Search Results (129)

Radiation use efficiency (RUE) is closely associated with cotton biomass and yield, yet the synergistic regulation of phenotypic structure and physiological potential remains unclear. A field experiment (2024–2025) in Anyang, China, utilized three independent trials: six sowing dates (from 12 April to 12 May at 6-day intervals, S1–S6), six planting densities (1.5, 3.3, 5.1, 6.9, 8.7, and 10.5 × 10⁴ plants·ha⁻¹, D1–D6), and ten cultivars with distinct architectures (V1–V10). Feature importance and structural relationships were quantified via random forest (RF) and partial least squares structural equation modeling (PLS-SEM). Results indicated that delaying sowing reduced true leaf number (TLN) and plant height (PH), with the April 24 sowing (S3) optimizing leaf area index (LAI, 2.57) and light interception rate (iPAR, 0.61). Increasing density significantly enhanced population-level LAI, above-ground biomass, and RUE, despite a progressive decline in TLN. Among cultivars, CCRI 60 (V6) exhibited superior structural traits (PH: 72.94 cm; iPAR: 0.61), while CCRI 113 (V8) exhibited the highest maximum carboxylation rate (V_cmax, 88.9 μmol·m⁻²·s⁻¹) and RUE (4.88 g·MJ⁻¹). Across the comprehensive dataset (integrating the density, sowing date, and cultivar trials), iPAR exhibited the highest relative importance (42.01%) for RUE variation, while associated structural traits (PH, LAI, TLN) yielded a cumulative relative importance of 41.69%. RUE was strongly associated with biomass accumulation (path coefficient > 0.97), which subsequently optimized yield components. Conversely, within the cultivar-comparison subset, the relative importance of iPAR decreased to 17.95%, while V_cmax rose significantly to 19.20%. PLS-SEM indicated that canopy structure exerted a significant negative association with photosynthetic potential (V_cmax, J_max) within this cultivar subset (path coefficient ≈ −0.51), whereas enhanced physiological potential was positively associated with resource allocation to yield components (path coefficient ≈ 0.57). Consequently, mitigating the inherent trade-off between canopy structure and leaf photosynthetic capacity is critical for further improving RUE and cotton yield under similar production environments. Full article

Understanding diurnal canopy orientation in crops is important for interpreting plant responses to light and environmental conditions, yet field-based quantification remains limited. In this study, we present Heliocot, a field RGB imaging approach that converts time-resolved images into reference-area standardized projected leaf area (PLA) time series to quantify within-day canopy orientation dynamics in early-season cotton. Leaf instance segmentation was performed using YOLOv8m-seg and refined through a 144-combination post-processing optimization. On the held-out early-stage validation/tuning set, the selected workflow showed strong agreement with manual ground truth (R² = 0.948; NRMSE = 0.082) and destructive leaf area measurements (R² = 0.836). Derived diurnal metrics, including Daily Orientation Amplitude (DOA) and Peak Orientation Index (POI), consistently revealed a midday maximum (13:15) in canopy projection. Exploratory genotype-level analysis suggested negative associations between orientation indices and selected plant traits, including specific leaf area (SLA) versus DOA (r = −0.71, p = 0.021, R² = 0.508), destructive leaf area (LA) versus DOA (r = −0.69, p = 0.028, R² = 0.471), and stem dry weight (SDW) versus POI (r = −0.74, p = 0.014, R² = 0.554), while plant height was not significantly associated with POI and DOA (p > 0.05). Although currently limited to early-season conditions and two field-imaging dates, this approach provides a practical workflow for field-based monitoring of canopy projection dynamics in cotton, while broader temporal and environmental validation remains necessary. Full article

