IntroductionWheat (Triticum aestivum L.) is a major staple crop for billions of people. Intercropping can increase wheat grain yield and contribute to food security. However, the physiological characteristics and molecular basis underlying yield increases in intercropped wheat remain insufficiently understood.MethodsThis study integrated physiological measurements with global transcriptional profiling of wheat leaves and roots to investigate responses associated with wheat yield increase under intercropping relative to sole cropping.ResultsIntercropping increased wheat grain yield by 19.12% and 14.94% and spike number per unit area by 27.4% and 25.3% in 2020 and 2021, respectively, whereas grain number per spike and thousand-grain weight were not significantly affected. Intercropping also increased relative chlorophyll content (SPAD value), net photosynthetic rate (Pn), leaf soluble protein content, peroxidase (POD) activity, and sucrose-phosphate synthase (SPS) activity, while decreasing malondialdehyde (MDA) content in wheat leaves. RNA sequencing (RNA-seq) analysis identified 1993 differentially expressed genes (DEGs) in leaves, including 1005 upregulated and 988 downregulated genes, and 17866 DEGs in roots, including 10782 upregulated and 7084 downregulated genes. Upregulated DEGs were mainly enriched in protein processing in the endoplasmic reticulum, plant–pathogen interaction, and photosynthesis–antenna proteins in leaves, and in phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism in roots. The expression trends of 15 of the 16 selected DEGs were consistent between RNA-seq and quantitative reverse-transcription PCR (qRT-PCR) analyses.DiscussionTaken together, the increased biomass accumulation and grain yield of intercropped wheat may be associated with coordinated changes in secondary-metabolite-related pathways, plant–pathogen interactions, protein synthesis and processing, and photosynthesis-related processes. These findings advance our understanding of the physiological and transcriptional responses of wheat to intercropping, identify candidate processes and pathways associated with its yield advantage, and provide a basis for further functional validation and breeding research in intercropping systems.

Background Salt stress is an important abiotic factor limiting yield formation and quality improvement in spring wheat. However, there is still a lack of systematic understanding of how root architectural maintenance and anatomical remodeling coordinately influence shoot growth maintenance during the development of salt tolerance in spring wheat. Methods To address this gap, a high-throughput paper-based cultivation platform was used to assess the shoot phenotypes, root architectural traits, and root anatomical characteristics of 28 spring wheat genotypes under control and Salt treatments. Principal component analysis, membership function analysis, and cluster analysis were combined to establish an integrated salt-tolerance evaluation system, and genotypes with contrasting salt tolerance were further selected to investigate differences in layered root architecture and anatomical responses. Results The results showed that salt stress significantly inhibited both shoot and root growth in spring wheat. The first five principal components explained 81.37% of the total variation, and the integrated evaluation system effectively distinguished salt-tolerance differences among genotypes and identified plant height, total root length, average root length, cortex/stele area ratio, and lacunar/cortex area ratio as key phenotypic indicators. Further analyses showed that root architectural maintenance and anatomical adjustment were significantly associated with shoot growth. Particularly in the deeper root system, salt-tolerant genotypes exhibited more stable salt tolerance, with root surface area reduced by only 18.68%–38.61%, whereas the corresponding reductions in salt-sensitive genotypes ranged from 28.57%–90.00%. Meanwhile, salt-tolerant genotypes showed more coordinated cortical contraction, stele maintenance, and lacunar adjustment, indicating that the key root adaptive basis of salt tolerance in spring wheat does not lie in any single structural trait, but rather in the coordinated optimization between sustained deeper-root maintenance and anatomical remodeling. Conclusion This study reveals the root basis of salt adaptation in spring wheat seedlings from the perspective of root architecture–anatomical coordination, provides new evidence for understanding the phenotypic–structural coupling mechanism underlying wheat salt tolerance, and offers operational indicators for salt-tolerant germplasm screening and targeted improvement of root traits.

