Rice (Oryza sativa) plant architecture and grain shape, which determine grain quality and yield, are modulated by auxin and brassinosteroid via regulation of cell elongation and proliferation. We review the signal transduction of these hormones and the crosstalk between their signals on the regulation of rice plant architecture and grain shape.

Auxin plays a crucial role in all aspects of plant growth and development. Auxin can induce the rapid and efficient expression of some genes, which are named auxin early response genes (AERGs), mainly including the three families: auxin/indole‐3‐acetic acid (Aux/IAA), Gretchen Hagen 3 (GH3), and small auxin-up RNA (SAUR). Aux/IAA encodes the Aux/IAA protein, which is a negative regulator of auxin response. Aux/IAA and auxin response factor (ARF) form a heterodimer and participate in a variety of physiological processes through classical or non-classical auxin signaling pathways. The GH3 encodes auxin amide synthetase, which catalyzes the binding of auxin to acyl-containing small molecule substrates (such as amino acids and jasmonic acid), and regulates plant growth and stresses by regulating auxin homeostasis. SAURs is a class of small auxin up-regulated RNAs. SAUR response to auxin is complex, and the process may occur at the transcriptional, post-transcriptional and protein levels. With the development of multi-omics, significant progress has been made in the study of Aux/IAA, GH3, and SAUR genes, but there are still many unknowns. This review offers insight into the characteristics of Aux/IAA, GH3, and SAUR gene families, and their roles in roots, hypocotyls, leaves, leaf inclinations, flowers, seed development, stress response, and phytohormone crosstalk, and provides clues for future research on phytohormone signaling and the molecular design breeding of crops.

With rising living standards, there is an increasing demand for high-quality rice. Rice quality is mainly defined by milling quality, appearance quality, cooking and eating quality, and nutrition quality. Among them, chalkiness is a key trait for appearance quality, which adversely affects cooking and eating quality, head rice yield, and commercial value. Therefore, chalkiness is undesirable, and reducing chalkiness is a major goal in rice quality improvement. However, chalkiness is a complex trait jointly influenced by genetic and environmental factors, making its genetic study and precision improvement a huge challenge. With the rapid development of molecular techniques, much knowledge has been gained about the genes and molecular networks involved in chalkiness formation. The present review describes the major environmental factors affecting chalkiness and summarizes the quantitative trait loci (QTL) associated with chalkiness. More than 150 genes related to chalkiness formation have been reported. The functions of the genes regulating chalkiness, primarily those involved in starch synthesis, storage protein synthesis, transcription regulation, organelle development, grain shape regulation, and high-temperature response, are described. Finally, we identify the challenges associated with genetic improvement of chalkiness and suggest potential strategies. Thus, the review offers insight into the molecular dynamics of chalkiness and provides a strong basis for the future breeding of high-quality rice varieties.

Plant height, spike, leaf, stem and grain morphologies are key components of plant architecture and related to wheat yield. A wheat (Triticum aestivum L.) mutant, wpa1, displaying temperature-dependent pleiotropic developmental anomalies, was isolated. The WPA1 gene, encoding a von Willebrand factor type A (vWA) domain protein, was located on chromosome arm 7DS and isolated by map-based cloning. The functionality of WPA1 was validated by multiple independent EMS-induced mutants and gene editing. Phylogenetic analysis revealed that WPA1 is monocotyledon-specific in higher plants. The identification of WPA1 provides opportunity to study the temperature regulated wheat development and grain yield.

Seed germination is a complex trait regulated by multiple genes in rice. However, the regulators of rice seed germination have yet to be sufficiently determined. Here, a quantitative trait locus (QTL) for rice seed germination was identified in a genome-wide association study. The candidate gene JASMONATE ZIM-DOMAIN 5 (OsJAZ5) of the QTL was verified that positively regulates seed germination. OsJAZ5 regulation of seed germination involves an OsABI3-mediated abscisic acid pathway. Overexpression of OsJAZ5 facilitated seed germination. The application of OsJAZ5 might be useful for increasing seed germination for rice direct seeding.

