane, first, and second ratoon. A total of 137,890 SNPs were selected after sequencing the 220 genotypes through GBS, RADSeq, and whole-genome sequencing. After GWAS analysis, a total of 77 markers were significantly associated with sucrose concentration at both ages, but only 39 were close to candidate genes previously reported for sucrose accumulation and/or production. Among the candidate genes, 18 were highlighted because they were involved in sucrose hydrolysis (SUS6, CIN3, CINV1, CINV2), sugar transport (i.e., MST1, MST2, PLT5, SUT4, ERD6 like), phosphorylation processes (TPS genes), glycolysis (PFP-ALPHA, HXK3, PHI1), and transcription factors (ERF12, ERF112). Similarly, 64 genes were associated with glycosyltransferases, glycosidases, and hormones.

CONCLUSIONS

These results provide new insights into the molecular mechanisms involved in sucrose accumulation in sugarcane and contribute with important genomic resources for future research in the humid environments of Colombia. Similarly, the markers identified will be validated for their potential application within Cenicaña's breeding program to assist the development of breeding populations.

Seasonal and Morphology Effects on Bioactive Compounds, Antioxidant Capacity, and Sugars Profile of Black Carrot (Daucus carota ssp. sativus var. atrorubens Alef.)

Black carrot (Daucus carota ssp. sativus var. atrorubens Alef.) is widely recognized for its bioactive compounds and antioxidant properties. The black carrot of Cuevas Bajas (Málaga) is a local variety characterized by a black/purple core, which differs from other black carrot varieties. Therefore, this autochthonous variety was characterized according to the root size and the harvesting season by means of a study of its antioxidant capacity analyzed by three methods, its total carotenoids content, and its sugars and phenolic compounds profile by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-MS). A total of 20 polyphenolic compounds were quantified in 144 samples analyzed. The anthocyanidins group was observed to be the most abundant, followed by the hydroxycinnamic acids group. Moreover, pelargonidin 3-sambubioside was observed in black carrot for the first time. The medium-sized carrots presented the highest content of phenolic compounds, largely due to their significantly higher anthocyanidins content. Comparatively, the small carrots showed a higher content of simple sugars than the large ones. Regarding the influence of season, significantly higher quantities of glucose and fructose were observed in the late-season carrots, while sucrose was the main sugar in early-season samples. No significant differences were observed in the total carotenoid content of black carrot.

SMS2, a Novel Allele of OsINV3, Regulates Grain Size in Rice

Grain size has an important effect on rice yield. Although several key genes that regulate seed size have been reported in rice, their molecular mechanisms remain unclear. In this study, a rice small grain size 2 (sms2) mutant was identified, and MutMap resequencing analysis results showed that a 2 bp insertion in the second exon of the LOC_Os02g01590 gene resulted in a grain length and width lower than those of the wild-type Teqing (TQ). We found that SMS2 encoded vacuolar acid invertase, a novel allele of OsINV3, which regulates grain size. GO and KEGG enrichment analyses showed that SMS2 was involved in endoplasmic reticulum protein synthesis, cysteine and methionine metabolism, and propionic acid metabolism, thereby regulating grain size. An analysis of sugar content in young panicles showed that SMS2 reduced sucrose, fructose, and starch contents, thus regulating grain size. A haplotype analysis showed that Hap2 of SMS2 had a longer grain and was widely present in indica rice varieties. Our results provide a new theoretical basis for the molecular and physiological mechanisms by which SMS2 regulates grain size.

The roles of non-structural carbohydrates in fruiting: a review focusing on mango (Mangifera indica)

Reproductive development of fruiting trees, including mango (Mangifera indica L.), is limited by non-structural carbohydrates. Competition for sugars increases with cropping, and consequently, vegetative growth and replenishment of starch reserves may reduce with high yields, resulting in interannual production variability. While the effect of crop load on photosynthesis and the distribution of starch within the mango tree has been studied, the contribution of starch and sugars to different phases of reproductive development requires attention. This review focuses on mango and examines the roles of non-structural carbohydrates in fruiting trees to clarify the repercussions of crop load on reproductive development. Starch buffers the plant's carbon availability to regulate supply with demand, while sugars provide a direct resource for carbon translocation. Sugar signalling and interactions with phytohormones play a crucial role in flowering, fruit set, growth, ripening and retention, as well as regulating starch, sugar and secondary metabolites in fruit. The balance between the leaf and fruit biomass affects the availability and contributions of starch and sugars to fruiting. Crop load impacts photosynthesis and interactions between sources and sinks. As a result, the onset and rate of reproductive processes are affected, with repercussions for fruit size, composition, and the inter-annual bearing pattern.