Polyploidization is a key pathway for species formation and genetic innovation; approximately 70% of angiosperms have undergone at least one whole-genome duplication event during their evolutionary history. To determine the genetic and phenotypic stability of artificially induced autotetraploids across generations, this study utilized a colchicine-induced autotetraploid of Gossypium herbaceum as experimental material and conducted systematic comparative analyses of morphological, cytological, and molecular marker characteristics in the S3 and S4 generations. The results showed that, compared with the 2×, seed weight in the S3 generation increased by 59.4% (to 89.22 mg), and in the S4 generation increased by 65.0% (to 92.40 mg), while there was no significant difference in fiber length. The leaf area of tetraploids decreased significantly during the flower-bell stage. Observation of pollen mother cell meiosis revealed that the proportions of normal tetrads in the S3 and S4 generations were 73.80% and 81.80%, respectively, and the proportions of normal pollen grains were 79.60% and 80.60%, respectively. Cytological stability was markedly improved in the S4 generation. A total of 34 alleles were amplified by SSR molecular marker analysis, of which 23 (67.60%) were polymorphic. The primers NBRI_G1015 and NAU1164 exhibited the highest polymorphism rates, at 87.50% and 83.30%, respectively. The average genetic diversity index (He) was 0.1411, indicating a highly inbred genetic background. The banding patterns of S3 and S4 are highly consistent, with strong signal intensity; not only do they amplify bands consistent with those of diploids, but they also exhibit specific new bands and band deletions. In summary, this autotetraploid material exhibits stable morphological advantages and genetic uniformity. As generations progress, its meiotic behavior and genetic structure tend to stabilize. The S4 generation exhibits greater cytological stability and genetic uniformity than the S3 generation, making it a highly promising new germplasm resource for cotton polyploid breeding. Full article

The simultaneous improvement of fiber strength (FS) and lint percentage (LP) is a critical objective for achieving high-quality and high-yield cotton production. Identifying key genes and their regulatory networks that govern the synergistic development of FS and LP is essential for achieving their simultaneous improvement. In our previous study, a stable chromosome segment, Seg-D06-2, was identified for its ability to concurrently enhance both FS and LP with high reliability. In the present study, homozygous individuals harboring the Seg-D06-2 segment within a nearly uniform genetic background were selected to construct a large BC₆F₂ chromosome segment substitution line (CSSL) population comprising 3324 individuals. Extreme individuals characterized by simultaneous improvement in FS and LP, which shared similar genetic and phenotypic backgrounds, were subjected to comparative transcriptomic and weighted gene co-expression network analysis (WGCNA) at 0, 5, 10, 15, 20, and 25 days post-anthesis (DPA). The results highlighted the ’blue’ and ’yellow’ modules as being significantly associated with the simultaneous improvement of FS and LP. Four hub genes (GH_D06G0542, GH_D06G1609, GH_D06G0627 and GH_D06G2689) and two DEGs (GH_D06G0564 and GH_D06G0723) were identified in the ’blue’ module. Three hub genes (GH_D06G0540, GH_D06G0558 and GH_D06G0636) and one DEG (GH_D06G0527) were identified in the ’yellow’ module. These 10 key genes likely play pivotal roles in regulating the synergistic development of FS and LP, warranting further investigation. The reliability of the RNA-seq data was confirmed by qRT-PCR. This study provides a valuable resource for molecular breeding aimed at the simultaneous improvement of FS and LP and offers new insights into the molecular mechanisms governing their synergistic development. Full article

Leucine-rich repeat extensins (LRXs) are essential regulators of plant development, cell wall integrity, and stress responses. However, genome-wide LRX studies in cotton are limited. Analysis of four Gossypium species identified 29, 28, 16, and 16 LRX genes in G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively. Phylogenetic analysis resolved these 89 genes into four subfamilies (I–IV). Structural annotation revealed that cotton LRX family members exhibit conserved domain architectures. This finding was corroborated by motif analysis, which revealed notable conservation in the motif compositions of most cotton LRX proteins, suggesting functional conservation across evolutionary lineages. Distinct spatiotemporal expression patterns were uncovered between G. hirsutum and G. barbadense. Prolonged exposure to extreme temperatures induced widespread down-regulation of most GhLRX genes, whereas genes in subgroup IV were significantly up-regulated under salt and drought stress conditions, respectively. Notably, GhLRX7 showed a more proactive responding profile to Verticillium wilt (VW) infection, which was therefore selected for functional validation employing virus-induced gene silencing in the cotton cultivars MBI9626 and CCRI36. Phenotypic analysis of silenced plants revealed exacerbated disease symptoms compared to wild-type controls, providing direct evidence implicating GhLRX7 as a key contributor to defense against VW. Full article

