Agrobacterium tumefaciens mediated plant transformation is a versatile tool for plant genetic engineering following its discovery nearly half a century ago. Numerous modifications were made in its application to increase efficiency, especially in the recalcitrant major cereals plants. Recent breakthroughs in transformation efficiency continue its role as a mainstream technique in CRISPR/Cas-based genome editing and gene stacking. These modifications led to higher transformation frequency and lower but more stable transgene copies with the capability to revolutionize modern agriculture. In this review, we provide a brief overview of the history of Agrobacterium-mediated plant transformation and focus on the most recent progress to improve the system in both the Agrobacterium and the host recipient. A promising future for transformation in biotechnology and agriculture is predicted.

Drought poses a significant challenge, restricting the productivity of medicinal and aromatic plants. The strain induced by drought can impede vital processes like respiration and photosynthesis, affecting various aspects of plants’ growth and metabolism. In response to this adversity, medicinal plants employ mechanisms such as morphological and structural adjustments, modulation of drought-resistant genes, and augmented synthesis of secondary metabolites and osmotic regulatory substances to alleviate the stress. Extreme water scarcity can lead to leaf wilting and may ultimately result in plant death. The cultivation and management of medicinal plants under stress conditions often differ from those of other crops. This is because the main goal with medicinal plants is not only to increase the yield of the above-ground parts but also to enhance the production of active ingredients such as essential oils. To elucidate these mechanisms of drought resistance in medicinal and aromatic plants, the current review provides a summary of recent literature encompassing studies on the morphology, physiology, and biochemistry of medicinal and aromatic plants under drought conditions.

In crop plants, various environmental stresses affect the balance of carbon, nitrogen, and phosphorus (C:N:P), leading to biochemical and physiological alterations and reductions in yield. Silicon (Si) is a beneficial element that alleviates plant stress. Most studies involving silicon have focused on physiological responses, such as improvements in photosynthetic processes, water use efficiency, and antioxidant defense systems. But recent research suggests that stressed plants facing either limited or excessive resources (water, light, nutrients, and toxic elements), strategically employ Si to maintain C:N:P homeostasis, thereby minimizing biomass losses. Understanding the role of Si in mitigating the impact of abiotic stresses on plants by regulating C:N:P homeostasis holds great potential for advancing sustainable agricultural practices in crop production. This review presents recent advances in characterizing the influence of environmental stresses on C:N:P homeostasis, as well as the role of Si in preserving C:N:P equilibrium and attenuating biological damage associated with abiotic stress. It underscores the beneficial effects of Si in sustaining C:N:P homeostasis and increasing yield via improved nutritional efficiency and stress mitigation.

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

Subclass III sucrose nonfermenting1-related protein kinase 2s (SnRK2s) function in ABA and abiotic stress responses by unknown mechanisms. We found that osmotic stress/ABA-activated protein kinase 10 (SAPK10), a member of rice SnRK2s, physically interacted with CBL-interacting protein kinase 1 (OsCIPK1). OsCIPK1 expression was up-regulated by ABA and PEG treatment, and overexpression increased the ABA sensitivity of seed germination and root growth and plant osmotic stress tolerance. Osmotic stress or ABA-induced activation of OsCIPK1 is dependent on SAPK10. SAPK10 phosphorylates Thr-24 of OsCIPK1 in vitro, and this phosphorylation increases the activity of OsCIPK1 and positively regulates the function of OsCIPK1 in ABA responses and plant osmotic stress tolerance. This study suggests that OsCIPK1 is a direct phosphorylated substrate of SAPK10, and SAPK10-mediated phosphorylation of OsCIPK1 functions in ABA signaling and increases rice osmotic stress tolerance.