Hybrid rice breeding depends on the development of elite parental lines with favorable traits such as grain quality, heading time, and plant architecture. However, improving restorer lines through conventional breeding is time-consuming and labor-intensive. Here, we employed a multiplex CRISPR/Cas9 editing strategy to simultaneously target Wx, Badh2, and Se14 in the elite restorer line FH676, aiming to generate glutinous, aromatic, and early-maturing lines. Through Agrobacterium-mediated transformation, we obtained Wx/Badh2 double mutants (Dm) and Wx/Badh2/Se14 triple mutants (Tm). Grain quality analysis revealed significantly reduced amylose content and enhanced aroma content in the edited lines, consistent with Wx and Badh2 knockouts. The triple mutants also exhibited significantly earlier heading compared to the wild type. The early-maturing Tm lines and the Dm lines achieved grain yields of 39.2 39.4 g and 42.9 43.0 g per plant, respectively, both exceeding yields of conventional glutinous cultivars used at present. To evaluate hybrid performance, we crossed Tm and Dm lines with two sterile lines: LX (aromatic) and NX (glutinous). The LX/Tm hybrid headed 4.8 days earlier than its wild-type counterpart, with no reduction in plant height or yield. The NX/Tm hybrid showed an advance of 6.3 days in heading but a 6.2 7.0

Grain size and stress resistance are key determinants of high and stable yield in rice. However, the genetic and regulatory mechanisms that coordinate these traits remain elusive. Here, we report that OsHOX24 encoding a HD-ZIP I transcription factor plays a dual role in regulating grain size and salt tolerance. OsHOX24 promotes grain length and weight by enhancing cell division and expansion in spikelet hulls, while it compromises salt tolerance. Additionally, we demonstrated that OsHOX24 participates in ABA signaling and directly activates OsPP2C09 transcription by binding to its promoter, thereby jointly regulate grain size and salt tolerance. Finally, haplotype analysis revealed differentiation of OsHOX24 between indica and japonica, with the prevalent indica haplotype (Hap1) associated with superior grain size and salt tolerance. Taken together, our study not only provides novel insights into the molecular mechanisms that regulate grain size and salt tolerance, but also offers a valuable haplotype-specific target for breeding high-yielding and salt-resilient rice.

Salt stress is an major abiotic factor limiting yield formation and quality improvement in spring wheat. Previous studies on wheat salt tolerance have mainly focused on shoot injury, ion homeostasis, biomass reduction, or whole-root morphological traits. However, these approaches generally treat the root system as a whole and rarely distinguish whether salt tolerance is associated with the maintenance of deeper roots or with specific anatomical remodeling within root tissues. To address this gap, a high-throughput paper-based cultivation platform was used to assess the shoot phenotypes, root architectural traits, and root anatomical characteristics in 28 spring wheat genotypes under control and salt-stress conditions. Salt tolerance coefficients were calculated for multiple traits and integrated using principal component analysis, membership function analysis, contribution-rate-based weighting, and comprehensive D-value clustering. Genotypes with contrasting salt tolerance were then selected for further comparison of stratified root architecture and root anatomical responses. The results showed that salt stress significantly inhibited both shoot and root growth in spring wheat. The first five principal components explained 81.37

Introducing genomic segments from related species into crops is an effective approach to enrich genetic diversity and create novel germplasm. African cultivated rice (Oryza glaberrima), as one of the two cultivated rice species, represents a valuable genetic resource for the improvement of Asian cultivated rice (O. sativa). Grain size/weight is one of the most important components of grain yield in rice. In this study, we isolated a chromosome segment introgression line harboring a single segment derived from O. glaberrima. Compare to the recurrent parent, this line displayed a significant increase in grain size, whereas other agronomic traits were not significantly affected. Using map-based cloning, we identified OgGS3.2 from this fragment as an ortholog of OsSLR1. A single nucleotide substitution in OgGS3.2 was identified as the causal mutation underlying the increased seed size phenotype. Haplotype analysis revealed that the vast majority of African rice germplasm carries the G haplotype at the GS3.2 locus. This study reveals the molecular mechanism by which OgGS3.2 regulates grain size and offers strategic genetic resources for yield improvement in cultivated rice.

