Search Results (2,312)

Cymbidium eburneum Lindl. is a valuable ornamental orchid and breeding parent, but its genetic background remains unclear due to habitat destruction and germplasm mixing. This study developed specific SSR markers to evaluate the genetic diversity and structure of 96 C. eburneum Lindl. accessions from China and Vietnam. Transcriptome analysis identified 47,248 SSR loci. Sixteen polymorphic core primer pairs detected 150 alleles (mean Na = 9.375) with an average Polymorphism Information Content (PIC) of 0.444. Observed heterozygosity (Ho = 0.290) was noticeably lower than expected (He = 0.478), indicating heterozygote deficiency. UPGMA clustering identified eight groups strongly correlated with geography. Principal Coordinate Analysis (PCoA) revealed a clear geographical differentiation pattern, featuring the most genetically cohesive group from Guangxi and more differentiated geographically marginal populations from Hainan and Vietnam. STRUCTURE analysis (K = 2) indicated two main gene pools with signals of genetic admixture. Geographical isolation was suggested as a potential driver of genetic differentiation. The Guangxi population represents a genetically consistent major reservoir, while marginal populations harbor unique variations. These findings provide a scientific basis for germplasm identification, conservation, and parental selection in C. eburneum Lindl. breeding. Full article

Aiming to clarify the spatial distribution characteristics of soil microbial assemblages and the environmental factors shaping them across a narrow altitudinal transect, this investigation concentrated on the surface soil layer within naturally occurring mixed forests of Picea crassifolia and Betula platyphylla, situated in the elevation band from 2400 to 2800 m along the southern flank of the Qilian Mountains. Leveraging the Illumina NextSeq 2000 high-throughput sequencing platform, integrated with α- and β-diversity analyses and redundancy analysis (RDA), we systematically characterized the composition and diversity traits of soil bacterial and fungal communities, as well as their associations with environmental factors. Notably, the bacterial communities were dominated by Pseudomonadota, Actinomycetota, and Acidobacteria with the abundance of Pseudomonadota decreasing with increasing altitude and that of Acidobacteria increasing with increasing altitude. Furthermore, Ascomycota and Basidiomycota were the dominant phyla in the fungal community. In contrast, bacterial α-diversity—as estimated by the Ace index—showed no significant variation across altitudes. Yet, the fungal alpha diversity metrics—namely Ace and Chao1—were markedly elevated at the 2800 m elevation relative to those observed at both intermediate and lower-altitude locations. Importantly, fungal diversity and community composition showed stronger altitudinal differentiation than bacterial communities in this dataset. Moreover, soil pH, total phosphorus, organic carbon, litter C:N:P stoichiometric ratios, and microbial biomass C:N:P stoichiometric ratios were strongly associated with soil microbial community variation along the altitude gradient, suggesting that they may act as important environmental filters. In conclusion, altitude-driven variations in litter characteristics and soil physicochemical properties jointly shape the assembly processes and spatial distribution patterns of soil microbial communities in this region. Full article

The integration of rooted plant flour into traditional noodle matrices, such as rice noodles and qingke noodles, represents a novel approach to enhancing the nutritional and sensory profiles of staple foods. This study investigates the volatile flavor components and functional compounds derived from rooted plant flours, including Gongmi “tribute rice”, qingke “highland barley” flour, kudzu vine flour, Gastrodia elata blume flour, dried ginger flour, and fishwort root flour, when incorporated into rice and qingke noodles. The novelty of this research lies in its comprehensive analysis of how these flours influence not only the nutritional and textural properties but also the volatile organic compounds (VOCs) that define sensory acceptance and health benefits. Using advanced gas chromatography mass spectrometry (GC-MS), we identified key VOCs, such as esters, aldehydes, and terpenes, which contribute to unique flavor profiles like umami, sweetness, and earthy notes in fortified noodles. Additionally, the study highlights the best functional compounds for health, including polyphenols, resistant starch, and polysaccharides, which demonstrate significant antioxidants, anti-inflammatory, and cholesterol-lowering properties. For instance, highland barley enriched flour exhibited high levels of phenolic compounds and carotenoids, which correlated with improved antioxidant activity and a reduced glycemic index. Similarly, Gongmi flour contributed elevated levels of γ-aminobutyric acid (GABA) and rutin, enhancing the rice noodles’ potential to manage metabolic diseases and support cardiovascular health. Molecular docking analyses predicted strong interactions between key volatile compounds (e.g., 3-dihydro-1, 3-trimethyl-33-phenyl-1H-indene) and metabolic targets like ACE and SGLT1, suggesting mechanisms for their cardioprotective and anti-diabetic effects. This research provides a groundbreaking framework for developing next generation functional foods by leveraging rooted plant flours to bridge the gap between sensory appeal and health efficacy, offering strategic insights for personalized nutrition and sustainable food production. Full article