Unveiling the mechanism of source-sink rebalancing in cucumber-pumpkin heterografts: the buffering roles of rootstock cotyledon

Grafting onto pumpkin rootstock is widely applied in cucumber production to improve growth and yield, as well as to overcome soil-borne diseases and enhance resistance to abiotic stresses. In this study, we constructed the cucumber-pumpkin heterografts with the one-cotyledon grafting method, and examined the effects of heterografting on biomass allocation and sugar partitioning, with cucumber and pumpkin self-grafts used as control. Compared with cucumber self-grafts, heterografting onto pumpkin rootstock promoted photosynthesis in cucumber scion, and led to higher sucrose contents in the 1st true leaf (source) and newly emerged leaf (sink). Thereby, the scion part of heterografts accumulated more biomass than cucumber self-grafts. In contrast, when compared to pumpkin self-grafts, grafting with cucumber scion reduced root vigor and biomass but promoted cotyledon growth in pumpkin rootstock. The roots (sink) of heterografts contained less sucrose and hexoses, and showed reduced sucrose synthase (SuSy) and hexokinase (HXK) activities. However, the rootstock cotyledon (source) contained more sucrose and starch, and showed higher activities of HXK, cell-wall invertase (CWIN), and enzymes for starch synthesis and degradation. Furthermore, removal or shade of rootstock cotyledon led to reduced growth of root and scion. Silencing of CmoMEX1a gene in rootstock cotyledon inhibited maltose export and reduced root growth of heterografts. These results indicated that rootstock cotyledon, especially its starch content, played a buffering role in the growth regulation of cucumber-pumpkin heterografts. Taken together, our results provided a major contribution to our understanding of source-sink sugar partitioning and scion-rootstock growth balancing in cucumber-pumpkin heterografts.

Unveiling the molecular regulatory mechanisms underlying sucrose accumulation and oil reduction in peanut kernels through genetic mapping and transcriptome analysis

Sucrose content is a key factor for the flavor of edible peanut, which determines the sweet taste of fresh peanut and also attribute to pleasant flavor of roasted peanut. To explore the genetic mechanism of the sucrose content in peanut, an F2 population was created by crossing the sweet cultivar Zhonghuatian 1 (ZHT1) with Nanyangbaipi (NYBP). A genomic region spanning 28.26 kb on chromosome A06 was identified for the sucrose content through genetic mapping, elucidating 47.5% phenotypic variance explained. As the sucrose content had a significantly negative correlation with the oil content, this region was also found to be related to the oil content explaining 37.2% of phenotype variation. In this region, Arahy.42CAD1 was characterized as the most likely candidate gene through a comprehensive analysis. The nuclear localization of Arahy.42CAD1 suggests its potential involvement in the regulation of gene expression for sucrose and oil contents in peanut. Transcriptome analysis of the developing seeds in both parents revealed that genes involved in glycolysis and triacylglycerol biosynthesis pathways were not significantly down-regulated in ZHT1, indicating that the sucrose accumulation was not attributed to the suppression of triacylglycerol biosynthesis. Based on the WGCNA analysis, Arahy.42CAD1 was co-expressed with the genes involved in vesicle transport and oil body assembly, suggesting that the sucrose accumulation may be caused by disruptions in TAG transportation or storage mechanisms. These findings offer new insights into the molecular mechanisms governing sucrose accumulation in peanut, and also provide a potential gene target for enhancing peanut flavor.