BACKGROUND:Patient-derived xenografts (PDX) models have been regarded as an important tool for preclinical research. The aim of this study was to establish a Chinese PDX library from gastrointestinal cancers, especially esophageal squamous cell carcinoma (ESCC), esophagogastric junction adenocarcinoma (EGJAC), and gastric adenocarcinoma (GAC). METHODS:1001 surgical tissues or endoscopic biopsy tissues of gastrointestinal cancers were subcutaneously implanted into NOD/SCID mice between January 2013 and August 2015. Engraftment rates, latency period of xenograft formation, patients' clinicopathological characteristics and survival associated with xenografts for ESCC, EGJAC and GAC were assessed. RESULTS:208 PDX models were established (20.8%, 208/1001), among which 82 were from ESCC (21.2%, 82/386), 31 from EGJAC (16.9%, 31/183), and 29 from GAC (10.9%, 29/266). The average latency period of xenograft formation of ESCC, EGJAC, and GAC was 76.2, 90.5, and 85.2 days, respectively, for the first passage, and decreased to 52.5, 54.8, and 52.6 days, respectively for the second passage. For ESCC, gender, specimen type and differentiation were associated with engraftment; and for GAC, the factors associated with engraftment were age, specimen type, differentiation, and Lauren classification. The median follow-up of patients with ESCC, EGJAC and GAC was 46, 64 and 64 months, respectively. For GAC, the survival time of patients from whom the tumor tissues achieved successful engraftment was significantly shorter than that without xenograft formation. CONCLUSIONS:We established a Chinese PDX library from gastrointestinal cancers, especially ESCC, a characteristic tumor type in China, providing a platform for drug development and individualized therapy.

African cultivated rice (Oryza glaberrima) was domesticated from its wild progenitor, Oryza barthii. The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication. A QTL analysis of 331 recombinant inbred lines (RILs) using 194 InDel markers identified five quantitative trait loci (QTL) associated with awn length. Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval. RNA-seq and RT-qPCR analyses, combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5. Genomic analysis revealed a large structural variation (SV) between W1411 and IRGC104165 within this region, characterized by an inversion and two large deletions. Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like (Dom-like) pattern, whereas non-cultivated accessions consisted of two distinct types: W1050-like and W1411-like. The W1411-like type was exclusively found in the AA genome of African wild rice. This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.

The current surveillance guideline of esophageal squamous cell carcinoma (ESCC) runs the risk of underestimation of early Lugol-unstained lesions (LULs), and extremely early genomic events in the carcinogenesis and their temporal order of occurrence remain unclear. Here, we performed whole-exome sequencing analyses of 148 biopsy samples obtained at different time points (with a median 4.6-year interval) from the same esophageal lesions of 74 asymptomatic subjects with LULs detected at community-based screening, of whom 33 individuals showed progression at the follow-up chromoendoscopy, while the other 41 did not. We found that progressors showed higher tumor mutational burden, chromosomal instability level, whole-genome doubling (WGD) events, and apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) activity at both index and follow-up compared to non-progressors. Sustained TP53 two-hit events, absence of NOTCH1 mutation, presence of CDKN2A mutation/deletion, and WGD were detected both before and after LUL progression in 64% (9/14) of progressors and none (0/19) of non-progressors with non-dysplastic LULs (ND-LULs). CCND1, FGFs, and MIR548K amplification in chromosome 11q13.3 only occurred in progressors with high-grade intraepithelial neoplasia or above lesions. TP53 two-hit events, absence of NOTCH1 mutation, and presence of CDKN2A mutation/deletion were positively correlated with WGD and successfully distinguished all 5 progressed individuals from the 24 subjects at so-called "low risk" of progression (ND-LULs with a size of ≤5 mm) under current surveillance criteria. Collectively, TP53 two-hit events, absence of NOTCH1 mutation, and presence of CDKN2A mutation/deletion are extremely early events in the carcinogenesis of ESCC, providing early warning markers for the surveillance of high-risk precursor lesions of ESCC.