Exogenous application of plant hormones has been considered a short-term and effective strategy to alleviate deleterious effects of water stress on plants. However, whether exogenous gibberellic acid (GA₃) directly enhances nitrogen accumulation and thereby alleviates drought stress in soybean (Glycine max (Linn.) Merr.) remains to be investigated. This study set three water treatments (75% CK, 50% MD, 25% SD), with half of the plants at each level sprayed with 10⁻⁶ mol·L⁻¹ GA₃, measuring growth, photosynthesis, nitrogen content, water status, and electrophysiological parameters and calculating cellular metabolic electronic energy (ΔG_B) based on Nernst equation. The results showed that drought reduced soybean nitrogen accumulation, photosynthesis, growth and yield. GA₃ increased soybean nitrogen accumulation, improving photosynthesis and yield under CK, which enhanced the consumption of intracellular stored energy and reduced ΔG_B. Under MD, GA₃ improved leaf water status, promoted soybean nitrogen accumulation and photosynthesis and reduced ΔG_B by allocating more energy to drought resistance; it could therefore mitigate the moderate drought stress on plants. ΔG_B negatively correlated with total nitrogen content and yield, indicating that ΔG_B was a potential indicator associated with nitrogen accumulation, which can guide the optimization of GA₃ spraying strategies. Further studies on GA₃ application details are necessary to improve the soybean yields under drought conditions. Full article

The common bean (Phaseolus vulgaris L.) is a major food legume and an important plant genetic resource for sustainable agriculture. Effective use of this diversity requires integrated evaluation of phenotypic variation and agronomic performance, with preliminary assessments of line performance across seasons. In this study, phenotypic diversity was evaluated in a subsample of the INCREASE R-core collection, a large and well-defined core set of common-bean SSD lines derived from heterogeneous germplasm lines. A total of 507 lines were characterized using 57 agro-morphological traits. Multivariate analyses revealed wide phenotypic diversity structured mainly by growth habit, phenology, and yield-related traits, with clear differentiation among lines. Mixed-data clustering identified cluster 4 as the main phenotypic group associated with higher seed- and yield-related performance and composed predominantly of indeterminate climbing landraces. Multi-trait selection indices generally ranked lines from this group highest, while early, small-seeded types tended to show lower overall performance. Evaluation of a selected subset of 19 lines across two growing seasons revealed marked year-to-year variation in yield performance, indicating contrasting responses among otherwise high-performing lines. The multi-trait genotype–ideotype distance index further distinguished lines with balanced performance across traits and years. Overall, this study shows that large-scale phenotypic characterization combined with multi-trait evaluation can provide a useful exploratory basis for identifying breeding-relevant ideotypes and promising lines for further validation for common-bean improvement. Full article

Background: Information on the autopolyploid of Gossypium herbaceum remains limited until now. Previously, the autotetraploid of G. herbaceum was successfully generated via colchicine-induced chromosome doubling from the diploid cultivar ‘Hongxing’ in our lab. Methods: To investigate the drought stress response mechanism of this tetraploid, the autotetraploid S4 was used as the experimental material. The plants were subjected to drought stress during the flowering stage, followed by measurements of physiological and biochemical indicators and transcriptomic sequencing analysis. Results: Under drought stress, MDA content increased, and cell membranes sustained oxidative damage. Photosynthetic parameters, such as net photosynthetic rate (Pn), were significantly suppressed, while the activity of osmotic regulators and key antioxidant enzymes increased significantly. After rehydration, all of the above physiological indicators showed varying degrees of recovery. Transcriptome analysis revealed that, when comparing the treatment group with the control group, a total of 5530 differentially expressed genes (DEGs) were identified, with 2714 up-regulated and 2816 down-regulated. Furthermore, this study investigated the drought resistance mechanism involving the interaction between the MAPK signaling pathway and other metabolic pathways in the autotetraploid. Nine drought-resistant genes, including MAPK3, bHLH47, GaRbohD, RIBA1, PIP1-3, RCA1, RbohD, CYP707A and HSP70, were selected and analyzed using real-time quantitative PCR; the results were generally consistent with the transcriptomic data. Conclusions: These findings substantially enhance our understanding of the molecular mechanisms underlying drought responses in autotetraploids. This novel autotetraploid genotype expands the available cotton germplasm resources and is expected to hold significant value for research on polyploidy evolution. Full article