Melatonin as a master regulatory hormone for genetic responses to biotic and abiotic stresses in model plant Arabidopsis thaliana: a comprehensive review

Melatonin is a naturally occurring biologically active amine produced by plants, animals and microbes. This review explores the biosynthesis of melatonin in plants, with a particular focus on its diverse roles in Arabidopsis thaliana , a model species. Melatonin affects abiotic and biotic stress resistance in A. thaliana . Exogenous and endogenous melatonin is addressed in association with various conditions, including cold stress, high light stress, intense heat and infection with Botrytis cinerea or Pseudomonas , as well as in seed germination and lateral root formation. Furthermore, melatonin confers stress resistance in Arabidopsis by initiating the antioxidant system, remedying photosynthesis suppression, regulating transcription factors involved with stress resistance (CBF, DREB, ZAT, CAMTA, WRKY33, MYC2, TGA) and other stress-related hormones (abscisic acid, auxin, ethylene, jasmonic acid and salicylic acid). This article additionally addresses other precursors, metabolic components, expression of genes (COR , CBF , SNAT , ASMT , PIN , PR1 , PDF1.2 and HSFA ) and proteins (JAZ, NPR1) associated with melatonin and reducing both biological and environmental stressors. Furthermore, the future perspective of melatonin rich agri-crops is explored to enhance plant tolerance to abiotic and biotic stresses, maximise crop productivity and enhance nutritional worth, which may help improve food security.

Nutritional composition of quinoa leafy greens: An underutilized plant-based food with the potential of contributing to current dietary trends

Quinoa (Chenopodium quinoa Willd.) leafy greens (QLGs) are plant-based foods of high nutritional value that have been scarcely studied. In this work, the nutritional and functional composition of three QLGs varieties was evaluated. A protein content higher than 35 g 100 g-1 dw with a well-balanced essential amino acid composition was found making them a good source of vegetable protein. In addition, elevated contents of dietary fibre and minerals, higher than those detected in quinoa seeds and other leafy vegetables, were found. The lipid profile showed higher contents of linoleic (C18:2, ω6) (20.2 %) and linolenic acids (C18:3, ω3) (52.8 %) with low ω6/ ω3 ratios (∼0.4/1). A total sugar content <1 g 100 g-1 dw was found for all varieties tested, lower than that obtained in seeds. The saponin content varied between 0.76 and 0.87 %. Also, high values of total phenolic compounds (969.8-1195.4 mg gallic acid 100 g-1), mainly hydroxycinnamic acids and flavonoids, and great antioxidant activities (7.64-8.90 g Trolox kg-1) were found. Multivariate analysis here used allowed us to classify the samples according to the quinoa variety evaluated, and the sequential stepwise multiple regression applied revealed that the PUFA and sucrose contents negatively influenced the protein content while the palmitic acid content affected positively this parameter. Overall, this study shows that QLGs are promising nutritious and functional plant-based foods supporting the necessity of promoting their cultivation, commercialization, and consumption.

Biostimulatory Effects of Chlorella fusca CHK0059 on Plant Growth and Fruit Quality of Strawberry

Green algae have been receiving widespread attention for their use as biofertilizers for agricultural production, but more studies are required to increase the efficiency of their use. This study aimed to investigate the effects of different levels of Chlorella fusca CHK0059 application on strawberry plant growth and fruit quality. A total of 800 strawberry seedlings were planted in a greenhouse and were grown for seven months under different Chlorella application rates: 0 (control), 0.1, 0.2, and 0.4% of the optimal cell density (OCD; 1.0 × 107 cells mL-1). The Chlorella application was conducted weekly via an irrigation system, and the characteristics of fruit samples were monitored monthly over a period of five months. The growth (e.g., phenotype, dry weight, and nutrition) and physiological (e.g., Fv/Fm and chlorophylls) parameters of strawberry plants appeared to be enhanced by Chlorella application over time, an enhancement which became greater as the application rate increased. Likewise, the hardness and P content of strawberry fruits had a similar trend. Meanwhile, 0.2% OCD treatment induced the highest values of soluble solid content (9.3-12 °Brix) and sucrose content (2.06-2.97 g 100 g-1) in the fruits as well as fruit flavor quality indices (e.g., sugars:acids ratio and sweetness index) during the monitoring, whilst control treatment represented the lowest values. In addition, the highest anthocyanin content in fruits was observed in 0.4% OCD treatment, which induced the lowest incidence of grey mold disease (Botrytis cinerea) on postharvest fruits for 45 days. Moreover, a high correlation between plants' nutrients and photosynthetic variables and fruits' sucrose and anthocyanin contents was identified through the results of principal component analysis. Overall, C. fusca CHK0059 application was found to promote the overall growth and performance of strawberry plants, contributing to the improvement of strawberry quality and yield, especially in 0.2% OCD treatment.

