Search Results (103)

Anaerobic digestion (AD) is a common waste management method for producing renewable energy from biogas. However, animal manures typically have low C/N ratios, which can limit biogas recovery. This study aims to optimize biogas production through the co-digestion of goat manure (GM) with high-C/N lignocellulosic rice husk (RH) and sludge as the inoculum. Characterization of the substrate and inoculum revealed a low GM C/N ratio (GM = 21.3), whereas RH has a high-C/N (RH = 107.3). The volatile solids-to-total solids (VS/TS) ratios were around 82–85% for GM and RH. Batch experiments were conducted at different organic loading rates, with an inoculum-to-substrate ratio of 2:1 (mL:g), at 36 ± 1 °C for 65 days. This study investigates optimizing biomethane recovery by using serum-bottle biomethane potential (BMP) and compares kinetic performance and yields across different GM-to-RH ratios with the characteristics of the influent and effluent. The highest BMP values (mL CH₄/g_VS) occurred at 100% GM (245.1), followed by 90% GM (233.6) and 30% GM (232.5), indicating a strong synergy between GM and RH at specific mixing ratios. Kinetic modeling using both the modified Gompertz and first-order models effectively described digestion dynamics, allowing for estimation of potential lag phases and maximum production rates. These models aligned well with experimental data across substrates, aiding process design. Overall, the results show that strategic co-digestion of GM with RH can maximize methane recovery, with defined substrate ratios and a clear understanding of the kinetics essential for scale-up and sustainable biogas production. Full article

Rho GTPase-activating proteins (RhoGAPs) are characterized by a conserved RhoGAP domain and function as negative regulators of Rho GTPases, playing important roles in plant growth, development, and responses to environmental stimuli. In this study, 19 GmRhoGAP genes were identified in the soybean genome and found to be unevenly distributed across 11 chromosomes. Comprehensive analyses were performed, including gene structure, conserved motifs, protein domains, gene duplication, synteny, cis-acting elements, tissue-specific expression, and quantitative real-time PCR under rhizobial infection. Structural analysis revealed substantial diversity in intron-exon organization but high conservation of motif composition, with all members containing the conserved RhoGAP domain. A total of 20 segmentally duplicated gene pairs were identified, indicating expansion of the GmRhoGAP family in soybean. Inter-species synteny analysis showed closer evolutionary relationships with Arabidopsis than with rice, and Ka/Ks analysis suggested strong purifying selection during evolution. Promoter analysis indicated potential involvement in development, phytohormone signaling, stress responses, and light responsiveness. Expression profiling demonstrated distinct tissue-specific patterns. qRT-PCR further showed that GmRhoGAP genes respond differentially to rhizobial infection, with 10 generally upregulated genes and 4 downregulated genes. These analyses provide a framework for understanding this gene family and identify candidate genes for future research. Full article

Cyclin-dependent kinases (CDKs) and cyclins are master regulators of the cell cycle, playing critical roles in plant growth, development, and stress responses. While these gene families have been extensively studied in model plants, a comprehensive analysis in soybean remains underexplored. To address this gap, we performed a genome-wide identification and systematic analysis of these families in soybean using bioinformatic approaches. Expression profiles and protein interactions of selected GmCDK and GmCyclin candidates were tested by qRT-PCR and BiFC assays. A total of 28 GmCDK and 101 GmCyclin genes were identified, revealing a significant expansion compared to Arabidopsis, rice, and maize, primarily driven by whole-genome and segmental duplications. Phylogenetic analysis classified GmCDKs into seven conserved clades (CDKA-CDKG) and GmCyclins into ten distinct subfamilies. Expression profiling demonstrated dynamic, tissue-specific patterns, with distinct modules active during seed development and in tissues. Promoter analysis further linked these genes to hormonal and stress-responsive pathways. Crucially, BiFC assay identified specific interactions between GmCDKA2, GmCDKA3, GmCDKB1 and GmCYCA3-3, suggesting evolutionary divergence in soybean CDK-Cyclin regulatory networks. This study provides a foundational resource for the soybean cell cycle regulome, highlighting its evolutionary plasticity and implicating specific CDK-Cyclin pairs as potential targets for manipulating agronomic traits such as seed development and stress resilience. Full article