The enzyme C-14 sterol reductase is involved in biosynthesis of brassinosteroids (BR) and sterols, as well as plant development. OsFK1, a member of the sterol biosynthesis pathway located in the endoplasmic reticulum (ER), encodes C-14 sterol reductase. However, there is little research on the function of C-14 sterol reductase in rice. Compared with the wild type, an osfk1 mutant showed dwarf phenotype and premature aging in the second leaf during the trefoil stage, and abnormal development of leaf veins during the tillering stage. The osfk1 mutant showed signs of aberrant PCD, as evidenced by TUNEL staining. This suggested that high ROS buildup caused DNA damage and ROS-mediated cell death in the mutant. The osfk1 mutant also showed decreased chlorophyll content and aberrant chloroplast structure. Sequencing of the osfk1 mutant allele revealed a non-synonymous G to A mutation in the final intron, leading to early termination. Here, we identified the OsFK1 allele, cloned it by Mutmap sequencing, and verified it by complementation. HPLC-MS/MS assays demonstrated that the osfk1 mutation caused lower phytosterol levels. These findings showed that the OsFK1 allele encoding C-14 sterol reductase is involved in phytosterol biosynthesis and mediates normal development of rice plants.

In four rice genomes, 85 ABC1-family genes were identified by comparative genomics, evolution, genetics, and physiology. One, OsABC1-13, was shown by knockdown and knockout experiments to affect plant height, grain size, and photosynthetic capability.

Temperature is an important environmental factor affecting heading date of rice. Despite its importance, genes responsible for temperature-sensitive heading in rice have remained elusive. Our previous study identified a quantitative trait locus qHd1 which advances heading date under high temperatures. A 9.5-kb insertion was found in the first intron of OsMADS51 in indica variety Zhenshan 97 (ZS97). However, the function of this natural variant in controlling temperature sensitivity has not been verified. In this study, we used CRISPR/Cas9 to knock out the 9.5-kb insertion in ZS97. Experiments conducted under cotrolled conditions in phytotrons confirmed that deletion increased temperature sensitivity and advanced heading by downregulating the expression level of OsMADS51. One-hybrid assays in yeast, ChIP-quantitative polymerase chain reaction, electrophoretic mobility shift, and luciferase-based transient transactivation assays collectively confirmed that OsMADS51 affects heading date by regulation of heading date gene Ehd1. We further determined that the long non-coding RNA HEATINR is generated from the first intron of OsMADS51, offering an explanation for how the 9.5-kb insertion affects temperature sensitivity. We also found that OsMADS51 was strongly selected in early/late-season rice varieties in South China, possibly accounting for their strong temperature sensitivity. These insights not only advance our understanding of the molecular mechanisms underlying the temperature-responsive regulation of heading date in rice but also provide a valuable genetic target for molecular breeding.

In acidic paddy fields of South China, rice (Oryza sativa L.) faces the dual challenges of cadmium (Cd) toxicity and silicon (Si) deficiency. Although previous studies have highlighted the functions of Si application timing and strategies in mitigating Cd-stressed rice, the precise mechanisms underlying the health restoration of Cd-toxic rice and the assurance of grain safety remain elusive. This study explored Cd translocation and detoxification in the shoots of rice regulated by various Si fertilization regimes: Si(T) (all Si added before transplanting), Si(J) (all Si added at jointing), and Si(TJ) (half Si added both before transplanting and at jointing). The findings revealed that the regime of Si(TJ) was more beneficial to rice health and grain safety than Si(T) and Si(J). The osmotic regulators such as proline, soluble sugars, and soluble proteins were significantly boosted by Si(TJ) compared to other Si treatments, and which enhanced membrane integrity, balanced intracellular pH, and increased Cd tolerance of rice. Furthermore, Si(TJ) was more effective than Si(T) and Si(J) on the Cd sequestration in the cell wall, Cd bio-passivation, and the down-regulated expression of the Cd transport genes. The concentrations of Cd in the xylem and phloem treated with Si(TJ) were reduced significantly. Additionally, Si(TJ) facilitated much more Cd bound with the outer layer proteins of grains, and promoted Cd chelation and complexation by phytic acid, phenolics, and flavonoids. Overall, Si (TJ) outperformed Si(T) and Si(J) in harmonizing the phycological processes, inhibiting Cd translocation, and enhancing Cd detoxification in rice plant. Thereby the split Si application strategy offers potential for reducing Cd toxicity in rice grain.

