The jasmonate ZIM-domain (JAZ) family of proteins serves as co-receptors and transcriptional repressors of jasmonic acid (JA) in plants. Their functional diversity and multiple roles make them important components of the regulatory network of JA and other hormonal signaling pathways. In this review, we provide an overview of the latest findings on JAZ family proteins and emphasize their roles in plant growth and development, and response to biotic and abiotic stress, along with their underlying mechanisms. Moreover, existing challenges and future applications are outlined with the aim of offering a reference for further research on JAZ proteins in the context of plant physiology.

The application of advanced omics technologies in plant science has generated an enormous dataset of sequences, expression profiles, and phenotypic traits, collectively termed “big data” for their significant volume, diversity, and rapid pace of accumulation. Despite extensive data generation, the process of analyzing and interpreting big data remains complex and challenging. Big data analyses will help identify genes and uncover different mechanisms controlling various agronomic traits in crop plants. The insights gained from big data will assist scientists in developing strategies for crop improvement. Although the big data generated from crop plants opens a world of possibilities, realizing its full potential requires enhancement in computational capacity and advances in machine learning (ML) or deep learning (DL) approaches. The present review discuss the applications of genomics, transcriptomics, proteomics, metabolomics, epigenetics, and phenomics “big data” in crop improvement. Furthermore, we discuss the potential application of artificial intelligence to genomic selection. Additionally, the article outlines the crucial role of big data in precise genetic engineering and understanding plant stress tolerance. Also we highlight the challenges associated with big data storage, analyses, visualization and sharing, and emphasize the need for robust solutions to harness these invaluable resources for crop improvement.

Inflorescence architecture is determined by inflorescence length, branch angles and the density of siliques, which affects planting density, lodging resistance and mechanical operation in rapeseed. However, the molecular mechanisms controlling inflorescence architecture are poorly understood, restricting the progress of breeding varieties with ideal plant architecture in oilseed rape. In this study, we have identified and characterized a rapeseed inflorescence development mutant, reduced inflorescence length (ril), which exhibits determinate and shortened inflorescences, reduced plant height, compact branches, and increased silique density. Through BSA-seq and map-based cloning, we find that RIL encodes a cyclic nucleotide-gated channel 20 (BnaA01.CNGC20). A substitution of proline at the 304th position to leucine (P304L) was identified in the conserved transmembrane domain of BnaA01.CNGC20. This P304L substitution neither affects the subcellular localization and self-assembly of BnaA01.CNGC20, nor disrupts the interactions with BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 (BAK1), which interacts with CNGC20 and phosphorylates it to regulate Ca²⁺ channel stability. However, the P304L substitution increases channel activity and Ca²⁺ influx, which in turn induces immune responses such as cell death, H₂O₂ accumulation, upregulation of pathogenesis-related genes, and pattern-triggered immunity. The enhanced immunity improves the resistance to Leptosphaeria biglobosa and Sclerotinia sclerotiorum. Transcriptome analysis further revealed that CNGC20 plays dual roles in regulating plant growth and immunity via the brassinosteroid and auxin signaling pathways. The findings in this study provide deeper insights into the intricate relationship between cytosolic Ca²⁺ level and plant development and immunity, as well as the trade-off between immunity and the performance of yield-related traits in the heterozygous plants (+/ril), which may serve as a guide for balancing yield and disease resistance in oilseed rape breeding.

Crop yield depends on biomass, which is primarily associated with photosynthesis. We previously demonstrated that two photorespiratory bypasses, i.e., GOC (glycolate oxidase + oxalate oxidase + catalase) and GCGT (glycolate oxidase + catalase + glyoxylate carboligase + tartronic semialdehyde reductase), significantly increased photosynthesis, biomass, and grain yield, but decreased seed-setting rates in rice. This study explored the underlying mechanism of how elevated photosynthetic efficiency impacted the seed-setting. First, pollen germination assessed in vivo and in vitro, revealed a reduced germination rate in GCGT rice. Subsequent analysis found that photosynthates highly accumulated in the leaves and stems; sucrose and soluble sugar levels were increased but the starch level was reduced in the anthers. Uridine diphosphate glucose (UDP-Glc) was increased but uridine diphosphate galactose (UDP-Gal) was unaltered, thus causing an imbalance in the UDP-Glc/UDP-Gal ratio in GCGT anthers. Most anthers in GCGT plants had two locules in contrast to four in the wild-type (WT). Pollen tapetum was developmentally abnormal, and genes related to sucrose synthesis, transport, and tapetal programmed cell death (PCD) were upregulated, whereas those involved in starch synthesis and conversion were downregulated in GCGT anthers. Taken together, our results demonstrated that an increase in sugar content was the primary factor causing reduced seed-setting rates in high photosynthetic efficiency rice, during which metabolic disorder of sugars and UDP sugar imbalance in anthers lead to impaired pollen fertility.