Morphological and physio-biochemical responses under heat stress in cotton: Overview

Cotton is an important cash crop in addition to being a fiber commodity, and it plays an essential part in the economies of numerous nations. High temperature is the most critical element affecting its yield from fertilization to harvest. The optimal temperature for root formation is 30 C -35 °C; however, root development ends around 40 °C. Increased temperature, in particular, influences different biochemical and physiological processes associated with cotton plant, resulting in low seed cotton production. Many studies in various agroecological zones used various agronomic strategies and contemporary breeding techniques to reduce heat stress and improve cotton productivity. To attain desired traits, cotton breeders should investigate all potential possibilities, such as generating superior cultivars by traditional breeding, employing molecular techniques and transgenic methods, such as using genome editing techniques. The main objective of this review is to provide the recent information on the environmental factors, such as temperature, heat and drought, influence the growth and development, morphology and physio-chemical alteration associated with cotton. Furthermore, recent advancement in cotton breeding to combat the serious threat of drought and heat stress.

Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation

Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.

Transcriptomic Analysis Reveals the Response Mechanisms of Bell Pepper (Capsicum annuum) to Phosphorus Deficiency

Phosphorus (P) is an important nutritional element needed by plants. Roots obtain P as inorganic phosphate (Pi), mostly in H2PO-4 form. It is vital for plants to have a sufficient supply of Pi since it participates in important processes like photosynthesis, energy transfer, and protein activation, among others. The physicochemical properties and the organic material usually make Pi bioavailability in soil low, causing crops and undomesticated plants to experience variations in accessibility or even a persistent phosphate limitation. In this study, transcriptome data from pepper roots under low-Pi stress was analyzed in order to identify Pi starvation-responsive genes and their relationship with metabolic pathways and functions. Transcriptome data were obtained from pepper roots with Pi deficiency by RNASeq and analyzed with bioinformatic tools. A total of 97 differentially expressed genes (DEGs) were identified; Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that metabolic pathways, such as porphyrin and chlorophyll metabolism, were down-regulated, and galactose and fatty acid metabolism were up-regulated. The results indicate that bell pepper follows diverse processes related to low Pi tolerance regulation, such as the remobilization of internal Pi, alternative metabolic pathways to generate energy, and regulators of root development.

Physiological and Agronomic Responses and Nutrient Uptake of Soybean Genotypes Cultivated Under Various Sowing Dates

Late or early sowing subjecting crop plants to stress conditions, this is simulating the climatic change effects. The global warming and climate change are critical issues in agriculture since progressive rise in temperature leads to exposure the crops to heat stress, hence low productivity. Since weather conditions are uncontrollable, it is impossible to modulate their negative impacts against crop growth and development. However, scientists should not be handcuffed about this serious problem. So, in open field conditions, the performance of some soybean genotypes was evaluated under different sowing dates. Along the two seasons of 2019 and 2020, field experiments were designed in a split-plot design using three replicates to evaluate the performance of four soybean genotypes (Giza-21, Giza-35, Giza-111, and Crawford) under four sowing dates (15th April, 30th April, 15th May, and 30th May). Various physiological and growth traits, yield attributes, seed nutrient contents, and oil and protein contents were estimated. Sowing Crawford (in both seasons) and Giza-35 (in the first season) on 15th April as well as Giza-111 either on 30th April or 15th May produced the highest catalase activity. In plots sown on 30th April, Crawford and Giza-21 (in the first season) and Giza-111 (in both seasons) exhibited the highest leaves area plant−1. Plots sown by Giza-111 on 30th April was the potent interaction for enhancing seed yield in both seasons. Under any sowing date in the second season and the sowing date of 30th April in the first season, Giza-111 was the effective genotype for recording the maximum seed oil content. For adopting a specific stress condition scenario, it is advisable to insert Giza-111 as an effective gene pool to improve soybean genotypes under unfavorable conditions, expressed in sowing dates.

Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield

The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.

Exploring the antibacterial potential of plant extracts and essential oils against Bacillus thermophilus in beet sugar for enhanced sucrose retention: a comparative assessment and implications

Sugar beet is one of the greatest sources for producing sugar worldwide. However, a group of bacteria grows on beets during the storage process, leading to a reduction in sucrose yield. Our study focused on identifying common bacterial species that grow on beets during manufacturing and contribute to sucrose loss. The ultimate goal was to find a potential antibacterial agent from various plant extracts and oils to inhibit the growth of these harmful bacteria and reduce sucrose losses. The screening of bacterial species that grow on beet revealed that a large group of mesophilic bacteria, such as Bacillus subtilis, Leuconostoc mesenteroides, Pseudomonas fluorescens, Escherichia coli, Acinetobacter baumannii, Staphylococcus xylosus, Enterobacter amnigenus, and Aeromonas species, in addition to a dominant thermophilic species called Bacillus thermophilus, were found to be present during the manufacturing of beets. The application of 20 plant extracts and 13 different oils indicated that the extracts of Geranium gruinum, Datura stramonium, and Mentha spicata were the best antibacterials to reduce the growth of B. thermophilus with inhibition zones equal to 40, 39, and 35 mm, respectively. In contrast, the best active oils for inhibiting the growth of B. thermophilus were Mentha spicata and Ocimum bacilicum, with an inhibitory effect of 50 and 45 mm, respectively. RAPD-PCR with different primers indicated that treating sugar juice with the most effective oils against bacteria resulted in new recombinant microorganisms, confirming their roles as strong antibacterial products. The characterization of Mentha spicata and Ocimum bacilicum oils using GC/MS analysis identified cis-iso pulegone and hexadecanoic acid as the two main bioactive compounds with potential antibacterial activity. An analysis of five genes using DD-PCR that have been affected due to antibacterial activity from the highly effective oil from Mentha spicata concluded that all belonged to the family of protein defense. Our findings indicate that the application of these pure antibacterial plant extracts and oils would minimize the reduction of sucrose during sugar production.

Determination of optimal NH4+/K + concentration and corresponding ratio critical for growth of tobacco seedlings in a hydroponic system

Inherently, ammonium (NH₄ ⁺) is critical for plant growth; however, its toxicity suppresses potassium (K⁺) uptake and vice-versa. Hence, attaining a nutritional balance between these two ions (NH₄ ⁺ and K⁺) becomes imperative for the growth of tobacco seedlings. Therefore, we conducted a 15-day experimental study on tobacco seedlings exposed to different concentrations (47 treatments) of NH₄ ⁺/K⁺ at different corresponding 12 ratios simultaneously in a hydroponic system. Our study aimed at establishing the optimal NH₄ ⁺-K⁺ concentration and the corresponding ratio required for optimal growth of different tobacco plant organs during the seedling stage. The controls were the baseline for comparison in this study. Plants with low or excessive NH₄ ⁺-K⁺ concentration had leaf chlorosis or dark greenish colouration, stunted whole plant part biomass, and thin roots. We found that adequate K⁺ supply is a pragmatic way to mitigate NH₄ ⁺-induced toxicity in tobacco plants. The optimal growth for tobacco leaf and root was attained at NH₄ ⁺-K⁺ concentrations 2-2 mM (ratio 1:1), whereas stem growth was optimal at NH₄ ⁺-K⁺ 1-2 mM (1:2). The study provided an insight into the right combination of NH₄ ⁺/K⁺ that could mitigate or prevent NH₄ ⁺ or K⁺ stress in the tobacco seedlings.