Salicylic acid (SA), a vital endogenous hormone, plays a crucial role in plant growth and the response to abiotic and biotic stress. Isochorismate synthase (ICS) and phenylalanine ammonia lyase (PAL) are critical rate-limiting enzymes for SA synthesis. Fusarium head blight (FHB) seriously threatens the safety of wheat production, but increasing the content of SA can enhance FHB resistance. However, the pathway of SA synthesis and regulation in wheat remains unknown. In this study, three wheat ICS (TaICSA, TaICSB, and TaICSD) were identified, and their functions were validated in vitro for isomerizing chorismate to isochorismate. The mutation of one or two homoeoalleles of TaICSA, TaICSB, and TaICSD in the wheat variety ‘Cadenza’ reduced SA levels under ultraviolet treatment and Fusarium graminearum infection, further enhancing sensitivity to FHB. Overexpression of TaICSA can significantly enhance SA levels and resistance to FHB. To further study SA synthesis pathways in wheat and avoid interference with pathogenicity related genes, the leaves of wild-type Cadenza and different TaICS mutant lines were subjected to ultraviolet treatment for transcriptomic analysis. The results showed that 37 PALs might be involved in endogenous SA synthesis, and 82 WRKY and MYB family transcription factors may regulate the expression of ICS and PAL. These results were further confirmed by RT-PCR. In conclusion, this study expands our knowledge of SA biosynthesis and identifies TaICSA, as well as several additional candidate genes that encode transcription factors for regulating endogenous SA levels, as part of an efficient strategy for enhancing FHB resistance in wheat.

Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors. Haploids/doubled haploids (DHs) derived from in vitro-cultured microspores are widely used in plant breeding and genetic engineering. However, the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly defined. Here, RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis (ME) in barley cultivars Golden Promise and Igri, which exhibit contrasting responsiveness to microspore-derived plant formation. Our experiments revealed fundamental regulatory networks, specific groups of genes, and transcription factor (TF) families potentially regulating the developmental switch. We identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to ME. Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition.

Grain water content (GWC) is a key determinant for mechanical harvesting of maize (Zea mays). In our previous research, we identified a quantitative trait locus, qGWC1, associated with GWC in maize. Here, we examined near-isogenic lines (NILs) NIL^L and NIL^H that differed at the qGWC1 locus. Lower GWC in NIL^L was primarily attributed to reduced grain water weight (GWW) and smaller fresh grain size, rather than the accumulation of dry matter. The difference in GWC between the NILs became more pronounced approximately 35 d after pollination (DAP), arising from a faster dehydration rate in NIL^L. Through an integrated analysis of the transcriptome, proteome, and metabolome, coupled with an examination of hormones and their derivatives, we detected a marked decrease in JA, along with an increase in cytokinin, storage forms of IAA (IAA-Glu, IAA-ASP), and IAA precursor IPA in immature NIL^L kernels. During kernel development, genes associated with sucrose synthases, starch biosynthesis, and zein production in NIL^L, exhibited an initial up-regulation followed by a gradual down-regulation, compared to those in NIL^H. This discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

Soybean mosaic virus (SMV), an RNA virus, is the most common and destructive pathogenic virus in soybean fields. The newly developed CRISPR/Cas immune system has provided a novel strategy for improving plant resistance to viruses; hence, this study aimed to engineer SMV resistance in soybean using this system. Specifically, multiple sgRNAs were designed to target positive- and/or negative-sense strands of the SMV HC-Pro gene. Subsequently, the corresponding CRISPR/CasRx vectors were constructed and transformed into soybeans. After inoculation with SMV, 39.02%, 35.77%, and 18.70% of T₁ plants were confirmed to be highly resistant (HR), resistant (R), and mildly resistant (MR) to SMV, respectively, whereas only 6.50% were identified as susceptible (S). Additionally, qRT-PCR and DAS-ELISA showed that, both at 15 and 30 d post-inoculation (dpi), SMV accumulation significantly decreased or was even undetectable in HR and R plants, followed by MR and S plants. Additionally, the expression level of the CasRx gene varied in almost all T₁ plants with different resistance level, both at 15 and 30 dpi. Furthermore, when SMV resistance was evaluated in the T₂ generation, the results were similar to those recorded for the T₁ generation. These findings provide new insights into the application of the CRISPR/CasRx system for soybean improvement and offer a promising alternative strategy for breeding for resistance to biotic stress that will contribute to the development of SMV-immune soybean germplasm to accelerate progress towards greater soybean crop productivity.