Low temperature causes rice yield losses of up to 30%-40%, therefore increasing its cold tolerance is a breeding target. Few genes in rice are reported to confer cold tolerance at both the vegetative and reproductive stages. This study revealed a rice-specific 24-nt miRNA, miR1868, whose accumulation was suppressed by cold stress. Knockdown of MIR1868 increased seedling survival, pollen fertility, seed setting, and grain yield under cold stress, whereas its overexpression conferred the opposite phenotype. Knockdown of MIR1868 increased reactive oxygen species (ROS) scavenging and soluble sugar content under cold stress by increasing the expression of peroxidase genes and sugar metabolism genes, and its overexpression produced the opposite effect. Thus, MIR1868 negatively regulated rice cold tolerance via ROS scavenging and sugar accumulation.

SNF1-related protein kinase 2 (SnRK2) family members are essential components of the plant abscisic acid (ABA) signaling pathway initiated by osmotic stress and triggering a drought stress response. This study characterized the molecular properties of TaSnRK2.4 and its function in mediating adaptation to drought in Triticum aestivum. Transcripts of TaSnRK2.4 were upregulated upon drought and ABA signaling and associated with drought- and ABA-responsive cis-elements ABRE and DRE, and MYB and MYC binding sites in the promoter as indicated by reporter GUS protein staining and activity driven by truncations of the promoter. Yeast two-hybrid, BiFC, and Co-IP assays indicated that TaSnRK2.4 protein interacts with TaPP2C01 and an ABF transcription factor (TF) TaABF2. The results suggested that TaSnRK2.4 forms a functional TaPP2C01-TaSnRK2.4-TaABF2 module with its upstream and downstream partners. Transgene analysis revealed that TaSnRK2.4 and TaABF2 positively regulate drought tolerance whereas TaPP2C01 acts negatively by modulating stomatal movement, osmotic adjustment, reactive oxygen species (ROS) homeostasis, and root morphology. Expression analysis, yeast one-hybrid, and transcriptional activation assays indicated that several osmotic stress-responsive genes, including TaSLAC1-4, TaP5CS3, TaSOD5, TaCAT1, and TaPIN4, are regulated by TaABF2. Transgene analysis verified their functions in positively regulating stomatal movement (TaSLAC1-4), proline accumulation (TaP5CS3), SOD activity (TaSOD5), CAT activity (TaCAT1), and root morphology (TaPIN4). There were high correlations between plant biomass and yield with module transcripts in a wheat variety panel cultivated under drought conditions in the field. Our findings provide insights into understanding plant drought response underlying the SnRK2 signaling pathway in common wheat.

Triosephosphate isomerase (TPI) is an enzyme that functions in plant energy production, accumulation, and conversion. To understand its function in maize, we characterized a maize TPI mutant, zmtpi4. In comparison to the wild type, zmtpi4 mutants showed altered ear development, reduced kernel weight and starch content, modified starch granule morphology, and altered amylose and amylopectin content. Protein, ATP, and pyruvate contents were reduced, indicating ZmTPI4 was involved in glycolysis. Although subcellular localization confirmed ZmTPI4 as a cytosolic rather than a plastid isoform of TPI, the zmtpi4 mutant showed reduced leaf size and chlorophyll content. Overexpression of ZmTPI4 in Arabidopsis led to enlarged leaves and increased seed weight, suggesting a positive regulatory role of ZmTPI4 in kernel weight and starch content. We conclude that ZmTPI4 functions in maize kernel development, starch synthesis, glycolysis, and photosynthesis.