Early leaf responses of cell physiological and sensor-based signatures reflect susceptibility of wheat seedlings to infection by leaf rust

Leaf rust caused by Puccinia triticina Erikss. can have devastating effects on wheat (Triticum aestivum L.), causing severe economic losses. This comprehensive study serves to facilitate our understanding of the impact of carbohydrate and antioxidant metabolism in association with sensor-based phenotyping and leaf rust stress responses in wheat seedlings. After 24 h of inoculation (hai) very susceptible variety to leaf rust (Ficko) increased cell-wall invertase (cwInv; EC 3.2.1.26), compared to other varieties that significantly increased cwInv later. This could mean that the Ficko variety cannot defend itself from leaf rust infections once symptoms have started to develop. Also, Ficko had significantly decreased amounts of cytoplasmic invertase (cytInv; EC 3.2.1.26) at 8 hai. The downregulation of cytInv in susceptible plants may facilitate the maintenance of elevated apoplastic sucrose availability favoring the pathogen. The significant role of vacuolar invertase (vacInv; EC 3.2.1.26) in moderately resistant varieties was recorded. Also, a significant decrease of glucose-6-phosphate dehydrogenase (G6PDH; EC 1.1.1.49) and UDP-glucose pyrophosphorylase (UGPase; EC 2.7.7.9) in moderately resistant varieties might restrict normal development of leaf rust due to reduced sugar. During plant-pathogen interaction, when the invader spreads systemically throughout the plant, the main role of ascorbate peroxidase (APX; EC 1.11.1.11) activity in one moderately resistant variety (Olimpija) and catalase (CAT; EC 1.11.1.6) activity in another moderately resistant variety (Alka) is to protect the plant against oxidative damage in the early stages of infection. Non-invasive phenotyping with a sensor-based technique could be used as a rapid method for pre-symptomatic determination of wheat leaf rust resistance or susceptibility.

Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers

Sucrose (Suc) and gibberellin (GA) can promote the elongation of certain internodes in bamboo. However, there is a lack of field studies to support these findings and no evidence concerning how Suc and GA promote the plant height of bamboo by regulating the internode elongation and number. We investigated the plant height, the length of each internode, and the total number of internodes of Moso bamboo (Phyllostachys edulis) under exogenous Suc, GA, and control group (CTRL) treatments in the field and analyzed how Suc and GA affected the height of Moso bamboo by promoting the internode length and number. The lengths of the 10th-50th internodes were significantly increased under the exogenous Suc and GA treatments, and the number of internodes was significantly increased by the exogenous Suc treatment. The increased effect of Suc and GA exogenous treatment on the proportion of longer internodes showed a weakening trend near the plant height of 15-16 m compared with the CTRL, suggesting that these exogenous treatments may be more effective in regions where bamboo growth is suboptimal. This study demonstrated that both the exogenous Suc and GA treatments could promote internode elongation of Moso bamboo in the field. The exogenous GA treatment had a stronger effect on internode elongation, and the exogenous Suc treatment had a stronger effect on increasing the internode numbers. The increase in plant height by the exogenous Suc and GA treatments was promoted by the co-elongation of most internodes or the increase in the proportion of longer internodes.

Identification and molecular characterization of novel sucrose transporters in the hexaploid wheat (Triticum aestivum L.)

Common wheat (Triticum aestivum) is a major cereal crop grown and consumed globally. Recent advances in sequencing technology have facilitated the exploration of large and repetitive genomes. Plant sucrose transporter (SUT) genes are vital components of energy transport systems that play prominent roles in various plant functions, such as signaling and stress regulation. In this study, we identified and analyzed five novel sucrose transporter genes in wheat. The wheat sucrose transporter genes were divided into five clades based on their phylogenetic relationships. Synteny analysis revealed that synteny in the genome is highly conserved between wheat and rye, barley, and Brachypodium. Furthermore, the cis-element analysis indicated that sucrose transporter genes might be regulated by light and some phytohormone-related transcriptional factors. Overall, plant tissue-specific gene expression revealed enhanced expression of the transporter genes in the root and stem, whereas they were differentially expressed under abiotic stress treatments (cold, heat, NaCl, PEG-6000, and sucrose). These results indicate that each TaSUT gene may play a crucial role in stabilizing plants under stress by actively regulating the energy demands of cells. The findings of this study may provide a basis for further research on sucrose transporters and their significant roles in plant energy metabolism as well as in abiotic stress response, signaling, and regulation.