Rapeseed (Brassica napus L.) is one of the main oil crops in the world, and increasing its yield is of great significance for ensuring the safety of edible oil. Presently, improving rapeseed plant architecture is an effective way to increase rapeseed yield with higher planting density. However, the regulatory mechanism of rapeseed plant architecture is poorly understood. In this study, a dwarf rapeseed mutant dwarf08 (df08) is obtained by ethyl methane sulfonate (EMS)-mutagenesis. The decrease in plant height of df08 is mainly caused by the reduction in main inflorescence length and first effective branch height and controlled by a single semi-dominant gene. The hybrid plants (F₁) show a semi-dwarf phenotype. Through map-based cloning and transgenic assay, we confirm that the nonsynonymous single nucleotide variant (SNV) (C to T) in BnaC03.BIN2, which is homologous with Arabidopsis (Arabidopsis thaliana) BIN2, is responsible for the dwarfism of df08. BnaC03.BIN2 interacts with BnaBZR1/BES1 and involves in brassinosteroids (BRs) signal transduction. Proline to Leucine substitution in 284 (P284L) enhances the protein stability of BnaC03.bin2-D, disrupts BRs signal transduction and affects the expression of genes regulating cell division, leading to dwarfism of df08. This study provides a new insight for the mechanism of rapeseed plant height regulation and creates an elite germplasm that can be used for genetic improvement of rapeseed architecture.

Cotton provides the most abundant natural fiber for the textile industry. The mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and lignin. To dissect the roles of hemicellulosic polysaccharides during fiber development, four IRREGULAR XYLEM 15 (IRX15) genes, GhIRX15-1/-2/-3/-4, were functionally characterized in cotton. These genes encode DUF579 domain-containing proteins, which are homologs of AtIRX15 involved in xylan biosynthesis. The four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening, and the encoded proteins were localized to the Golgi apparatus. Each GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double mutant. Silencing of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild type. Intriguingly, GhIRX15-2 and GhIRX15-4 formed homodimers and heterodimers. In addition, the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C, GhGT47A and GhGT47B, which are responsible for synthesis of the xylan backbone and reducing end sequence. Moreover, the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis, such as GhGUX1/2, GhGXM1/2 and GhTBL1. These findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.

Cotton architecture is determined by the differentiation fate transition of axillary meristem (AM), and influences cotton yield and the efficiency of mechanized harvesting. We observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of AM. The RNA-Seq and expression level analyses showed that genes FLAVIN BINDING, KELCH REPEAT, F-BOX1 (GhFKF1), and GIGANTEA (GhGI) were in response to circadian rhythms, and involved in the regulation of cotton flowering. The gene structure, predicted protein structure, and motif content analyses showed that in Arabidopsis, cotton, rapseed, and soybean, proteins GhFKF1 and GhGI were functionally conserved and share evolutionary origins. Compared to the wild type, in GhFKF1 mutants that were created by the CRISPR/Cas9 system, the initiation of branch primordium was inhibited. Conversely, the knocking out of GhGI increased the number of AM differentiating into flower primordium, and there were much more lateral branch differentiation and development. Besides, we investigated that proteins GhFKF1 and GhGI can interact with each other. These results suggest that GhFKF1 and GhGI are key regulators of cotton architecture development, and may collaborate to regulate the differentiation fate transition of AM, ultimately influencing plant architecture. We describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture.

Verticillium dahliae is an important soil-borne fungal pathogen that causes great yield losses in many cash crops. Effectors of this fungus are known to regulate plant immunity but the mechanism much remains unclear. A glycine-rich nuclear effector, VdCE51, was able to suppress immune responses in tobacco against Botrytis cinerea and Sclerotinia sclerotiorum. This effector was a required factor for full virulence of V. dahliae, and its nuclear localization was a requisite for suppressing plant immunity. The thioredoxin GhTRXH2, identified as a positive regulator of plant immunity, was a host target of VdCE51. Our findings show a virulence regulating mechanism whereby the secreted nuclear effector VdCE51 interferes with the transcription of PR genes, and the SA signaling pathway by inhibiting the accumulation of GhTRXH2, thus suppressing plant immunity.