Histidine triad (HIT) family proteins contain a conserved histidine triad motif and play key roles in fungal metabolism and pathogenicity. This study focused on VD9136, a member of the HIT family in Verticillium dahliae, aiming to elucidate its biological function and mechanism underlying its role in cotton pathogenesis. A systematic investigation of the VD9136 gene in V. dahliae was conducted using bioinformatics analysis, gene knockout, genetic complementation, and pathogenicity assays. The results showed that VD9136 protein consists of 136 amino acids and is a stable, neutral, and weakly hydrophilic protein that lacks transmembrane domains and signal peptides; it is localized to the extracellular space via a non-classical secretion pathway. Its secondary structure is predominantly composed of α-helices and random coils. Phylogenetic analysis revealed that VD9136 is closely related to VliHIT, a homologous protein from V. longisporum, the pathogen responsible for Verticillium wilt in rapeseed. The promoter region of VD9136 contains multiple cis-acting elements, including light-responsive, hormone-responsive, and stress-responsive elements, indicating that its transcription may be regulated by multiple signaling pathways. VD9136 was significantly upregulated during the early stage of cotton infection (6–24 h post-inoculation). Pathogenicity assays demonstrated that V. dahliae knockout mutants lacking VD9136 exhibited a significant reduction in virulence, as evidenced by a lower disease index, decreased fungal biomass within plant tissues, and attenuated vascular browning in cotton plants. The pathogenic phenotype was successfully restored in genetic complementation strains. This study identified VD9136 as a key regulatory factor in the pathogenic process of V. dahliae, and its loss of function reduces the pathogenicity of V. dahliae. The findings provide a theoretical basis for elucidating the pathogenic mechanism of cotton Verticillium wilt and for developing corresponding prevention and control strategies. Full article

Fruit branch length in cotton is a key trait influencing plant architecture and suitability for mechanisation; elucidating its molecular regulatory mechanisms is crucial for breeding varieties with desirable plant architecture. In this study, an F₂ segregating population was established using the long-fruit-branch upland cotton line L16 and the short-fruit-branch line S14 as parents. By integrating morphological, cytological, and omics approaches, we systematically analysed the underlying mechanisms of variation in fruit branch length. Phenotypic analysis indicated that the inter-node elongation rate of the first fruit branch in L16 was significantly higher than that in S14. Tissue section observations revealed that the length of cortical parenchyma cells in L16 was significantly greater than that in S14, suggesting that the difference in fruit branch length primarily stems from variations in the extent of cortical parenchyma cell elongation. BSA-Seq analysis identified five QTL regions significantly associated with fruit branch length, encompassing 82 coding genes. Further RNA-Seq analysis of the fruit branch initiation stage (T0) and rapid elongation stage (T1) identified 3106 differentially expressed genes common to both stages. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in pathways related to plant hormone signalling, the cytoskeleton, and microtubule organisation. By integrating BSA-Seq and RNA-Seq data, three candidate genes were screened that simultaneously harboured non-synonymous mutations and were significantly highly expressed in the short fruit branch line S14. Combined with bioinformatics analysis, GH_D02G0744 was predicted to be the most likely key candidate gene regulating cotton fruit branch length. This study provides important genetic resources to elucidate the molecular regulatory mechanisms of cotton fruit branch length and lays a theoretical foundation for molecular breeding to improve cotton plant architecture. Full article