Genome-Wide Identification and Analysis of Stress Response of Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase Genes in Quinoa

Saline-alkali stress seriously affects the yield and quality of crops, threatening food security and ecological security. Improving saline-alkali land and increasing effective cultivated land are conducive to sustainable agricultural development. Trehalose, a nonreducing disaccharide, is closely related to plant growth and development and stress response. Trehalose 6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are key enzymes catalyzing trehalose biosynthesis. To elucidate the effects of long-term saline-alkali stress on trehalose synthesis and metabolism, we conducted an integrated transcriptome and metabolome analysis. As a result, 13 TPS and 11 TPP genes were identified in quinoa (Chenopodium quinoa Willd.) and were named CqTPS1-13 and CqTPP1-11 according to the order of their Gene IDs. Through phylogenetic analysis, the CqTPS family is divided into two classes, and the CqTPP family is divided into three classes. Analyses of physicochemical properties, gene structures, conservative domains and motifs in the proteins, and cis-regulatory elements, as well as evolutionary relationships, indicate that the TPS and TPP family characteristics are highly conserved in quinoa. Transcriptome and metabolome analyses of the sucrose and starch metabolism pathway in leaves undergoing saline-alkali stress indicate that CqTPP and Class II CqTPS genes are involved in the stress response. Moreover, the accumulation of some metabolites and the expression of many regulatory genes in the trehalose biosynthesis pathway changed significantly, suggesting the metabolic process is important for the saline-alkali stress response in quinoa.

Stage-specific metabolomics suggests a trade-off between primary and secondary metabolites for nutritional advantage in Lepidium latifolium L

Lepidium latifolium L. is an established phytofood of the Ladakh Himalayas that contains differential content of important glucosinolates (GLS) in specific stages of sprouts. Therefore, in order to harness its nutraceutical potential, a comprehensive mass spectrometry-based stage-specific untargeted metabolomic analysis was performed. A total of 318 metabolites were detected, out of which 229 were significantly (p ≤ 0.05) changed during different stages. The Principal Component Analysis plot clearly differentiated different growth stages into three clusters. The nutritionally important metabolites, including amino acids, sugars, organic acids, and fatty acids, were found significantly (p ≤ 0.05) higher in the first cluster consisting of 1st, 2nd and 3rd week sprouts. The higher energy requirements during the early growth stages were observed with the higher metabolites of glycolysis and the TCA cycle. Further, the trade-off between primary and secondary sulfur-containing metabolites was observed, which may explain the differential GLS content in different growth stages.

Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency

Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.

Light Intensity Affects the Assimilation Rate and Carbohydrates Partitioning in Spinach Grown in a Controlled Environment

The cultivation of spinach (Spinacia oleracea L.) has been increasing during the last years in controlled environment agriculture, where light represents a key factor for controlling plant growth and development and the highest energetic costs. The aim of the experiment was to evaluate the plant's response to two light intensities, corresponding to an optimal and a reduced level, in terms of the photosynthetic process, photoassimilates partitioning, and the biosynthesis of sucrose and starch. Plants of spinach cv. 'Gigante d'Inverno' were grown in a phytotron under controlled conditions, comparing two values of photosynthetic photon flux density (PPFD), 800 μmol m-2 s-1 (800 PPFD) and 200 μmol m-2 s-1 (200 PPFD), at a 10 h light/14 h dark regime. Compared to 800 PPFD, under 200 PPFD, plants showed a reduction in biomass accumulation and a redirection of photoassimilates to leaves, determining a leaf expansion to optimize the light interception, without changes in the photosynthetic process. A shift in carbon partitioning favouring the synthesis of starch, causing an increase in the starch/sucrose ratio at the end of light period, occurred in low-light leaves. The activity of enzymes cFBAse, SPS, and AGPase, involved in the synthesis of sucrose and starch in leaves, decreased under lower light intensity, explaining the rate of accumulation of photoassimilates.