Wild soybean (Glycine soja Siebold & Zucc.) has valuable genetic diversity for improved disease resistance, stress tolerance, seed protein content and seed sulfur-containing amino acid concentrations. Many studies have reported loci controlling seed composition traits based on cultivated soybean populations, but wild soybean has been largely overlooked. In this study, a nested association mapping (NAM) population consisting of 10 families and 1107 recombinant inbred lines was developed by crossing 10 wild accessions with the common cultivar NC-Raleigh. Seed composition of the F6 generation grown at two locations was phenotyped, and genetic markers were identified for each line. The average number of recombination events in the wild soybean-derived population was significantly higher than that in the cultivated soybean-derived population, which resulted in a higher resolution for QTL mapping. Segregation bias in almost all NAM families was significantly biased toward the alleles of the wild soybean parent. Through single-family linkage mapping and association analysis of the entire NAM population, new QTLs with positive allele effects were identified from wild parents, including 5, 6, 18, 9, 16, 17 and 20 for protein content, oil content, total protein and oil content, methionine content, cysteine content, lysine content and threonine content, respectively. Candidate genes associated with these traits were identified based on gene annotations and gene expression levels in different tissues. This is the first study to reveal the genetic characteristics of wild soybean-derived populations, landscapes and the extent of effects of QTLs and candidate genes controlling traits from different wild soybean parents.

The soybean cyst nematode (SCN) is one of the most destructive pests affecting soybean production worldwide. Wild soybean (Glycine soja) germplasm offers valuable genetic resources for developing SCN-resistant cultivars. Here, we present a telomere-to-telomere assembly of the wild soybean Glycine soja accession YSD56, which is resistant to the highly virulent SCN race X12. The assembled genome has a total length of 1,008.52 Mb, with a contig N50 of 51.97 Mb, and successfully resolves all 20 centromeres and 40 telomeres. The assembly is high quality, with 99.7% completeness based on conserved single-copy orthologs (BUSCO) and a base-level accuracy of QV 52.16. A total of 57,712 protein-coding genes were predicted, 98.79% of which were functionally annotated. This high-quality reference genome provides a valuable resource for investigating SCN resistance and accelerating soybean genetic improvement.

Accurate prediction of molecular properties is a key component of Artificial Intelligence-driven Drug Design (AIDD). Despite significant progress in improving these predictive models, balancing accuracy with computational complexity remains a challenge. Molecular topological and geometric features provide rich spatial information, crucial for improving prediction accuracy, but their extraction typically increases model complexity. To address this, we propose TGF-M (Topology-augmented Geometric Features for Molecular Property Prediction), a novel predictive model that optimizes feature extraction to enhance information capture and improve model accuracy, and reduces model complexity to lower computational cost. This approach enhances the model's ability to leverage both topological and geometric features without unnecessary complexity. On the re-segmented PCQM4Mv2 dataset, TGF-M performs remarkably, achieving a low mean absolute error (MAE) of 0.0647 in the HOMO-LUMO gap prediction task with only 6.4M parameters. Compared to two recent state-of-the-art models evaluated within a unified validation framework, TGF-M demonstrates comparable performance with less than one-tenth of the parameters. We conducted an in-depth analysis of TGF-M's chemical interpretability. The results further validate the method's effectiveness in leveraging complex molecular topology and geometry during model learning, underscoring its potential and advantages. The trained models and source code of TGF-M are publicly available at https://github.com/TiAW-Go/TGF-M.

Drought and seed aging severely impact crop yield and seed vigor, respectively. Here, we identified the rice protein OsNAT9, a nucleobase-ascorbate transporter, as being crucial for seed vigor and drought tolerance. Knockout of OsNAT9 resulted in a significant reduction in seed vigor; however, the application of exogenous ascorbic acid (AsA) and the breaking of seed dormancy restored this phenotype, suggesting that OsNAT9 regulates seed vigor by modulating seed dormancy. Furthermore, the Osnat9 mutants exhibited decreased AsA concentration in the endosperm, impairing the scavenging of reactive oxygen species (ROS) in aged seeds, which disrupted starch structure and seed vigor. During the aging process, both the knockout and overexpression of OsNAT9 affected AsA efflux, disrupting the redox homeostasis of AsA pools, increasing ROS accumulation, and ultimately reducing embryo vigor. In addition, the Osnat9 mutants displayed reduced drought tolerance, accompanied by decreased AsA concentration and increased ROS accumulation, whereas OsNAT9-overexpressed lines showed the opposite phenotypes. The OsNAT9 protein exhibited either a uniform or punctate distribution on the cytomembrane. Protoplast secretion assays and microscale thermophoresis experiments further confirmed that OsNAT9 functions as a cytomembrane-localized efflux transporter responsible for AsA secretion. This study highlights the dual role of OsNAT9 in regulating seed vigor and drought tolerance by maintaining the homeostasis of AsA pools and reducing ROS accumulation. These findings provide novel insights into AsA efflux transport and its implications for seed vigor and stress adaptation. Furthermore, this study identifies OsNAT9 as a potential target for enhancing crop stress tolerance and seed longevity.