In flowering plants, callose (β-1,3-glucan) plays a vital role in pollen development, especially in the separation and development of microspores. However, the molecular mechanism of callose deposition during rice pollen development remains unclear. In this study, we isolated and characterized a novel rice pollen defective mutant, non-separated microspores 1 (nsm1), which produced “dyad” or “tetrad” pollen grains. Cytological analysis indicated disrupted interstitial callose deposition at the cell plate of dyads and tetrads in nsm1 pollens. This disruption caused sporopollenin to be massively deposited outside of the junction where the interstitial callose wall connected with the peripheral callose wall, or unevenly distributed on the interstitial pollen primexine at the late meiosis stage. Consequently, an excess tectum-like layer was formed outside of the junction, connecting with the tectum of two microspores during later developmental stages, which prevented the separation of microspores. Additionally, in the linkage area, the tectum of two microspores gradually fused or degenerated, resulting in a decreased contact area between microspores and the anther locule. Therefore, the defect in callose deposition resulted in unsuccessful separation of microspores, abnormal deposition of pollen exine, and also affected the accumulation of materials in microspores, resulting in pollen semi-sterility. NSM1, encoding a callose synthase located in the Golgi body, is ubiquitously expressed in anthers with its peak expression at the young microspore stage. The in vitro enzyme activity assay confirmed that NSM1 possesses callose synthase activity, and the enzyme activity in the nsm1 mutants was significantly reduced. Phylogenetic analysis indicated that NSM1 and its orthologs play a highly conserved role in callose biosynthesis among plant species. Taken together, we propose that NSM1 plays an essential role in male meiotic callose synthesis and later pollen wall development.

Tiller number and grain size are important agronomic traits that determine grain yield in rice. Here, we demonstrate that DEFECTIVE TILLER GROWTH 1 (DTG1), a member of the casein kinase 1 protein family, exerts a co-regulatory effect on tiller number and grain size. We identified a single amino acid substitution in DTG1 (I357K) that caused a decrease in tiller number and an increase in grain size in NIL-dtg1. Genetic analyses revealed that DTG1 plays a pivotal role in regulation of tillering and grain size. The DTG1^I357K allelic variant exhibited robust functionality in suppressing tillering. We show that DTG1 is preferentially expressed in tiller buds and young panicles, and negatively regulates grain size by restricting cell proliferation in spikelet hulls. We further confirm that DTG1 functioned in grain size regulation by directly interacting with Grain Width 2 (GW2), a critical grain size regulator in rice. The CRISPR/Cas9-mediated elimination of DTG1 significantly enhanced tiller number and grain size, thereby increasing rice grain yield under field conditions, thus highlighting potential value of DTG1 in rice breeding.

Amino acids are the primary form of nitrogen utilization in higher plants, mainly transported by amino acid transporters. In this study, we analyzed the natural variation of amino acid transporter-like 4 (OsATL4) in rice germplasm resources, identified its spatiotemporal expression characteristics, determined its substrate transport, and validated its function using transgenic plants. We found that the promoter sequence of OsATL4 varied across 498 rice varieties. The expression level of OsATL4 was higher in japonica rice, which was negatively correlated with tiller number and grain yield. OsATL4 was highly expressed in the basal part, leaf sheath, stem, and young panicle, with its two splicing variants localized to the cell membrane. OsATL4a (the long splicing variant) had a high affinity for transporting Ser, Leu, Phe, and Thr, while OsATL4b (the short splicing variant) had a high affinity for transporting Ser, Leu, and Phe. Blocking OsATL4 promoted axillary bud outgrowth, rice tillering, and grain yield, whereas overexpression lines exhibited the opposite phenotype. Exogenous application of low concentrations of Ser promoted axillary bud outgrowth in overexpression lines, while high concentrations of Ser inhibited it. Conversely, the mutant lines showed the opposite response. Altered expression of OsATL4 might affect the expression of genes in nitrogen, auxin, and cytokinin pathways. We propose that two splicing variants of OsATL4 negatively regulate rice tillering and yield by mediating the transport of amino acids, making it a significant target for high-yield rice breeding.