Co-utilization of milk vetch as green manure (GM) and rice straw is an effective practice for reducing nitrogen (N) input while maintaining crop productivity in rice-based agroecosystems in southern China. The effects of soil carbon (C) and N pools and their fractions under green manuring and rice straw return, combined with reduced N fertilization remain to be clarified. A four-year field experiment was carried out to explore the effects of synergistic utilization of GM and rice straw (GMS) on rice yield, soil C and N fractions, and their contributions to rice productivity. The study demonstrated that compared with winter fallow (WF), GMS increased rice yield by 20.3% under 40% reduction in N fertilization (N60). GM application increased soil total N content by 16.5% and 18.0% significantly relative to WF under N0 and N60, respectively. GMS treatment demonstrated improvements in the soil organic C pool and enhanced soil N activity. Compared with WF, soil organic C, mineral-associated organic C and particulate organic C under GMS increased by 11.1% and 24.9%, 31.3% and 13.8%, 13.1% and 47.3% at N0 and N60 levels, respectively. Under N60, GMS increased heavy-fraction organic C content by 42.6% while reducing light-fraction organic C content by 28.0% compared to WF, thereby enhancing soil C pool stability. Regarding soil N fractions, GMS increased particulate organic N content by 60.8% and 79.3%, and mineral-associated organic N content by 89.7% and 43.4% at N0 and N60 levels, respectively. Under N60, GMS reduced heavy-fraction organic N content while increasing light-fraction organic N content, thereby enhancing soil N availability. Based on the results of Mantel tests and random forest prediction, our analysis found that N and particulate organic C served as the key factors affecting rice yield. In conclusion, GMS combined with 60% of the conventional N rate enhanced rice yield by mediating soil C sequestration and N availability, proving to be an effective strategy for improving soil fertility and ensuring food security in the rice-growing region of southern Jiangsu, China. Full article

Seed weight is a key agronomic trait determining soybean yield and quality, yet only a few of genes regulating this trait have been functionally characterized to date. In this study, we identified 155 homologous genes in the soybean genome through BLAST searches using 78 functionally validated rice grain weight-related genes as queries. Haplotype analysis prioritized 40 candidate genes exhibiting significant differences in seed weight between haplotypes. To further refine the candidate list, we integrated haplotype frequency analysis, expression–trait association mapping, and tissue-specific expression profiling, ultimately delineating eight key genes. Given the established role of ubiquitination in seed development, we focused on homologs of OsUBP15 and identified three candidate genes, GmUBP5, GmUBP11, and GmUBP33, that exhibited significant haplotype-dependent variation in seed weight. Subcellular localization assays confirmed their nuclear localization. Haplotype frequency analysis revealed that the superior haplotypes of these genes have been preferentially retained during modern breeding and are widely distributed across major soybean-producing regions. Leveraging non-synonymous SNP variants, we developed and validated robust KASP markers that efficiently discriminate germplasm with contrasting seed weight phenotypes. Collectively, our study provides not only high-confidence genetic targets and actionable molecular markers but also insights into pyramiding breeding strategies for improving seed weight in soybean. Full article