Cotton Verticillium wilt seriously threatens global cotton production, necessitating the development of resistant cultivars through molecular breeding. Members of the ethylene response factor (ERF) family function as pivotal transcriptional regulators of the ethylene signaling pathway, orchestrating plant defensive responses against pathogen invasion. Here, through comprehensive phenotypic and transcriptional analyses of lignin biosynthesis genes in AtERF49-overexpressing lines, loss-of-function mutants, dominant repressor plants, and GhERF49-silenced cotton plants (TRV-VIGS), we demonstrate that AtERF49 functions as a negative regulator of Verticillium wilt resistance. Overexpression of AtERF49 significantly compromised defense responses in Arabidopsis thaliana, whereas GhERF49 silencing enhanced cotton resistance to Verticillium wilt. Transcription analysis showed that ERF49-mediated susceptibility correlates with suppression of lignin biosynthesis-related genes following pathogen challenge, suggesting that ERF49 interferes with inducible cell wall fortification. These findings elucidate a previously unrecognized negative regulatory node linking ethylene signaling to lignin-mediated disease resistance, providing promising biotechnological targets for engineering durable Verticillium wilt resistance in cotton and related crops. Full article

Agricultural robots and unmanned farmland management require real-time and precise parsing of crop leaves at the edge to support variable application of pesticides, seedling condition monitoring, and phenotypic analysis. However, the field environment features drastic changes in light, leaf occlusion, and interference from background weeds, which can cause semantic fragmentation and boundary artifacts in lightweight models. This paper presents ES2-LeafSeg, a lightweight framework for leaf semantic segmentation tailored for edge deployment. The method employs EfficientNetV2 as the backbone encoder and introduces the State Space Semantic Enhancement Module (S2FEM) on skip connection features, modeling long-range dependencies and suppressing local texture noise through SSM pooling in row and column directions. Meanwhile, a cross-scale decoder (CSD) and a global context transformation (GCT) are designed to achieve multi-scale semantic fusion and boundary refinement. On the three-class segmentation task of the SoyCotton dataset, ES2-LeafSeg achieved mIoU of 0.817, mDice of 0.869, Fβw of 0.925, and MAE of 0.011, outperforming multiple classic and recent baselines while maintaining 23.67 M parameters and 49.62 FPS. Ablation experiments further verified the complementary contributions of S2FEM and GCT to regional consistency and boundary quality. Full article

Plant viral vectors are powerful tools for the transient expression of exogenous genes, enabling not only virus-induced gene silencing (VIGS) but also virus-induced genome editing (VIGE). However, technical systems capable of simultaneously achieving gene silencing and gene editing in cotton have been rarely reported to date. Therefore, the development of a virus vector system that can concurrently mediate both gene editing and gene silencing would provide a valuable platform for advancing functional genomics studies and molecular design breeding in cotton. To address this gap, we established a system in cotton that concurrently enables gene silencing and gene editing. This system utilizes cotton Cas9 overexpression (Cas9-OE) as a receptor and CLCrV and TRV as vectors for targeting the GhCLA1 gene, which yields an albino phenotype upon silencing and mutation. Initially, CLCrV and TRV were used independently as vectors for gene editing and gene silencing, respectively. However, our results demonstrated persistent GhCLA1 gene silencing via TRV, but no systemic gene editing via CLCrV, suggesting viral cross-protection may occur between CLCrV and TRV for simultaneous actions. Subsequently, we constructed tandem assemblies of GhCLA1 silencing fragments and sgRNA expression elements in both TRV and CLCrV vectors resulted in successful gene silencing and editing, albeit with low editing efficiency. Further optimization through shortening the gene silencing fragments led to a substantial 2.61 to 3.11-fold increase in editing efficiency, while still maintaining effective GhCLA1 silencing. This refined system provides a robust tool for gene editing in cotton. Full article