The mechanisms underlying hydrogen peroxide (HP)-induced oxidative stress damage in the muscle of Nile tilapia (Oreochromis niloticus) remain poorly understood. In this study, an oxidative stress model was established through 2 mM HP exposure for 4 weeks to elucidate the effects of oxidative stress on tilapia muscle and regulatory mechanisms. The results demonstrated that prolonged oxidative stress inhibited the antioxidant response in tilapia muscle and significantly reduced body weight. Concurrently, oxidative stress downregulated the gene expression of muscle proliferation and development, leading to a loss of muscle mass and the deterioration of muscle texture. Furthermore, oxidative stress altered muscle cell fate and exacerbated inflammatory responses. Further transcriptomic analysis revealed that Pten played a critical regulatory role in the muscle antioxidant response and growth. Mechanistically, activation of Pten ameliorated antioxidant capacity and promoted cell proliferation. In conclusion, HP-mediated oxidative stress significantly inhibited muscle proliferation and development, while targeted regulation of Pten effectively alleviated the suppression of muscle antioxidant capacity and cell proliferation. This study provided a theoretical basis for the prevention and control of oxidative stress injury in tilapia aquaculture. Full article

Silage serves as a cornerstone for the advancement of the livestock industry and a critical method for biomass preservation and utilization. This study investigated the impact of geographical and environmental factors—including longitude, latitude, temperature, relative humidity, precipitation, altitude, and sunshine duration—on fermentation parameters and bacterial communities in natural forage silage. Fresh samples of Saccharum arundinaceum and Leucaena leucocephala were collected from Changjiang, Haikou, Wanning, Danzhou, Qiongzhong and Sanya in Hainan Province, China. After 60 days of anaerobic fermentation, fermentation parameters and bacterial communities were analyzed. Results showed that fermentation parameters of the same plant exhibited significant variations across different regions. For instance, Leucaena leucocephala silage from Haikou showed the lowest pH value (4.32), while that from Danzhou recorded the highest pH value (5.63). In Saccharum arundinaceum silages, the prevalent genera in HGH (Saccharum arundinaceum silage from Haikou) were Weissella (49.85%) and Leuconostoc (20.42%), while the bacterial community of DGH (Saccharum arundinaceum silage from Danzhou) was dominated by Klebsiella (62.69%). These results revealed significant variations in fermentation characteristics and microbial community structure of the same plant species across different geographical regions. The Mantel-test network heatmap analysis demonstrated that longitude, latitude, altitude, precipitation, and relative humidity were identified as influential factors shaping silage microbial communities, with latitude being the most important geographical factor influencing silage microbiota. In conclusion, these findings highlight the critical need for region-specific adaptation of silage production strategies, particularly in response to latitudinal variations, to accommodate local environmental conditions, even when processing identical plant species. Full article

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating threatening to global rice production. The narrow genetic background of modern rice cultivars exacerbates the shortage of durable resistance resources. In contrast, the wild rice species Oryza officinalis harbors abundant stress-resistance alleles and represents a valuable gene pool for identifying novel broad blast-resistance genes. The cloned resistance gene Pid2 is encoded in a receptor-like protein kinase conferring race-specific resistance against the M. oryzae isolate ZB15. In this study, three Pid2 homologs were isolated from O. officinalis. The special allele Pid2of-MD33 was transformed into “Yunjing 37(YG37), a blast-susceptible japonica rice cultivar” via Agrobacterium-mediated transformation. Quantitative real-time PCR analysis showed that Pid2of-MD33 was consistently expressed in various tissues of O. officinalis, with the highest transcript abundance detected in leaf mesophyll cells and plasma membranes. Inoculation with the M. oryzae isolate ZB15 revealed that transgenic YG37 lines expressing Pid2of-MD33 displayed significantly reduced lesion size and pathogen proliferation, suggesting recovered race-specific resistance. These results enrich the resistance gene resources for rice blast research and provide a promising candidate gene for rice blast resistance breeding. Full article