Receptor kinases play a pivotal role in detecting environmental signals, and consequently, gene pleiotropy is frequently observed within this family. However, the trade-off in trait expression resulting from gene pleiotropy poses a constraint on the utilization of such genes in agricultural breeding. In this study, we identified the receptor kinase gene FERONIA-Like Receptor 13 (FLR13) as a pleiotropic gene influencing plant height, tillering, grain yield, and disease resistance. Using promoter editing, we generated novel alleles (FLR13^T5T6-1, FLR13^T5T6-2) that confer resistance to rice blast and increase per-plant yield. The knockout of the T5T6 segment alleviates the inhibitory effects of two transcription factors, OsGBP1 and OsWRKY53, on FLR13 expression. In summary, our study presents a promising avenue for enhancing the pivotal attributes of receptor-like kinases through a promoter-editing strategy.

The transition from the vegetative to reproductive stage (flowering) is a critical stage in the life cycle of plants. Transition to flowering is controlled by a complex photoperiod-dependent network. Here, we report the functional analysis of NAC transcription factor ONAC005 as a positive regulator of flowering in rice. An onac005-1 T-DNA insertion mutant showed late flowering only under long-day (LD) conditions, indicating that ONAC005 is an LD-dependent flowering activator. Expression analysis of flowering time genes revealed that ONAC005 negatively regulates expression of OsLFL1, which is a LD-specific repressor of flowering in rice. Consequently, ONAC005 up-regulates expression of downstream genes Ehd1, Hd3a, and RFT1 under LD conditions. ONAC005 physically interacts with previously reported upstream regulators of OsLFL1, OsMADS50 and OsMADS56. Binding assays showed that ONAC005 binds to the promoter regions of OsLFL1. We further found that the ONAC005-OsMADS50-OsMADS56 complex weakly repressed OsLFL1 at the early vegetative stage and then gradually repressed it at the transcriptional level as the plant developed. Taken together, our results suggest that ONAC005 specifically affects flowering under LD-dependent conditions by interacting with an antagonistic protein complex.

A novel rice mutant lmi1 showed increased resistance to bacterial blight. LMI1 encodes a DUF292 protein and regulates defense immune responses and cell death via vesicle trafficking in chloroplasts.

The involvement of the endoplasmic reticulum (ER)-localized adenylate transporter1 (ER-ANT1) in photorespiratory metabolism has been established, yet its precise physiological function remains uncertain. Rice er-ant1 mutant plants grown in ambient air exhibited stunted growth and substantial alterations in amino acid metabolites, but recovery in a high CO₂ condition (1.5%). We show that the absence of ER-ANT1 hindered the breakdown of glycine without affecting its synthesis, leading to a substantial accumulation of glycine, diminished levels of serine, and depleted reserves of glutamate and alanine. Intriguingly, the er-ant1 plants grown in high CO₂ and later exposed to ambient air displayed reduced serine levels within 12 h, yet they accumulated serine a week after transferring to ambient air due to induced phosphorylated serine synthesis pathways. Furthermore, knockout of ER-ANT1 marginally impacted the transcription of genes governing core enzymes in photorespiration, but notably upregulated BOU expression that encodes a putative mitochondrial glutamate transporter and AGAT1 that encodes an alanine:glyoxylate aminotransferase gene. Surprisingly, AGAT1, an ER-localized protein, exhibited higher activity that correlates with the decreased alanine levels observed in the er-ant1 mutant. Lack of ER-ANT1 activity also led to a significantly elevated NADH/NAD⁺ ratio that potentially hinders the glycine-to-serine conversion process. This supports the hypothesis that the lack of ER-ANT1-induced limitation of ATP usage might inhibit GDC activity by modulating the NADH/NAD⁺ ratio. Moreover, non-proteinogenic amino acids, including β-alanine and γ-aminobutyrate (GABA), underwent significant alterations, even under high CO₂ conditions in the er-ant mutant, implying additional non-photorespiration roles of ER-ANT1. Taken together, our results indicate that ER-localized ER-ANT1 plays a crucial role in amino acid metabolism during photorespiration.