Grain size is a key factor influencing grain weight in rice. In this study, a chromosome segment substitution line (CSSL9-17) was identified, that exhibits a significant reduction in both grain size and weight compared to its donor parent 93-11. Further investigation identified two quantitative trait loci (QTL) on chromosome 11, designated qGW11a and qGW11b, which contribute to 1000-grain weight with an additive effect. LOC_Os11g05690, encoding the amino acid permease OsCAT8, is the target gene of qGW11a. Overexpression of OsCAT8 resulted in decreased grain weight, while OsCAT8 knockout mutants exhibited increased grain weight. The 287-bp located within the OsCAT8 promoter region of 93-11 negatively regulates its activity, which is subsequently correlated with an increase in grain size and weight. These results suggest that OsCAT8 functions as a negative regulator of grain size and grain weight in rice.

Flag leaf angle is one of the key target traits in high yield wheat breeding. A smaller flag leaf angle reduces shading and enables plants to grow at a higher density, which increases yield. Here we identified a mutant, je0407, with an 84.34%-89.35% smaller flag leaf angle compared with the wild type. The mutant also had an abnormal lamina joint and no ligule or auricle. Genetic analysis indicated that the ligule was controlled by two recessive genes, which were mapped to chromosomes 2AS and 2DL. The mutant allele on chromosome 2AS was named Tafla1b, and it was fine mapped to a 1 Mb physical interval. The mutant allele on chr. 2DL was identified as Taspl8b, a novel allele of TaSPL8 with a missense mutation in the second exon, which was used to develop a cleaved amplified polymorphic sequence marker. F₃ and F₄ lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b alleles. Plants with the Tafla1b/Taspl8a genotype had 58.41%-82.76% smaller flag leaf angles, 6.4%-24.9% shorter spikes, and a greater spikelet density (0.382 more spikelets per cm) compared with the wild type. Plants with the Tafla1a/Taspl8b genotype had 52.62%-82.24% smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild type. Tafla1b/Taspl8b plants produced erect leaves with an abnormal lamina joint. The two alleles had dosage effects on ligule formation and flag leaf angle, but no significant effect on thousand-grain weight. The mutant alleles provide novel resources for improvement of wheat plant architecture.

Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region on chromosome 2AL when crossed with Yangmai 16. To fine-map the YR86 locus, we developed two large F₂ populations from crosses Emai 580/Zhongmai 895 and Avocet S/Zhongmai 895. Remarkably, both populations exhibited suppressed recombination in the same 2AL region. Collinearity analysis across Chinese Spring, Aikang 58, and 10+ wheat genomes revealed a 4.1 Mb chromosomal inversion spanning 708.5-712.6 Mb in the Chinese Spring reference genome. Molecular markers were developed in the breakpoint and were used to assess a wheat cultivar panel, revealing that Chinese Spring, Zhongmai 895, and Jimai 22 shared a common sequence named Inv^CS, whereas Aikang 58, Yangmai 16, Emai 580, and Avocet S shared the sequence named Inv^AK58. The inverted configuration explained the suppressed recombination observed in all three bi-parental populations. Normal recombination was observed in a Jimai 22/Zhongmai 895 F₂ population, facilitating mapping of YR86 to a genetic interval of 0.15 cM corresponding to 710.27-712.56 Mb falling within the inverted region. Thirty-three high-confidence genes were annotated in the interval using the Chinese Spring reference genome, with six identified as potential candidates for YR86 based on genome and transcriptome analyses. These results will accelerate map-based cloning of YR86 and its deployment in wheat breeding.

In a wheat breeding line XQ-0508 showing consistent resistance to powdery mildew disease, a recessive gene, designated PmXQ-0508, was identified and mapped to a distal region on chromosome arm 2BS. Of three resistance-associated genes in this region, one encoding a protein kinase was selected as the primary candidate for PmXQ-0508. Ten closely linked DNA markers developed in the study could be used for marker-assisted selection for powdery-mildew resistance in breeding programs.