Mitochondrial calcium uniporter (MCU) is a conserved calcium ion (Ca²⁺) transporter in the mitochondrial inner membrane of eukaryotic cells. How MCU proteins regulate Ca²⁺ flow and modulate plant cell development remain largely unclear. Here, we identified the gene GhMCU4 encoding a MCU protein that negatively regulates plant development and fiber elongation in cotton (Gossypium hirsutum). GhMCU4 expressed constitutively in various tissues with the higher transcripts in elongating fiber cells. Knockdown of GhMCU4 in cotton significantly elevated the plant height and root length. The calcium signaling pathway was significantly activated and calcium sensor genes, including Ca²⁺ dependent modulator of interactor of constitutively active ROP (GhCMI1), calmodulin like protein (GhCML46), calcium-dependent protein kinases (GhCPKs), calcineurin B-like protein (GhCBLs), and CBL-interacting protein kinases (GhCIPKs), were dramatically upregulated in GhMCU4-silenced plants. Metabolic processes were preferentially enriched, and genes related to regulation of transcription were upregulated in GhMCU4-silenced plants. The contents of Ca²⁺ and H₂O₂ were significantly increased in roots and leaves of GhMCU4-silenced plants. Fiber length and Ca²⁺ and H₂O₂ contents in fibers were significantly increased in GhMCU4-silenced plants. This study indicated that GhMCU4 plays a negative role in regulating cell elongation in cotton, thus expanding understanding in the role of MCU proteins in plant growth and development.

Knowledge of the function of growth-regulating factors (GRFs) in sugarcane (Saccharum officinarum and S. spontaneum) growth and development could assist breeders in selecting desirable plant architectures. However, limited information about GRFs is available in Saccharum due to their polyploidy. In this study, 22 GRFs were identified in the two species and their conserved domains, gene structures, chromosome location, and synteny were characterized. GRF7 expression varied among tissues and responded to diurnal rhythm. SsGRF7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional cofactor. SsGRF7 positively regulated the size and length of rice leaves, possibly by regulating cell size and plant hormones. Of seven potential transcription factors binding to the SsGRF7 promoter in S. spontaneum, four showed positive expression patterns, and two showed negative expression patterns relative to SsGRF7.

Plant height influences plant architecture, lodging resistance, and yield performance. It is modulated by gibberellic acid (GA) metabolism and signaling. DELLA proteins, acting as central repressors of GA signaling, integrate various environmental and hormonal signals to regulate plant growth and development in Arabidopsis. We examined the role of two DELLA proteins, GmRGAa and GmRGAb, in soybean plant height control. Knockout of these proteins led to longer internodes and increased plant height, primarily by increasing cell elongation. GmRGAs functioned under different light conditions, including red, blue, and far-red light, to repress plant height. Interaction studies revealed that GmRGAs interacted with the blue light receptor GmCRY1b. Consistent with this, GmCRY1b partially regulated plant height via GmRGAs. Additionally, DELLA proteins were found to stabilize the protein GmSTF1/2, a key positive regulator of photomorphogenesis. This stabilization led to increased transcription of GmGA2ox-7b and subsequent reduction in plant height. This study enhances our understanding of DELLA-mediated plant height control, offering Gmrgaab mutants for soybean structure and yield optimization.

Anthocyanins play crucial roles in pollen protection and pollinator attraction in flowering plants. However, the mechanisms underlying flower color determination and whether floral anthocyanin regulators participate in other processes remain largely unresolved in soybeans (Glycine max). In this study, we investigated the genetic components and mechanisms governing anthocyanin biosynthesis in soybean flowers. Molecular and genetic studies have characterized two antagonistic regulators, the positive activator GmMYBA3 and the negative repressor GmMYBR1, that modulate the gene expression of anthocyanin biosynthesis in soybean flowers. Further findings revealed a regulatory interplay between GmMYBA3 and GmMYBR1 bridged by GmTT8a, highlighting the complexity of anthocyanin regulation in different soybean organs. Exploration of additional soybean cultivars demonstrated the universality of GmMYBA3 and GmMYBR1 in regulating floral anthocyanin biosynthesis- related genes, with GmF3′5′H identified as a crucial determinant of white flower color. This study provides a molecular mechanism underlying soybean flower color determination, paving the way for the molecular modification of soybean flowers to probably enhance their resistance to abiotic stresses and attractiveness to pollinators.