Globally, 5.94 million accessions are conserved across 867 genebanks, of which 41.5% (2.47 million) are cereal crop accessions. Only a small portion of global germplasm diversity has been marker-genotyped or genome-sequenced. Accurate identification of genebank accessions is essential to improve the efficiency and effectiveness of global genebanking. It is crucial for preserving the legacy knowledge associated with the germplasm and for maintaining its value to current plant science and breeding efforts. Existing practices generally fall into two categories: either expensive and complex, or inefficient, labour-intensive, and inaccurate. The first relies on high-resolution genomic sequences or saturated markers, while the second relies on morphological comparisons of regenerated plants with historical records. We propose a genotyping method based on a minimal set of Single Nucleotide Polymorphism (SNP) markers and exemplify its use on a genebank scale. We identified a small, effective set of SNPs that can differentiate between the global diversity of genebank accessions of barley (Hordeum vulgare and Hordeum spontaneum) and tetraploid wheat collections (Triticum turgidum) maintained at the Germplasm Resources National Capability at the John Innes Centre, UK. This approach offers a straightforward, automatable, and inexpensive alternative to traditional genebank crop descriptors used during seed regeneration and distribution. By establishing the minimal genomic resolution needed to distinguish genetically distinct accessions, we show that as few as 24 and 25 carefully chosen SNP markers for barley and durum wheat, respectively, can effectively differentiate individual accessions. Unlike morphology-based identification, which can detect mislabelling or contamination but often cannot prevent or correct such errors, our SNP-based molecular labelling enables error correction and the retrieval of lost germplasm identity. This study highlights how accuracy and reliability in germplasm management can be improved without costly whole-genome sequencing or resource-intensive analysis. We discuss the impact of this method on enhancing quality assurance in genebanks and its broader usefulness for the user community. Full article

The diploid distant hybrid (2nBY) derived from female blunt snout bream (Megalobrama amblycephal, BSB) × male Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT). To investigate the hypoxia tolerance and the regulatory mechanisms of hypoxia-inducible factor-1α/2α (hif-1α/2α) in 2nBY, BSB, and YT, experiments consisting of 24 h of hypoxia treatment (DO = 2.0 ± 0.1 mg/L) followed by 6 h of reoxygenation were conducted. The loss of equilibrium critical oxygen pressure (LOEcrit), gill tissue structure, and antioxidant indices, as well as the full-length sequences and expression of hif-1α/2α in 2nBY, BSB, and YT, were compared. The results showed that the LOEcrit value of 2nBY was significantly lower than that of BSB but higher than that of YT (p < 0.05). After hypoxia treatment, the changes in gill tissue structure and antioxidant indices of 2nBY were less obvious than those of BSB, and the recovery rate was faster after reoxygenation. Sequence analysis revealed high similarity of hif-1α/2α between YT and 2nBY. After hypoxia treatment, hif-1α/2α were upregulated in the liver but showed distinct gill expression among the three groups. Their gill expression differences may contribute to varied hypoxic tolerance. Distant hybridization between BSB and YT successfully generated hybrid offspring with enhanced hypoxia tolerance relative to BSB. These results provide theoretical and technical support for the breeding of a new hypoxia-tolerant germplasm resource of bream. Full article

Understanding the genetic diversity and population structure of Cucurbita species is essential for effective germplasm conservation and the development of improved cultivars. This study aimed to evaluate the genetic diversity, population structure, and genetic relationships among accessions of C. pepo, C. moschata and C. maxima and their interspecific hybrids (Tetsukabuto hybrid C. maxima × C. moschata). A total of 92 accessions were analyzed using 22 polymorphic simple sequence repeat (SSR) markers selected from previous studies due to their high polymorphic information content (PIC). Genetic diversity parameters were estimated, and population structure was inferred using Bayesian clustering, complemented by dendrogram and principal component analysis (PCA). All markers were successfully amplified in C. pepo, C. moschata, C. maxima, and the hybrids, with polymorphic information content (PIC) values ranging from 0.191 (CMTm232) to 0.448 (CMTm48) and average of 0.274. The AMOVA analysis showed that 50% of the total variation was attributed to differences both within and among groups. PCA revealed clear genetic differentiation among the analyzed species, with C. maxima and hybrid accessions clustering closely and exhibiting lower genetic dissimilarity. In contrast, C. pepo displayed greater genetic divergence, supporting its distinct evolutionary trajectory. According STRUCTURE analysis the accessions can be divided into four subpopulations, which are closely related to the species. PCA and dendrogram showed similar results for genetic structure of Cucurbita germplasm; C. maxima and hybrid accessions clustering closely and C. pepo as a distinct group. These findings provide valuable insights for breeding programs, germplasm management, and conservation strategies aimed at preserving genetic diversity and exploiting interspecific variation. Full article