Low temperatures during germination inhibit seed growth, lead to small and weak seedlings, and significantly reduce the wheat yield. Alleviating the adverse effects of low temperature on wheat seed germination is highly important for achieving high and stable wheat yields. In this study, Tongmai 6 (insensitive) and Zhengmai 113 (sensitive), which have different low-temperature sensitivities during germination were treated with low temperature during germination. The transcriptome, metabolome and physiological data revealed that low temperature decreased the germination rate, downregulated the expression of a large number of genes involved in regulating glycometabolism, and inhibited carbon, nitrogen (especially amino acids) and energy metabolism in the seeds. Arginine content increased at low temperature, and its increase in the low-temperature-tolerant variety was significantly greater than that in the sensitive variety. Arginine priming experiment showed that treatment with an appropriate concentration of arginine improved the seed germination rate. The conversion of starch to soluble sugar significantly increased under exogenous arginine conditions, the content of key metabolites in energy metabolism increased, and the utilization of ATP in the seeds increased. Taken together, arginine priming increased seed germination at low temperature by relieving inhibition of seed carbon and nitrogen metabolism and improving seed energy metabolism.

Promoting more floret primordia within a spike to acquire fertile potential during the differentiation and pre-dimorphism phases is critical for increasing the number of fertile florets per spike (NFFs). However, it is yet unknown the physiological mechanism regulating the complex and dynamic process. This study aimed to clarify how intra-spike hormones, pigments, and assimilates coordinate with each other to regulate spike morphology and then floret primordia development. A two-year field experiment was conducted with two winter wheat genotypes: N50 (big-spike with greater NFFs) and SM22 (medium-spike with fewer NFFs). We monitored high temporal and spatial-resolution changes in the number and morphology of floret primordia within a spike, as well as in intra-spike hormones, pigments, and assimilates. Our results revealed that the big-spike genotype had more NFFs than the medium-spike genotype, not only because they had more spikelets, but also because they had greater NFFs mainly at central spikelets. More floret primordia at central spikelets had sufficient time to develop and acquire fertile potential during the differentiation phase (167-176 d after sowing, DAS) and the pre-dimorphism phase (179 DAS) for the big-spike genotype than the medium-spike genotype. Floret primordia with fertile morphology during the pre-dimorphism phase always developed into fertile florets during the dimorphism phase. Those early-developed floret primordia most proximal and intermediate to the rachis in the big-spike genotype developed faster than the medium-spike genotype. Correspondingly, the spike dry matter and pigments (chlorophyll a, chlorophyll b, carotene, and carotenoids) content during 170-182 DAS, auxin (IAA) and cytokinin (CTK) content on 167 DAS were significantly higher in the big-spike genotype than in the medium-spike genotype, while jasmonic acid (JA) content was significantly lower in the big-spike genotype compared to the medium-spike genotype during 167-182 DAS. Since the significant differences in intra-spike hormone content of the two genotypes appear earlier than those in dry matter and pigments, we propose a possible model that helped the N50 genotype (big-spike) to form more fertile florets, taking the intra-spike hormone content as a signaling molecule induced assimilates and pigments synthesis, which accelerated the development of more floret primordia during the differentiation phase and then acquired fertile potential during the pre-dimorphism phase, finally improved the NFFs. Our high temporal and spatial-resolution analysis provides an accurate time window for precision cultivation and effective physiological breeding to improve the number of fertile florets in wheat.

Direct-seeding rapeseed production at high plant density raises the risk of lodging. We investigated the use of dwarf genes to improve rapeseed plant architecture to balance yield and lodging. Three genotypes with different plant architectures (dwarf sca^HS5, semi-dwarf +/sca^HS5, and tall HS5) were evaluated under varying nitrogen rates (N1, N2, and N3: 120, 240, and 360 kg N ha⁻¹) and plant densities (D1, D2, and D3: 15, 45, and 75 plants m⁻²) from 2019 to 2022. The results showed that increasing N rate positively influenced yield while decreasing lodging resistance in all genotypes. Increasing plant density (D2-D3) enhanced lodging resistance and yield in sca^HS5 and +/sca^HS5, but reduced yield in HS5. Compared to the two parents, +/sca^HS5 exhibited moderate expressions of IAA3, GH3.15, and SAUR30 in stems under N2D3, resulting in reduced plant height and increased compactness. Additionally, +/sca^HS5 had a thicker silique layer than HS5 by 14.7%, and it had a significant correlation between branch height/angle and yield. Increasing N rate led to increased lignin and pectin contents, while cellulose content decreased. Increasing plant density resulted in greater stem cellulose content and CSLA3/7 expression in sca^HS5 and +/sca^HS5, but decreased in HS5. Compared to HS5, +/sca^HS5 exhibited higher expressions of ARAD1 and GAUT4, along with a 51.1% increase in pectin content, leading to improved lodging resistance under N2D3. Consequently, +/sca^HS5 showed a 46.4% higher yield and 38.9% lodging resistance than HS5 under N2D3, while sca^HS5 demonstrated strong lodging resistance but lower yield potential. Overall, this study underscores the potential of utilizing auxin dwarf genes to optimize the trade-off between yield and lodging resistance in rapeseed and the possibility of maximizing yield potential by optimizing the plant architecture of +/sca^HS5 through nitrogen reduction and dense planting.