Effective weed control is essential for sustainable and safe rice production, particularly under the long-term and widespread use of chemical herbicides. Oilseed rape (Brassica napus L.) is one of the most important oil crops worldwide, and the oilseed rape–rice rotation system is widely practiced in China. It has been reported to exhibit strong allelopathy on various plants, but the feasibility of using its straw incorporation for weed control in transplanted rice fields remains unclear. In this study, a natural weed management strategy based on shallow tillage of oilseed rape straw (ORS) was evaluated through laboratory bioassays, greenhouse experiments, and field trials. The results indicated that soil decomposition liquids (SDLs) of ORS exhibited strong dose- and decomposition time-dependent allelopathic effects on seven paddy weed species, while rice showed markedly lower sensitivity. ORS incorporated at 700–1100 g/m² generally exhibited high integrated allelopathic inhibition (in lab) and population control effects (in greenhouse) on paddy weeds, especially Leptochloa chinensis (L.) Nees, Cyperus iria L., and Cyperus difformis L. Among the growth parameters of ORS allelopathic stress, root growth was the most sensitive indicator, followed by shoot growth and seed germination. Greenhouse experiments displayed variety-dependent impact on the transplanted rice seedlings, with Xiushui134 and Yongyou1540 showing relatively high tolerance. Field trials revealed that ORS incorporation at 1100 g/m² for 10 d achieved a satisfactory control of population (77.7–84.9%) and fresh weight (80.7–95.6%) across Gramineae, Cyperaceae and Broadleaf weeds, without adverse impact on the growth of transplanted rice seedlings (Yongyou1540). This treatment also significantly promoted theoretical grain yield by 13.4–19.4%. Overall, shallow tillage of oilseed rape straw provides a feasible and environmentally friendly weed control strategy for transplanted rice systems. Full article

In this study, rice-husk fiber (RHF) extracted via alkali hydrolysis was used as a reinforcing material (0–10 wt%) in a pectin-sodium alginate (PE/SA) matrix to develop biofilms by the casting method. These biofilms were characterized by using FTIR, XRD, TGA, and DSC. The thickness, moisture content, water solubility, swelling behavior, water-contact angle, water-vapor permeability, optical transparency, and mechanical properties of biofilms were investigated. It was observed that the PE/SA/RHF film loaded with 5% RHF had better visual attributes, and a further increase in reinforcement was not found to be as favorable. The addition of 10 wt% RHF significantly enhanced the thickness from 0.094 to 0.127 mm, water solubility from 49.25 to 56.13%, water-contact angle from 48.4 to 62.6°, and tensile strength from 4.17 to 10.23 MPa. However, decreases in water-vapor permeability from 1.94 × 10⁻⁹ to 1.32 × 10⁻⁹ g·m⁻¹·Pa⁻¹·s⁻¹ and in elongation at break from 19.24 to 2.87% were observed in the biofilms. Structurally, FTIR confirmed intermolecular hydrogen bonding between components. XRD revealed that the films remained predominantly amorphous, without significant crystalline alterations. Furthermore, thermal stability improved with the addition of RHF. Finally, these PE/SA/RHF composite films may be potential eco-friendly biodegradable packaging candidates for food industry applications. Full article

Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation. Full article

Isopentenyltransferase (IPT) is the rate-limiting enzyme in cytokinin biosynthesis and plays a critical role in plant acclimation to abiotic stress. To explore soybean IPT genes, we performed genome-wide identification, bioinformatics analysis, and molecular experimental validation to systematically characterize the features and functions of the soybean IPT (GmIPT) gene family. We identified 15 GmIPT genes in the soybean genome, which are unevenly distributed across 12 chromosomes; their evolutionary expansion is primarily driven by whole-genome duplication events. Phylogenetic analysis of soybean IPT proteins with those from Arabidopsis, rice and maize clustered them into four groups, exhibiting lineage-specific functional specialization. GmIPT genes exhibit significant variations in conserved motifs, gene structure, and cis-acting elements; their promoter regions are enriched in light-responsive, abiotic stress-responsive, and hormone-responsive elements, indicating their involvement in complex transcriptional regulatory networks. Tissue expression profiling revealed that GmIPT7 and GmIPT10 are highly expressed in various tissues, whereas GmIPT14 shows specific expression in flowers and the shoot apical meristem. Transcriptomic analysis and qRT-PCR validation demonstrated that GmIPT7, GmIPT10 and GmIPT15 respond differentially to drought, salt and low-temperature stress, with GmIPT15 exhibiting a transient upregulation at 3 h (p < 0.01) followed by a gradual decline to levels close to the pre-treatment control at 6–12 h under low-temperature stress. We further performed haplotype analysis of GmIPT15 and identified a putative elite haplotype (hap1) associated with cold tolerance based on low-temperature germination index assessment. This study provides useful insights for the future functional characterization of plant IPT genes and offers potential genetic resources and molecular markers that may support molecular-assisted breeding for soybean abiotic stress tolerance. Full article