Transcription factors regulating crop uptake and translocation of the micronutrient Cu have not been identified. We isolated a novel R2R3-MYB transcription factor, OsMYB84, and showed that it was a positive regulator involved in uptake and transport of Cu via activation of OsCOPT2 and OsHMA expression. OsMYB84 was highly expressed in roots and anthers and induced by Cu. Overexpression of OsMYB84 promoted uptake and root-to-shoot translocation of Cu in rice, facilitated Cu distribution into grain and increased grain yield. In contrast, mutation of OsMYB84 reduced Cu concentration in xylem sap. OsMYB84 bound to the promoter region of OsCOPT2 and OsHMA5 and upregulated their expression. OsCOPT2 mutants showed reduced uptake of Cu and OsHMA5 overexpression lines showed increased root-to-shoot translocation of Cu.

Diverse bacterial and fungal pathogens attack plants, causing biotic stress and severe yield losses globally. These losses are expected to become more serious as climate change improves conditions for many pathogens. Therefore, identifying genes conferring broad-spectrum disease resistance and elucidating their underlying mechanisms provides important resources for plant breeding. WRKY transcription factors affect plant growth and stress responses. However, the functions of many WRKY proteins remain to be elucidated. Here, we demonstrated the role of rice (Oryza sativa) WRKY group III transcription factor OsWRKY65 in immunity. OsWRKY65 localized to the nucleus and acted as transcriptional repressor. Genetic and molecular functional analyses showed that OsWRKY65 increases resistance to the fungal pathogen Fusarium fujikuroi through downregulation of GA signaling and upregulation of JA signaling. Moreover, OsWRKY65 modulated the expression of the key genes that confer susceptibility or resistance to Xanthomonas oryzae pv. oryzae to enhance immunity against the pathogen. In particular, OsWRKY65 directly bound to the promoter region of OsSWEET13 and repressed its expression. Taken together, our findings demonstrate that the OsWRKY65 enhances resistance to fungal and bacterial pathogens in rice.

Avirulence effectors (Avrs), encoded by plant pathogens, can be recognized by plants harboring the corresponding resistance proteins, thereby initiating effector-triggered immunity (ETI). In susceptible plants, however, Avrs can function as effectors, facilitating infection via effector-triggered susceptibility (ETS). Mechanisms of Avr-mediated ETS remain largely unexplored. Here we report that the Magnaporthe oryzae effector Avr-PikD enters rice cells via the canonical cytoplasmic secretion pathway and suppresses rice basal defense. Avr-PikD interacts with an LSD1-like transcriptional activator AKIP30 of rice, and AKIP30 is also a positive regulator of rice immunity, whereas Avr-PikD impedes its nuclear localization and suppresses its transcriptional activity. In summary, M. oryzae delivers Avr-PikD into rice cells to facilitate ETS by inhibiting AKIP30-mediated transcriptional regulation of immune response against M. oryzae.

The necrotrophic fungus, Sclerotinia sclerotiorum, employs an array of cell wall-degrading enzymes (CWDEs), including cellulase, to dismantle host cell walls. However, the molecular mechanisms through which S. sclerotiorum degrades cellulose remain elusive. Here, we unveil a novel secretory cellobiohydrolase, SsdchA, characterized by a signal peptide and a Glyco_hydro_7 (GH7) domain. SsdchA exhibits a robust expression of during early infection stages. Interestingly, colony morphology and growth rates remain unaffected across the wild-type, SsdchA deletion strains and SsdchA overexpression strains on potato dextrose agar (PDA) medium. Nevertheless, the pathogenicity and cellobiohydrolase activity decreased in the SsdchA deletion strains, but enhanced in the SsdchA overexpression strains. Moreover, the heterologous expression of SsdchA in Arabidopsis thaliana leads to reduced cellulose content and heightened susceptibility to S. sclerotiorum. Collectively, our data underscore the pivotal role of the novel cellobiohydrolase SsdchA in the pathogenicity of S. sclerotiorum.