Achieving the green development of agriculture requires the reduction of chemical nitrogen (N) fertilizer input. Previous studies have confirmed that returning green manure to the field is an effective measure to improve crop yields while substituting partial chemical N fertilizer. However, it remains unclear how to further intensify the substituting function of green manure and elucidate its underlying agronomic mechanism. In a split-plot field experiment in spring wheat, different green manures returned to the field under reduced chemical N supply was established in an oasis area since 2018, in order to investigate the effect of green manure and reduced N on grain yield, N uptake, N use efficiency (NUE), N nutrition index, soil organic matter, and soil N of wheat in 2020-2022. Our results showed that mixed sown common vetch and hairy vetch can substitute 40% of chemical N fertilizer without reducing grain yield or N accumulation. Noteworthily, mixed sown common vetch and hairy vetch under reduced N by 20% showed the highest N agronomy efficiency and recovery efficiency, which were 92.0% and 46.0% higher than fallow after wheat harvest and conventional N application rate, respectively. The increase in NUE of wheat was mainly attributed to mixed sown common vetch and hairy vetch, which increased N transportation quantity and transportation rate at pre-anthesis, enhanced N harvest index, optimized N nutrition index, and increased activities of nitrate reductase and glutamine synthetase of leaf, respectively. Meanwhile, mixed sown common vetch and hairy vetch under reduced N by 20% improved soil organic matter and N contents. Therefore, mixed sown common vetch and hairy vetch can substitute 40% of chemical N fertilizer while maintaining grain yield and N accumulation, and it combined with reduced chemical N by 20% or 40% improved NUE of wheat via enhancing N supply and uptake.

In a nine-year field experiment in a wheat-maize-sunflower cropping system in Hetao Irrigation Area, Inner Mongolia, China, organic amendments applied as straw, manure, green manure, and the combination of green manure and straw increased wheat and maize yield, soil aggregate stability, and soil microbial activity in comparison with chemical fertilizer, without changing greenhouse gas emission intensity.

Accurate nitrogen (N) nutrition diagnosis is essential for improving N use efficiency in crop production. The widely used critical N (Nc) dilution curve traditionally depends solely on agronomic variables, neglecting crop water status. With three-year field experiments with winter wheat, encompassing two irrigation levels (rainfed and irrigation at jointing and anthesis) and three N levels (0, 180, and 270 kg ha⁻¹), this study aims to establish a novel approach for determining the Nc dilution curve based on crop cumulative transpiration (T), providing a comprehensive analysis of the interaction between N and water availability. The Nc curves derived from both crop dry matter (DM) and T demonstrated N concentration dilution under different conditions with different parameters. The equation Nc = 6.43T^−0.24 established a consistent relationship across varying irrigation regimes. Independent test results indicated that the nitrogen nutrition index (NNI), calculated from this curve, effectively identifies and quantifies the two sources of N deficiency: insufficient N supply in the soil and insufficient soil water concentration leading to decreased N availability for root absorption. Additionally, the NNI calculated from the Nc-DM and Nc-T curves exhibited a strong negative correlation with accumulated N deficit (Nand) and a positive correlation with relative grain yield (RGY). The NNI derived from the Nc-T curve outperformed the NNI derived from the Nc-DM curve concerning its relationship with Nand and RGY, as indicated by larger R² values and smaller AIC. The novel Nc curve based on T serves as an effective diagnostic tool for assessing winter wheat N status, predicting grain yield, and optimizing N fertilizer management across varying irrigation conditions. These findings would provide new insights and methods to improve the simulations of water-N interaction relationship in crop growth models.