Heterosis is a landmark innovation in modern agriculture, which has been widely exploited to boost crop productivity. As a staple food for over half of the global population, rice depends heavily on heterosis for yield improvement. Notably, hybrid rice has made remarkable contributions to global food security over the past several decades. Male sterility serves as the fundamental basis for efficient hybrid rice breeding, with cytoplasmic male sterility (CMS) and genic male sterility (GMS) as the core systems employed in practical production. CMS, induced by mitochondrial genes, can be restored to fertility by nuclear restorer genes, thereby forming the essential genetic basis for the three-line hybrid rice system. GMS, mainly regulated by the nuclear genome, includes dominant and recessive nuclear sterility. Specifically, recessive environment-sensitive genic male sterility (EGMS) has facilitated the development of the two-line hybrid rice system for commercial hybrid seed production. The third-generation hybrid rice technology (TGHRT) is a transgenic approach developed for propagating stable recessive GMS lines. This review comprehensively summarizes the latest advances in rice male sterility systems, focusing on their genetic classification, origin, and molecular mechanisms. It further analyzes their application status, inherent limitations, future research directions, and development trends in hybrid rice production, aiming to deepen our understanding of the innovation and optimization of hybrid rice breeding technologies. Full article

Northern japonica rice holds a significant position in China’s food security. However, the traditional nitrogen fertilizer management model (nitrogen application rate > 225 kg/ha, base fertilizer proportion > 50%) has led to serious sustainability problems: the nitrogen utilization rate is only 25–30%, resulting in a large amount of fertilizer waste and economic losses. At the same time, it causes a decline in rice quality, manifested as a 15–20% increase in chalkiness and an 8–12% decrease in palatability value. It has also brought about environmental problems such as soil acidification and eutrophication of water bodies. As an important japonica rice production area, the Liaohe Plain has significant differences in the response of semi-upright and curved panicle varieties to nitrogen fertilizer. However, the agronomic physiological mechanism for the coordinated improvement of yield and quality of japonica rice with different panicle types is still unclear at present, which limits the sustainable development of rice production in this region. For this purpose, in this study, the typical semi-upright spike variety Shendao 47 and the curved spike variety Shendao 11 from the Liaohe Plain were used as materials, and five nitrogen fertilizer treatments were set up: N1, no nitrogen application; N2–N4, conventional nitrogen application rate of 165–225 kg/ha; and N5, and optimized nitrogen application rate of 195 kg/ha allocated in the proportion of 40% base fertilizer, 15% tillering fertilizer, 25% tillering fertilizer, 15% panicle fertilizer, and 5% grain fertilizer. The synergistic regulatory effect of nitrogen fertilizer management on yield and rice quality was systematically explored, and the key agronomic physiological mechanisms were analyzed. The research results show that: (1) The optimized nitrogen fertilizer treatment (N5) achieved a significant increase in yield while reducing the input of nitrogen fertilizer. The yields of Shendao 47 and Shendao 11 reached 10.71–11.82 t/ha and 9.50–10.62 t/ha, respectively, increasing by more than 35% compared with the treatment without nitrogen. (2) The N5 treatment simultaneously improved the processing quality (the whole polished rice rate increased by 4.11%) and the appearance quality (the chalkiness decreased by 63.8% to 77%). (3) The dry matter accumulation during the tillering stage (≥3.2 t/ha) and the net assimilation rate during the scion development stage (≥12 g/m²/d) were identified as key agronomic physiological indicators for regulating the yield-quality synergy. Optimizing nitrogen fertilizer management ensures an adequate supply of photosynthetic products through the high photosynthetic rate of flag-holding leaves and the extended lifespan of functional leaves. The phased nitrogen application strategy of “40% base fertilizer + 25% tillering fertilizer + 15% panicle fertilizer + 5% grain fertilizer” proposed in this study provides a theoretical and practical basis for the sustainable development of japonica rice production in the Liaohe Plain. This plan has achieved the coordinated realization of multiple goals including resource conservation (reducing nitrogen by 13%), environmental protection (lowering the risk of nitrogen loss), food security guarantee (stable increase in yield), and quality improvement (enhancement of rice quality), effectively promoting the development of the northern japonica rice industry towards a green, efficient and sustainable direction. Develop in the right direction. Full article