The ratios of red light (R)/blue light (B) and R/far-red light (Fr) stay relatively constant, which is the unique properties of sunlight. It may be a new way to optimise plant development in artificial lighting conditions. We assayed the potential effects of white light (W), 50% R 50% B (RB), and the unique properties of sunlight (N, R/Fr=1.4, R/Fr=1.1) under 500μmol m-2 s-1 on soybean (Glycine max ) plant growth. Our results showed that total leaf dry weight under N rapidly increased compared with the W and RB treatments from 30days to 60days. Soybean plants under N treatment had higher Rubisco activity and chlorophyll content than the W treatment at 50days. Stem and petiole dry weight under N treatment grew by 454.3% from 30 days to 60days. Compared with W and RB treatments, lignin content in the stems was also 26.9% and 34.5% higher at 50days under N treatment, respectively. N treatment caused 22.9% and 26.2% higher cellulose content than the W and RB treatments at 50days, respectively. N treatment led to 10.5% higher 13 C assimilation than the RB treatment in stems. The spectral combination of sunlight enhanced soybean plant growth and stem strength in artificial light environment.

Excessive use of nitrogen (N) in crops, such as potatoes, can lead to economic and environmental repercussions. We hypothesized that potato genotypes with resilient root systems and high genetic capabilities for nitrogen-use efficiency (NUE) could effectively mitigate these challenges. Consequently, we investigated intraspecific variations and characteristics within six distinct potato genotypes exhibiting diverse NUEs in response to varying nitrogen levels in an aeroponic system. The morpho-physiological and biochemical properties showed significant genotypic variations, especially related to the N-assimilating enzyme levels and root characteristics. Notably, the root systems of all genotypes demonstrated greater responsiveness to low nitrogen levels, with genotype C17 showcasing the most substantial root system irrespective of nitrogen concentration. Root morphological traits displayed robust positive correlations with NUtE, primarily influenced by genotype rather than nitrogen concentration. Conversely, nitrogen levels, displaying positive correlations with NUpE, influenced growth and activities of N-assimilating enzymes. Based on their distinct root systems, metabolic activities, and NUE profiles, genotypes C17 and C11 were determined to be N-efficient and N-inefficient, respectively. This study provides novel insights into the physiological and biochemical mechanisms underlying nitrogen use efficiency in potato genotypes under aeroponic conditions, offering potential targets for breeding programs, optimizing fertilizer management and cultivation strategies to improve crop performance under nitrogen-deficient conditions. Future investigations, employing multi-omics approaches, will elucidate key genes and pathways in nitrogen metabolism, potentially offering avenues to enhance root architecture and improve NUE.

The transcription factor TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP) is a tiny family that is exclusive to plants, which is crucial for both abiotic stress and plant growth and development. Many different types of plants have been found to contain TCP transcription factors. Carya illinoensis is an important economic forest species, but the function of TCP transcription factors in pecan has not been reported so far. Based on the highly conserved TCP (PF03634) domain, we identified 35 TCP genes (CiTCPs) in pecan and divided them into three subfamilies. Analysis of conserved motifs and gene structure of the CiTCP gene family indicated that the gene family was highly conserved. Through bioinformatics and qRT-PCR analysis, we have identified a gene that may be related to salt stress, CiTCP8, which has typical transcription factor characteristics. Phenotypic analysis of CiTCP8 transgenic Arabidopsis indicates that CiTCP8 can enhance salt tolerance in plant. Overexpression of CiTCP8 in Arabidopsis enhance plant tolerance to salt stress, as determined through some physiological and biochemical indicators. In addition, the expressions of stress-related genes were also activated in CiTCP8 transgenic Arabidopsis.