Verticillium longisporum (Vl43) is a soilborne hemibiotrophic fungal pathogen causing stem striping on oilseed rape (OSR) and severe yield losses. Breeding for resistant varieties is the most promising approach to control this disease. Here, we report the identification of Hva22c as a novel susceptibility factor and its potential for improving OSR resistance. Hva22c is a member of the Hva22 gene family, originally described for barley (Hordeum vulgare). Several Hva22 members have been located at the endoplasmic reticulum. Hva22c is up-regulated in response to Vl43 in both Arabidopsis and OSR. We demonstrate that knock-out of Hva22c in OSR by CRISPR/Cas9 and its homolog in Arabidopsis by T-DNA insertion reduced plants’ susceptibility to Vl43 infection and impaired the development of disease symptoms. To understand the underlying mechanism, we analysed transcriptomic data from infected and non-infected roots of hva22c knock-out and wild type plants. We identified a homozygous mutant with frame-shifts in all four BnHva22c loci displaying a vastly altered transcriptional landscape at 6 dpi. Significantly, a large set of genes was suppressed under mock conditions including genes related to the endomembrane systems. Among the up-regulated genes we found several defense-related and phytohormone-responsive genes when comparing mutant to the wild type. These results demonstrate that Hva22c is functionally required for a fully compatible plant-fungus interaction. Its loss of function reduces plant susceptibility, most likely due to endoplasmatic reticulum and Golgi dysfunction accompanied by additionally activated defense responses. These findings can help improve OSR resistance to V. longisporum infection.

“Synthetic” allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement. Such synthetic allopolyploids often undergo rapid genomic structural variation (SV). However, how such SV arises, is inherited and fixed, and how it affects important traits, has rarely been comprehensively and quantitively studied in advanced generation synthetic lines. A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs. Here, we analyzed three genetic mapping populations (735 DH lines) derived from crosses between advanced synthetic and conventional Brassica napus (rapeseed) lines, using whole-genome sequencing to determine genome composition. We observed high tolerance of large structural variants, particularly toward the telomeres, and preferential selection for balanced homoeologous exchanges (duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs), including stable events involving whole chromosomes (“pseudoeuploidy”). Given the experimental design (all three populations shared a common parent), we were able to observe that parental SV was regularly inherited, showed genetic hitchhiking effects on segregation, and was one of the major factors inducing adjacent novel and larger SV. Surprisingly, novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines. However, incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits. Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs, and support the use of synthetic parents as an important source of novel trait variation.

As an essential crop that provides vegetable oil and protein, soybean (Glycine max (L.) Merr.) is widely planted all over the world. However, the scarcity of water resources worldwide has seriously impacted on the quality and yield of soybean. To address this, exploring excellent genes for improving drought resistance in soybean is crucial. In this study, we identified natural variations of GmFNSII-2 (flavone synthase II) significantly affect the drought resistance of soybeans. Through sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were identified. The full-length allele GmFNSII-2^C, but not the truncated allele GmFNSII-2^A possessing a nonsense nucleotide variation, increased enzyme activity. Further research found that GmDREB3, known to increase soybean drought resistance, bound to the promoter region of GmFNSII-2^C. GmDREB3 positively regulated the expression of GmFNSII-2^C, increased flavone synthase abundance and improved the drought resistance. Furthermore, a single-base mutation in the GmFNSII-2^C promoter generated an additional drought response element (CCCCT), which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought conditions. The frequency of drought-resistant soybean varieties with Hap 1 (Pro:GmFNSII-2^C) has increased, suggesting that this haplotype may be selected during soybean breeding. In summary, GmFNSII-2^C could be used for molecular breeding of drought-tolerant soybean.

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), is one of the destructive wheat diseases worldwide. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW), a tetraploid progenitor of common wheat, is a valuable genetic resource for wheat disease resistance breeding programs. We developed three hexaploid pre-breeding lines with PM resistance genes derived from three WEW accessions. These resistant pre-breeding lines were crossed with susceptible common wheat accessions. Segregations in the F₂ populations were 3 resistant : 1 susceptible, suggesting a single dominant allele in each resistant parent. Mapping of the resistance gene in each line indicated a single locus on the long arm of chromosome 7A, at the approximate location of previously cloned Pm60 from T. urartu. Sanger sequencing revealed three different Pm60 haplotypes (Hap 3, Hap 5, and Hap 6). Co-segregating diagnostic markers were developed for identification and selection of each haplotype. The resistance function of each haplotype was verified by the virus-induced gene silencing (VIGS). Common wheat lines carrying each of these Pm60 haplotypes were resistant to most Bgt isolates and differences in the response arrays suggested allelic variation in response.

Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F₂ populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F₃ populations offering notable advantages over F₂ populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F₃ population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F₃ populations and multi-environment experiments can achieve high power, resolution, and reliability.

Maize stalk rot reduces grain yield and quality. Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait. Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection. We performed a genome-wide association study (GWAS) and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpeño and non-Tuxpeño heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms (SNPs). Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses. More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines. Incorporating genotype-by-environment (G × E) interaction increased genomic prediction accuracy.

The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement. Currently available genome-editing tools have a limited number of targets, restricting their application in genetic research. In this study, we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors, eight donor vectors, four destination vectors, and one primer-design software package. By combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombination to assemble large fragments and by changing the structure of the amplicons used to assemble sgRNA expression cassettes, the plant ultra-multiplex genome editing system can assemble a single binary vector targeting more than 40 genomic loci. A rice knockout vector containing 49 sgRNA expression cassettes was assembled and a high co-editing efficiency was observed. This plant ultra-multiplex genome editing system advances synthetic biology and plant genetic engineering.

To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination, it is desirable to identify the optimal marker combinations. We describe a marker combination screening model based on the genetic algorithm (GA) and implemented in a software tool, LociScan. Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions. Among GA parameters, an increase in population size and generation number enlarged optimization depth but also calculation workload. Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time. In comparison with two other software tools, LociScan accommodated missing data, reduced calculation time, and offered more fitness functions. In large datasets, the sample size of training data exerted the strongest influence on calculation time, whereas the marker size of training data showed no effect, and target marker number had limited effect on analysis speed.

A two-year field experiment was conducted to measure the effects of densification methods on photosynthesis and yield of densely planted wheat. Inter-plant and inter-row distances were used to define rate-fixed pattern (RR) and row-fixed pattern (RS) density treatments. Meanwhile, four nitrogen (N) rates (0, 144, 192, and 240 kg N ha⁻¹, termed N0, N144, N192, and N240) were applied with three densities (225, 292.5, and 360 × 10⁴ plants ha⁻¹, termed D225, D292.5, and D360). The wheat canopy was clipped into three equal vertical layers (top, middle, and bottom layers), and their chlorophyll density (ChD) and photosynthetically active radiation interception (FIPAR) were measured. Results showed that the response of ChD and FIPAR to N rate, density, and pattern varied with different layers. N rate, density, and pattern had significant interaction effects on ChD. The maximum values of whole-canopy ChD in the two seasons appeared in N240 combined with D292.5 and D360 under RR, respectively. Across two growing seasons, FIPAR values of RR were higher than those of RS by 29.37% for the top layer and 5.68% for the middle layer, while lower than those of RS by 20.62% for the bottom layer on average. With a low N supply (N0), grain yield was not significantly affected by density for both patterns. At N240, increasing density significantly increased yield under RR, but D360 of RS significantly decreased yield by 3.72% and 9.00% versus D225 in two seasons, respectively. With an appropriate and sufficient N application, RR increased the yield of densely planted wheat more than RS. Additionally, the maximum yield in two seasons appeared in the combination of D360 with N144 or N192 rather than of D225 with N240 under both patterns, suggesting that dense planting combined with an appropriate N-reduction application is feasible to increase photosynthesis capacity and yield.