The objectives of this study were to select Thai rice that are tolerant at the seedling stage and investigate their growth, physiological and yield responses at the reproductive stage in comparison with the standard salt-tolerant Pokkali (PK). Twenty-two local, commercial and improved Thai rice genotypes along with PK and salt-susceptible IR29 were evaluated at the seedling stage for salt tolerance using a 15 dS m⁻¹ saline solution with five replications. Ten selected genotypes were grown in pots with four replications and exposed to a 15 dS m⁻¹ saline level from early booting to the flowering stage. During the grain-filling stage, salt treatments decreased from 15 to 12 dS m⁻¹ and were sustained at this level until harvest. The experimental design for both experiments was a randomized complete block design (RCBD). Based on the physiology of flag leaves, almost all genotypes exceled in the protection of chlorophyll, relative water content (RWC), membrane integrity and lipid peroxidation. In contrast, the photosynthesis, growth and grain yield of all were dramatically reduced. The rice genotypes exhibited varying degrees of osmotic adjustment (OA), ranging from 1.598 to 2.541 MPa. The cultivar RD73 and line TSKC1–144, which were genetically improved from KDML105 by the introgression of a salt-tolerant QTL/gene from PK, showed the least reduction in grain yield (60 and 53% reduction, respectively) along with PK (60%). Among the five Thai local rice varieties, Go Main Surin (GMS) showed the least reduction in grain weight (58%), total plant dry weight (28%) and green leaf dry weight (1%), while Khao Gaew (KG) and Leuang Puang Tawng (LPT) were the most reduced. PK and RD73 showed a high level of tolerance at both the seedling and reproductive stages. In contrast, KG and LPT, which exhibited high tolerance at the seedling stage, showed high susceptibility in growth, yield and most physiological traits. On the other hand, TSKC1–144 was sensitive at the seedling stage but showed increased tolerance at the reproductive stage. This result implies that suitable cultural practices should be performed to obtain the best field conditions for growing rice genotypes having different levels of salt tolerance at the seedling and reproductive stages. Future research should focus on molecular characterization of tolerance mechanisms of the promising local genotypes and the potential to use them as tolerance gene donors. Full article

Soil salinization poses a significant threat to global agricultural productivity. Among crops, soybean (Glycine max), an important source of oil and protein, is more susceptible to salt stress compared to other major crops such as wheat (Triticum aestivum) and rice (Oryza sativa). To better utilize saline land resources, understanding the mechanisms underlying salt tolerance in soybean is essential for developing new salt-tolerant soybean varieties that contribute to food security. This review synthesizes current knowledge on the molecular mechanisms of salt tolerance in soybean, with a focus on ion homeostasis, osmotic adjustment, oxidative balance restoration, structural adaptations, and transcriptional regulatory networks. Key findings highlight the critical roles of ion transporters—such as GmNHX1, GmSOS1, GmHKT1, and GmCLC1—in maintaining Na⁺/K⁺ and Cl⁻ balance; the accumulation of osmoprotectants like proline and LEA proteins to alleviate osmotic stress; and the activation of antioxidant systems—including SOD, CAT, and APX—to scavenge reactive oxygen species (ROS). Additionally, structural adaptations, such as salt gland-like features observed in wild soybean (Glycine soja), and transcriptional regulation via ABA-dependent and independent pathways (e.g., GmDREB, GmbZIP132, GmNAC) further enhance tolerance. Despite these advances, critical gaps remain regarding Cl⁻ transport mechanisms, rhizosphere microbial interactions, and the genetic basis of natural variation in salt tolerance. Future research should integrate genomic tools, omics-based breeding, genome editing techniques such as CRISPR-Cas9, microbial technologies, and traditional breeding methods to develop salt-tolerant soybean varieties, providing sustainable solutions for the utilization of saline–alkali soils and enhancing global food security. Full article