Background/Objectives: Among cotton species, Gossypium barbadense produces the strongest fibers. Examining cytoskeletal dynamics in single epidermal cells of G. barbadense ovules offers a direct approach to investigating fiber quality. Microtubules are major cytoskeletal components whose organization and dynamics are precisely regulated by microtubule-associated proteins (MAPs). However, information on the TPX2 family remains limited, and characterizing its features in G. barbadense is critical to clarifying the role of TPX2 family members in fiber strength formation. Methods: Using the Arabidopsis thaliana TPX2 sequence as a reference, 40, 49, 26, and 26 TPX2 family members were identified in the genomes of G. barbadense, Gossypium hirsutum, Gossypium arboreum, and Gossypium raimondii, respectively. We further analyzed the expression pattern of GbTPX2-35 and validated its function via virus-induced gene silencing (VIGS). Results: In G. barbadense, GbTPX2-35 (Gbar_D11G59825.1) was significantly upregulated in fiber samples of the parental lines at 25 days post-anthesis, and this expression pattern was further validated in G. barbadense lines with extreme fiber strength phenotypes. Next, VIGS-mediated silencing of GbTPX2-35 downregulated the transcript levels of cellulose synthase and microtubule-related protein genes, a finding further validated by mature fiber strength phenotypic data. Conclusions: This study preliminarily validated a pathway in which GbTPX2-35 regulates fiber strength by coordinating cellulose biosynthesis with microtubule cytoskeleton dynamics, providing valuable candidate genes and theoretical support for molecular breeding of high-strength cotton fibers. Full article

Soil salinization is a major constraint on sustainable agriculture worldwide, highlighting the need for stress-tolerant plant growth-promoting rhizobacteria (PGPR) for salt-affected soils. A moderately halophilic and alkali-tolerant bacterium, Staphylococcus succinus NYN-1, was isolated from the rhizosphere soil of the halophyte Suaeda dendroides collected from a highly salinized site in Xinjiang, China. This study aimed to evaluate its salt–alkali tolerance and plant growth-promoting potential through integrated phenotypic characterization, pot experiments, and whole-genome analysis. NYN-1 grew over a broad salinity range [0–15% (w/v)] and pH range (6.0–11.0), and showed plant growth-promoting activities including organic phosphorus mineralization, inorganic phosphate solubilization, potassium solubilization, and NH₄⁺ production. In pot experiments under 300 mM NaCl, inoculation with NYN-1 significantly improved the growth performance of maize (Zea mays L.), cotton (Gossypium hirsutum L.), and sunflower (Helianthus annuus L.). Genome analysis identified multiple Na⁺/H⁺ antiporter-related genes and genes encoding compatible-solute transport systems that are consistent with adaptation to salt–alkali stress. The genome also harbors a broad set of genes related to phosphorus metabolism, as well as other plant growth-promoting functions, including potassium solubilization-related pathways and siderophore biosynthesis. Collectively, these findings identify S. succinus NYN-1 as a promising native halophilic PGPR candidate and a potential microbial resource for developing inoculant strategies in salt-affected agricultural systems. Full article

Drought stress severely constrains cotton yield and fiber quality, but conventional evaluation methods are inefficient and time-consuming. To address this, we developed a high-throughput, non-destructive phenotyping framework by integrating UAV-based multispectral remote sensing with machine learning, using 225 upland cotton (Gossypium hirsutum L.) accessions. The accessions were subjected to well-watered (CK) and drought stress (DS) treatments at the flowering and boll-setting stage. Canopy multispectral imagery (Green/Red/Red_edge/Near-infrared bands) was acquired via DJI Mavic 3 Multispectral UAV, and 16 vegetation indices (VIs) were derived. Concurrently, 15 agronomic and fiber quality traits were measured to calculate drought resistance coefficients (DRCs), which were used for principal component analysis (PCA) and comprehensive drought tolerance index (D) construction. Hierarchical clustering categorized the accessions into 6 drought tolerance grades (Groups I–VI). Variable importance analysis identified GNDVI, NGRVI, and NDRE as the most drought-sensitive VIs (% IncMSE > 11). Among four regression models (LR, KNN, LGBM, XGBoost), XGBoost achieved the best performance for D prediction (test set: R² = 0.785, RMSE = 0.032, MAE = 0.024). This study demonstrates that UAV multispectral data coupled with XGBoost enables accurate, efficient drought tolerance assessment, providing a robust tool for high-throughput germplasm screening and smart agricultural management. Full article