Although thousands of genes have been identified or cloned in rice (Oryza sativa) in the last two decades, the majority of them have only been separately characterized in specific varieties or single-gene modified backgrounds, thus limiting their practical application. We developed an optimized multiplex genome editing (MGE) toolbox that can efficiently assemble and stably express up to twelve sgRNA targets in a single plant expression vector. In this study, we established the MGE-based Rapid Directional Improvement (MRDI) strategy for directional improvement of complex agronomic traits in one small-scale rice transformation. This approach provides a rapid and practical procedure, encompassing sgRNA assembly, transgene-free screening and the creation of promising germplasm, by combining the precision of gene editing with phenotype-based field breeding. The MRDI strategy was used to generate the full diversity of twelve main agronomic genes in rice cultivar FXZ for the directional improvement of its growth duration and plant architecture. After applying the MRDI to FXZ, ideal plants with the desired traits of early heading date reduced plant height, and more effective panicles were generated without compromising yield, blast resistance and grain quality. Furthermore, the results of whole-genome sequencing (WGS), including the analysis of structural variations (SVs) and single nucleotide variations (SNVs) in the MGE plants, confirmed the high specificity and low frequency of unwanted mutations associated with this strategy. The MRDI breeding strategy would be a robust approach for exploring and applying crucial agronomic genes, as well as for generating novel elite germplasm in the future.

The plant AT-rich sequence and zinc-binding proteins (PLATZ) are a new class of zinc-dependent DNA-binding proteins that play important roles in plant growth and development. But it has not been systematically identified in flax (Linum usitatissimum L.), as an important seed crop with high nutritional value. In this study, 28 LuPLATZ proteins were identified from flax and divided into six phylogenetic groups. Fragment duplication was an important driving factor in the evolution of LuPLATZ genes. The RNA-seq results showed that the LuPLATZ genes had different expression patterns. Quantitative analysis of 16 LuPLATZ genes was performed, and the qRT-PCR results were consistent with the RNA-seq results. The expression of LuPLATZ6, LuPLATZ23, and LuPLATZ27 increased significantly during seed development. The observed change in the expression pattern suggests that these three genes could have significant regulatory functions during seed formation. These three LuPLATZ proteins were localized to the nucleus, suggesting that they could be conventional transcription factors. LuPLATZ23 and LuPLATZ27 were co-expressed with LuNAC1 and LuNAC75, suggesting an interactive relationship. This study aims to offer a theoretical foundation for high-yielding molecular breeding of flax.

Polyaspartic Acid-Calcium (PASP-Ca) is a versatile and eco-friendly amino acid complex, primarily recognized for bolstering nitrogen use efficiency and crop productivity. However, the core significance of this complex remains enigmatic in potato crop. We hypothesized that simultaneous application of PASP-Ca with potato genotypes characterized by substantial root systems and high genetic potentials for nitrogen-use efficiency (NUE) would best address this knowledge gap. The synergistic effect of various PASP-Ca treatments on morph physiological, N-related, and enzymatic parameters coupled with their transcript levels (shoot and root) in four potato genotypes having contrasting NUEs under low and high N supplies in aeroponics. PASP-Ca markedly boosted plant growth, yield components, and photosynthetic efficiency, with pronounced effects observed in nitrogen-efficient genotypes, especially Qingshu-9, emphasizing the importance of genotype selection in optimizing nitrogen utilization. Moreover, PASP-Ca treatments, particularly LN-P100 significantly enhances root system architecture (RSA), contributing to expanded root dimensions and improved nutrient acquisition capacity, especially under nitrogen-deficient conditions. Carbohydrate metabolism in potato tubers benefits from PASP-Ca treatment, leading to increased starch content, thereby impacting tuber quality. Among the N-assimilating enzymes, a large genotypic variation was observed for glutamine synthetase (GS), which may be considered a potential trait for improving NUE. Molecular analysis further elucidated the underlying mechanisms, demonstrating the upregulation of essential genes involved in nitrogen metabolism. The potential efficacy of PASP-Ca synergist as a novel accelerant for enhancing potato crop growth, biomass production, and nitrogen utilization efficiency, all coalescing seamlessly with the ethos of sustainable agricultural practices.