Heavy-metal-associated (HMA) isoprenylated plant proteins (HIPPs) play crucial roles in plant responses to biotic/abiotic stresses and heavy-metal homeostasis. However, the involvement of HIPP genes in the response of soybean (Glycine max) to aluminum (Al) toxicity remains unexplored. This study aimed to comprehensively characterize the GmHIPP gene family and investigate its role in Al toxicity. A total of 76 GmHIPP genes were identified in the soybean genome. Phylogenetic and synteny analyses revealed that HIPP evolution was highly conserved among soybean, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). Cis-element analysis indicated that GmHIPP genes might be involved in phytohormone response, abiotic and biotic stresses, and plant growth. RNA-seq analysis further revealed that the expression of 20 GmHIPPs was up-regulated, and three GmHIPPs were down-regulated under Al stress in roots. Among them, six genes (GmHIPP9/13/29/43/58/73) were highly induced by Al, with GmHIPP29 exhibiting particularly high expression in root tips. Subcellular localization demonstrated that GmHIPP29 is a plasma membrane-localized protein. GmHIPP29-overexpression significantly increased Al accumulation in the cell sap of the transgenic soybean hairy root tips, leading to increased Al sensitivity. Collectively, these results demonstrate that GmHIPP29 acts as a negative regulator of Al tolerance by promoting Al accumulation in soybean roots. Full article

Understanding how organic amendments affect microbial carbon use efficiency (CUE) and necromass C (MNC) is crucial for understanding soil organic C (SOC) formation and accrual in paddy fields, but the underlying mechanisms remain largely unclear. In this study, the microbial CUE, MNC, and microbial community composition, as well as SOC fractions and chemical composition, were measured under long-term organic amendments: rice straw (RS), green manure (GM), and pig manure (PM) in paddy soils. Four treatments were included: (1) chemical fertilizers (CF); (2) CF plus RS (CF + RS); (2) CF plus GM (CF + GM); and (4) CF plus PM (CF + PM). The CUE, MNC, and microbial community were determined by ¹⁸O-H₂O incubation, amino sugars levels, and phospholipid fatty acids (PLFAs) content, respectively. Results showed that SOC, particulate organic C (POC), and mineral-associated organic C (MAOC) concentrations were significantly increased by organic amendments compared with chemical fertilization alone. The O-alkyl C decreased, but aromatic C increased with long-term organic amendments, suggesting enhanced SOC hydrophobicity. GM and PM inputs significantly enhanced microbial CUE, but straw return did not affect microbial CUE compared to CF. Microbial growth and C uptake increased by 25.2–42.4% and 19.8–30.0% under organic amendments relative with CF. Microbial respiration was increased by RS and GM amendments. Turnover time was more rapid in CF + RS and CF + GM than in CF and CF + PM. Compared to CF, organic amendments increased the MNC concentration due to the increase in microbial biomass. In addition, CF + RS and CF + GM enhanced the MNC contribution to SOC, but PM had no effect, suggesting that PM contributed more organic C from non-microbial sources. The SOC, POC, and MAOC increased with microbial CUE and MNC, indicating that microbial traits play a crucial role in SOC accrual. Higher microbial CUE and biomass explained the increased MNC accumulation under organic amendments. Our study highlights the crucial role of microbe-mediated processes in SOC accrual under long-term organic amendments in paddy soils. Our findings show that organic amendments are an effective management practice for accumulating more SOC in paddy soils. Full article