Gibberellins (GAs) play a crucial regulatory role in the growth and development of cotton (Gossypium hirsutum L.). Through bioinformatics analyses, we identified a total of 39 GA2ox genes (encoding gibberellin 2-oxidases) in the cotton genome, designated GhGA2ox1 to GhGA2ox39. Based on phylogenetic analysis, these genes were classified into five groups. We further examined their gene structures, conserved motifs, and chromosomal distributions, revealing that members within the same group shared similar structural and motif organizations. Collinearity and cis-element analyses provided important insights into the evolutionary history and regulatory potential of the GA2ox gene family in cotton. Notably, using nucleotide diversity (π) and population differentiation (F_ST) analyses across the entire family, we screened and identified nine candidate genes that underwent strong artificial selection during cotton domestication and improvement. Further haplotype-phenotype association analysis identified GH_D09G0919 (GhGA2ox31) as a key regulator of Plant Height (PH). To validate their regulatory roles, we analyzed the genotype distribution in accessions with extreme phenotypes. The results revealed divergent selection histories for these two loci: the favorable allele of GH_D01G0720 (GhGA2ox23) was already fixed in the tested population, whereas GH_D09G0919 maintained significant natural variation. Specifically, the Hap2 allele of GH_D09G0919 was significantly enriched in the shortest accessions compared to the tallest ones. Importantly, quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed that the Hap2 allele drives significantly higher gene expression in leaves, suggesting that enhanced GA catabolism underlies the compact phenotype. Additionally, transcriptomic profiling revealed the tissue-specific expression patterns of candidate genes, implying their functional roles in development. Furthermore, functional validation using the Arabidopsis mutant of the homologous gene (AtGA2ox8) confirmed its conserved role in regulating plant height, as the mutant exhibited a distinct short-stature phenotype. These results uncover valuable genetic resources for molecular breeding to shape compact cotton architecture. Collectively, this study aims to analyze the evolutionary patterns of the cotton GA2ox gene family and to identify key genes that regulate plant height under artificial selection, providing theoretical support for molecular breeding of compact plant types. Full article

Cotton is one of the most significant economic crops cultivated worldwide. Cottonseed is a strategic reservoir of high-quality plant protein and an underexploited resource for the food and feed industries. To quantify nutritional diversity and identify superior germplasm, we evaluated 312 upland cotton (Gossypium hirsutum L.) accessions over two consecutive growing seasons and characterized 30 agronomic and nutritional traits. Protein content varied widely (29.6–48.8%), with a coefficient of variation of 7.5–11.7% and a two-year mean of 37.0%. Glutamic acid (Glu; 154.0 mg/g) and aspartic acid (Asp; 90.7 mg/g) were the most abundant amino acids, and lysine and arginine were relatively high among essential amino acids. Correlation analysis based on genotype best linear unbiased estimates (BLUEs) showed that most nutritional traits were positively or neutrally associated with key yield-related traits, particularly lint percentage (LP) (e.g., protein vs. LP: r = 0.18, p < 0.01), indicating the feasibility of simultaneous improvement in seed nutritional quality and lint yield potential. Using 29 core traits with complete two-year data, we developed an integrated evaluation framework combining principal component analysis (PCA), grey relational analysis (GRA), TOPSIS, and the analytic hierarchy process (AHP) to rank accessions comprehensively. This framework identified 10 elite germplasm lines with high protein content and favorable yield potential, exemplified by “Xinluzhong 34” (Rank 1; phenotypic comprehensive value, P_i = 0.733). These results provide a quantitative foundation for value-added cottonseed utilization and support breeding strategies aimed at developing cultivars with both high yield and enhanced nutritional quality. Full article