Effect of Interactions between Phosphorus and Light Intensity on Metabolite Compositions in Tea Cultivar Longjing43

Light intensity influences energy production by increasing photosynthetic carbon, while phosphorus plays an important role in forming the complex nucleic acid structure for the regulation of protein synthesis. These two factors contribute to gene expression, metabolism, and plant growth regulation. In particular, shading is an effective agronomic practice and is widely used to improve the quality of green tea. Genotypic differences between tea cultivars have been observed as a metabolic response to phosphorus deficiency. However, little is known about how the phosphorus supply mediates the effect of shading on metabolites and how plant cultivar gene expression affects green tea quality. We elucidated the responses of the green tea cultivar Longjing43 under three light intensity levels and two levels of phosphorus supply based on a metabolomic analysis by GC×GC-TOF/MS (Two-dimensional Gas Chromatography coupled to Time-of-Flight Mass Spectrometry) and UPLC-Q-TOF/MS (Ultra-Performance Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometry), a targeted analysis by HPLC (High Performance Liquid Chromatography), and a gene expression analysis by qRT-PCR. In young shoots, the phosphorus concentration increased in line with the phosphate supply, and elevated light intensities were positively correlated with catechins, especially with epigallocatechin of Longjing43. Moreover, when the phosphorus concentration was sufficient, total amino acids in young shoots were enhanced by moderate shading which did not occur under phosphorus deprivation. By metabolomic analysis, phenylalanine, tyrosine, and tryptophan biosynthesis (PTT) were enriched due to light and phosphorus effects. Under shaded conditions, SPX2 (Pi transport, stress, sensing, and signaling), SWEET3 (bidirectional sugar transporter), AAP (amino acid permeases), and GSTb (glutathione S-transferase b) shared the same analogous correlations with primary and secondary metabolite pathways. Taken together, phosphorus status is a crucial factor when shading is applied to increase green tea quality.

Differential Effects of Ammonium (NH4+) and Potassium (K+) Nutrition on Photoassimilate Partitioning and Growth of Tobacco Seedlings

Plants utilize carbohydrates as the main energy source, but much focus has been on the impact of N and K on plant growth. Less is known about the combined impact of NH₄⁺ and K⁺ nutrition on photoassimilate distribution among plant organs, and the resultant effect of such distribution on growth of tobacco seedlings, hence this study. Here, we investigated the synergetic effect of NH₄⁺ and K⁺ nutrition on photoassimilate distribution, and their resultant effect on growth of tobacco seedlings. Soluble sugar and starch content peaks under moderate NH₄⁺ and moderate K⁺ (2-2 mM), leading to improved plant growth, as evidenced by the increase in tobacco weight and root activity. Whereas, a drastic reduction in the above indicators was observed in plants under high NH₄⁺ and low K⁺ (20-0.2 mM), due to low carbohydrate synthesis and poor photoassimilate distribution. A strong positive linear relationship also exists between carbohydrate (soluble sugar and starch) and the activities of these enzymes but not for invertase. Our findings demonstrated that NH₄⁺ and K⁺-induced ion imbalance influences plant growth and is critical for photoassimilate distribution among organs of tobacco seedlings.

Mechanism of [CO2] Enrichment Alleviated Drought Stress in the Roots of Cucumber Seedlings Revealed via Proteomic and Biochemical Analysis

Cucumber is one of the most widely cultivated greenhouse vegetables, and its quality and yield are threatened by drought stress. Studies have shown that carbon dioxide concentration ([CO₂]) enrichment can alleviate drought stress in cucumber seedlings; however the mechanism of this [CO₂] enrichment effect on root drought stress is not clear. In this study, the effects of different drought stresses (simulated with 0, 5% and 10% PEG 6000, i.e., no, moderate, and severe drought stress) and [CO₂] (400 μmol·mol^-1 and 800 ± 40 μmol·mol^-1) on the cucumber seedling root proteome were analyzed using the tandem mass tag (TMT) quantitative proteomics method. The results showed that after [CO₂] enrichment, 346 differentially accumulating proteins (DAPs) were found only under moderate drought stress, 27 DAPs only under severe drought stress, and 34 DAPs under both moderate and severe drought stress. [CO₂] enrichment promoted energy metabolism, amino acid metabolism, and secondary metabolism, induced the expression of proteins related to root cell wall and cytoskeleton metabolism, effectively maintained the balance of protein processing and degradation, and enhanced the cell wall regulation ability. However, the extent to which [CO₂] enrichment alleviated drought stress in cucumber seedling roots was limited under severe drought stress, which may be due to excessive damage to the seedlings.