Genetic diversity is fundamental for the conservation and sustainable utilization of plant species. Triadica cochinchinensis, a tree species native to southern China, is an important ornamental and nectar-producing plant with considerable economic value. However, the levels of genetic diversity and the patterns of population differentiation across its natural populations remain unexplored. Here, we developed 24 highly polymorphic SSR markers and used them to assess the genetic diversity and differentiation among 280 individuals collected from 10 natural populations of T. cochinchinensis. The results showed that the average expected heterozygosity (He) revealed by the SSR markers was 0.774, and the average Shannon diversity index (I) was 1.660, indicating a high level of genetic diversity at the species level of T. cochinchinensis. Analysis using SSR markers revealed a low average observed heterozygosity (Ho = 0.323) and a relatively high average inbreeding coefficient within populations (F = 0.466). These findings suggest that inbreeding is likely occurring, which may contribute to a loss of heterozygosity within the studied populations. Notably, not all populations had high genetic diversity. For example, the He of SC2 population (0.490), QY population (0.568), and SC1 population (0.585) were all below the mean He (0.607), suggesting that attention should be given to protecting populations with low genetic diversity. The results further showed that the average genetic differentiation coefficient (F_ST) between populations was 0.094, and the average gene flow (Nm) was 2.278, indicating that the natural populations of T. cochinchinensis had low genetic differentiation and relatively high gene flow. AMOVA indicated that 74% of the total variation was distributed within populations. Notably, populations SC1 and SC2 exhibited higher genetic differentiation from all others (F_ST > 0.1), which is likely attributed to mountain barriers restricting gene flow. Therefore, it is recommended to enhance in situ conservation efforts while also facilitating assisted gene flow, such as through artificial introduction. For the first time, this study reveals the genetic information of natural populations of T. cochinchinensis at the molecular level, thereby offering a valuable reference for the conservation and utilization of its germplasm resources. Full article

Rice–crab coculture, as China’s third-largest integrated farming model, is pivotal for sustainable Chinese mitten crab aquaculture. This study conducted untargeted metabolomics and 16S rRNA gene sequencing on gut contents of crabs from rice fields and ponds, integrating metabolic and microbial profiles. We aimed to reveal the chemical traits of rice-field Chinese mitten crab linked to gut microbiota, providing scientific guidance for optimizing culture practices and developing microbial additives. Both groups were dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidota, but the phylum Bdellovibrionota was not detected in group R. A total of 1271 distinct amplicon sequence variants (ASVs) were identified, which were annotated to 649 genera. At the ASV level, the Chao1 index for the R group (197.12 ± 17.88) was notably lower compared to the P group (288.75 ± 30.59) (p < 0.01). In contrast, the Shannon index for the R group (3.90 ± 0.06) was significantly greater than that of the P group (3.70 ± 0.06) (p < 0.01). The PCA plot demonstrated a distinct discrimination between the groups. The P group had more microbial species but was dominated by Candidatus_Bacilloplasma, resulting in uneven distribution. In contrast, the R group had fewer species but a more balanced distribution. Among 3531 metabolites identified in both groups, 865 differed significantly. Compared to P, 736 metabolites were significantly upregulated and 129 were significantly downregulated in R. Key metabolic pathways included amino acid, carbohydrate, cofactor and vitamin metabolism, signaling, and xenobiotics biodegradation. Group R had higher levels of L-leucine, L-phenylalanine, L-tyrosine, 2-amino-1-phenylethanol, choline, and pyrophaeophorbide a, which correlated with genera like Candidatus_Hepatoplasma and Aeromonas (p < 0.05), suggesting better nutritional value, flavor, and metabolic health in rice-field crabs. Full article

A comprehensive management framework integrating environmental and agronomic factors is critical for stable and resource-efficient rice production. The primary objective of this study was to develop an optimization framework for transplanted rice in Jiangsu Province, China, using a Generalized Additive Model (GAM). The framework was used to quantify the inter-annual stability of optimized management schemes and assess their sensitivity to future climate scenarios. The study evaluated the model’s generalization capability using two cross-validation strategies: Leave-One-Year-Out (LOYO) and Leave-One-Site-Out (LOSO). By predicting the yield of each candidate, the scheme maximizing yield was selected as the annual optimal management practice. Validation results demonstrated robust generalization capabilities across both spatial and temporal dimensions, with the model achieving an R² of 0.66 and an RMSE of 836 kg ha⁻¹ in LOSO validation, and an R² of 0.61 and an RMSE of 848 kg ha⁻¹ in LOYO validation. Analysis of the optimized schemes revealed that transplanting date and seedling age functioned as relatively stable planning benchmarks across years, whereas inter-annual adaptation was achieved primarily through adjustments in planting density and nitrogen inputs. Beyond yield prediction alone, this framework translates interpretable GAM response surfaces into spatially differentiated management prescriptions and highlights both soil-conditioned variable-rate strategies and the distinction between stable and adaptive management components under future climate scenarios. Full article