Regulating planting density and nitrogen (N) fertilization could delay chlorophyll (Chl) degradation and leaf senescence in maize cultivars. This study measured changes in ear leaf green area (GLA_ear), Chl content, the activities of Chl a-degrading enzymes after silking, and the post-silking dry matter accumulation and grain yield under multiple planting densities and N fertilization rates. The dynamic change of GLA_ear after silking fitted to the logistic model, and the GLA_ear duration and the GLA_ear at 42 d after silking were affected mainly by the duration of the initial senescence period (T₁) which was a key factor of the leaf senescence. The average chlorophyllase (CLH) activity was 8.3 times higher than pheophytinase activity and contributed most to the Chl content, indicating that CLH is a key enzyme for degrading Chl a in maize. Increasing density increased the CLH activity and decreased the Chl content, T₁, GLA_ear, and GLA_ear duration. Under high density, appropriate N application reduced CLH activity, increased Chl content, prolonged T₁, alleviated high-density-induced leaf senescence, and increased post-silking dry matter accumulation and grain yield.

Upland crop-rice cropping systems (UCR) facilitate sustainable agricultural intensification. Accurate UCR cultivation mapping is needed to ensure food security, sustainable water management, and rural revitalization. However, datasets describing cropping systems are limited in spatial coverage and crop types. Mapping UCR is more challenging than crop identification and most existing approaches rely heavily on accurate phenology calendars and representative training samples, which limits its applications over large regions. We describe a novel algorithm (RRSS) for automatic mapping of upland crop-rice cropping systems using Sentinel-1 Synthetic Aperture Radar (SAR) and Sentinel-2 Multispectral Instrument (MSI) data. One indicator, the VV backscatter range, was proposed to discriminate UCR and another two indicators were designed by coupling greenness and pigment indices to further discriminate tobacco or oilseed UCR. The RRSS algorithm was applied to South China characterized by complex smallholder rice cropping systems and diverse topographic conditions. This study developed 10-m UCR maps of a major rice bowl in South China, the Xiang-Gan-Min (XGM) region. The performance of the RRSS algorithm was validated based on 5197 ground-truth reference sites, with an overall accuracy of 91.92%. There were 7348 km² areas of UCR, roughly one-half of them located in plains. The UCR was represented mainly by oilseed-UCR and tobacco-UCR, which contributed respectively 69% and 15% of UCR area. UCR patterns accounted for only one-tenth of rice production, which can be tripled by intensification from single rice cropping. Application to complex and fragmented subtropical regions suggested the spatiotemporal robustness of the RRSS algorithm, which could be further applied to generate 10-m UCR datasets for application at national or global scales.

The grass spikelet is a unique inflorescence structure that determines grain size. Although many genetic factors have been well characterized for grain size and glume development, the underlying molecular mechanisms in rice are far from established. Here, we isolated rice gene, AGL1 that controlled grain size and determines the fate of the sterile lemma. Loss of function of AGL1 produced larger grains and reduced the size of the sterile lemma. Larger grains in the agl1 mutant were caused by a larger number of cells that were longer and wider than in the wild type. The sterile lemma in the mutant spikelet was converted to a rudimentary glume-like organ. Our findings showed that the AGL1 (also named LAX1) protein positively regulated G1 expression, and negatively regulated NSG1 expression, thereby affecting the fate of the sterile lemma. Taken together, our results revealed that AGL1 played a key role in negative regulation of grain size by controlling cell proliferation and expansion, and supported the opinion that rudimentary glume and sterile lemma in rice are homologous organs.

Sorghum (Sorghum bicolor (L.) Moench) is a world cereal crop used in China for producing Baijiu, a distilled spirit. We report a telomere-to-telomere genome assembly of the Baijiu cultivar Hongyingzi, HYZ-T2T, using ultralong reads. The 10 chromosome pairs contained 33,462 genes, of which 93% were functionally annotated. The 20 telomeres and 10 centromeric regions on the HYZ-T2T chromosomes were predicted and two consecutive large inversions on chromosome 2 were characterized. A 65-gene reconstruction of the metabolic pathway of tannins, the flavor substances in Baijiu, was performed and may advance the breeding of sorghum cultivars for Baijiu production.