To improve the amylose content (AC) and resistant starch content (RSC) of maize kernel starch, we employed the CRISPR/Cas9 system to create mutants of starch branching enzyme I (SBEI) and starch branching enzyme IIb (SBEIIb). A frameshift mutation in SBEI (E1, a nucleotide insertion in exon 6) led to plants with higher RSC (1.07%), lower hundred-kernel weight (HKW, 24.71 ± 0.14 g), and lower plant height (PH, 218.50 ± 9.42 cm) compared to the wild type (WT). Like the WT, E1 kernel starch had irregular, polygonal shapes with sharp edges. A frameshift mutation in SBEIIb (E2, a four-nucleotide deletion in exon 8) led to higher AC (53.48%) and higher RSC (26.93%) than that for the WT. E2 kernel starch was significantly different from the WT regarding granule morphology, chain length distribution pattern, X-ray diffraction pattern, and thermal characteristics; the starch granules were more irregular in shape and comprised typical B-type crystals. Mutating SBEI and SBEIIb (E12) had a synergistic effect on RSC, HKW, PH, starch properties, and starch biosynthesis-associated gene expression. SBEIIa, SS1, SSIIa, SSIIIa, and SSIIIb were upregulated in E12 endosperm compared to WT endosperm. This study lays the foundation for rapidly improving the starch properties of elite maize lines.

Amylose content (AC) is a crucial determinant of the eating and cooking quality (ECQ) of rice, with low AC varieties exhibiting a softer texture and greater stickiness −attributes that enhance palatability and are desirable in specific culinary contexts. To harness these traits, significant efforts have been made to manipulate AC to improve rice ECQ. Our research utilized the MutMap⁺ approach to identify LAC6/TL1, a gene that is an allele of Du13, responsible for low AC. LAC6 encodes a C2H2 zinc finger protein, which specifically increases the splicing efficiency of the Wx^b allele without affecting the Wx^a allele. Functional studies of LAC6 revealed that its proper integration could rectify the undesirable AC phenotype, whereas mutations within this gene led to reduced AC and were associated with shorter grain length and decreased thousand-grain weight. Despite these drawbacks, such mutations positively impact rice palatability, presenting a trade-off between grain size and eating quality. To address the challenges posed by the reduced grain weight associated with LAC6 mutations, we developed a specific molecular marker for LAC6, which has been effectively used in breeding programs to select lac6/tl1/du13 homozygous individuals with larger grain size. Our findings demonstrate that the “small grain” trait associated with lac6/tl1/du13 can be effectively mitigated through combined phenotype-based and marker-assisted selection. This study highlights the potential of lac6/tl1/du13 as a valuable gene for breeding novel, high-quality soft rice varieties through targeted breeding strategies.

Jute (Corchorus capsularis L.) is the second most important natural plant fiber source after cotton. However, developing an efficient gene editing system for jute remains a challenge. In this study, the transgenic hairy root system mediated by Agrobacterium rhizogenes strain K599 was developed for Meifeng 4, an elite jute variety widely cultivated in China. The transgenic hairy root system for jute was verified by subcellular localization and bimolecular fluorescence complementation (BiFC) assays. The CHLOROPLASTOS ALTERADOS 1 (CcCLA1) gene, which is involved in the development of chloroplasts, was targeted for editing at two sites in Meifeng 4. Based on this hairy root transformation, the gRNA scaffold was placed under the control of cotton ubiquitin GhU6.7 and -GhU6.9 promoters, respectively, to assess the efficiency of gene editing. Results indicated the 50.0% (GhU6.7) and 38.5% (GhU6.9) editing events in the target 2 alleles (gRNA2), but no mutation was detected in the target 1 allele (gRNA1) in transgenic-positive hairy roots. CcCLA1 gene editing at gRNA2 under the control of GhU6.7 in Meifeng 4 was also carried out by Agrobacterium tumefaciens-mediated transformation. Two CcCLA1 mutants were albinic, with a gene editing efficiency of 5.3%. These findings confirm that the CRISPR/Cas9 system, incorporating promoter GhU6.7, can be used as a gene editing tool for jute.