WUSCHEL-related homeobox (WOX) transcription factors play a crucial role in lateral organ development in several plant species; however, their precise functions in soybean (Glycine max [L.] Merr.) were unclear. Here, we identified two independent multi-leaflet soybean mutants, mlw48-8 and mlw48-161, from a CRISPR/Cas9-engineered mutant library in the Williams 82 background. Both mutants exhibited irregular leaf margins, and the upper leaves were narrow and almost lanceolate at maturity. Molecular analysis revealed that these are allelic mutants with independent mutations in the WUSCHEL-related homeobox1 (GmWOX1A) gene. A transcriptome analysis demonstrated that GmWOX1A modulates the expression of auxin- and leaf development-related genes. Yeast two-hybrid and split-luciferase complementation imaging assays revealed that GmWOX1A interacts with the YABBY family protein GmYAB5, providing further evidence of its potential involvement in leaf development. Notably, the mlw48-161 mutant showed an increased seed number per plant. Consequently, our study not only provides valuable insights into the role of GmWOX1A in soybean leaf development but also offers a potential strategy for high-yield breeding.

MicroRNAs (miRNAs) are versatile regulators of gene expression at both the transcription and post-transcription levels. The microRNA miR396 plays vital roles in growth, development, and resistance to abiotic stresses in many plant species. However, the roles and functions of miR396 in soybeans are not well understood. Here, we report that Gm-miR396a influences soybean development and salinity tolerance. We found that soybean miR396a was responsive to salt stress. Gm-miR396a gene-edited lines (miR396a-GEs), created using CRISPR/Cas9, exhibited more branches, higher grain yields, and greater salinity tolerance than control plants. The transcripts in lines with altered abundance of miR396a-GE were significantly enriched for biological processes related to hormone regulation. Overexpression of the Gm-miR396a precursor (pre-miR396a-OE) resulted in developmental deficiencies including dwarfness, abnormal inflorescences and flowers, smaller and fewer seeds, and small leaves with larger and more numerous stomata. Transcriptome analysis indicated photosynthesis-related genes were downregulated in pre-miR396a-OE plants. These results contribute valuable insights into the function of Gm-miR396a in soybeans and hold promise for enhancing soybean yield and salinity tolerance through germplasm innovation.

A glutathione S-transferase (GST) gene IbGSTL2 was cloned and characterized from sweetpotato. It harbored a variation associated with starch content in storage roots. Overexpression of IbGSTL2 increased starch content and amylopectin proportion, decreased gelatinization temperature, and improved degree of crystallinity in sweetpotato storage roots, while its RNA interference resulted in the opposite trends. IbGSTL2 physically interacted with IbcPGM, an enzyme of sucrose metabolism, and improve starch content and quality by regulating genes involved in starch biosynthesis.

Doubled haploid (DH) technology is an efficient method used in commercial maize breeding. Chromosome doubling is a vital step of DH technology; however, the underlying processes regulating chromosome doubling of haploid is still not well understood, which is key to optimize the technology. In this study, the immature haploid embryos of the maize inbred line Zheng58 treated with amiprophos-methyl (APM) or colchicine were used to analyze transcriptomic and metabolomic changes, 75 and 60 differential expressed metabolites (DEMs) were identified between control treatment, respectively. Most differentially expressed genes (DEGs) related to artificial chromosome doubling were down regulated; these were mainly involved in mitosis process. Both DEMs and DEGs co-expression analyses showed that, compared to controls, zeatin biosynthesis and cofactor and vitamin metabolism were significantly enriched in both APM and colchicine treatments. In a parallel experiment, exogenous vitamins including thiamine, nicotinic acid, vitamin B6, or trans-zeatin were added to colchicine treatment; there were synergistic effects between vitamins or zeatin and colchicine in haploid artificial chromosome doubling. These results provide novel insights in exploring the molecular responses to antimitotic reagents at both the transcriptomic and metabolomic levels. In addition, the application efficiency of haploid breeding will be greatly improved by the key factors for artificial chromosome doubling.

Genotyping arrays based on single nucleotide polymorphisms (SNPs) provide a low-cost, high-throughput platform. The development of a SNP array that fully reflects the genetic diversity of maize (Zea mays L.) germplasm and is applicable to molecular breeding programs is desirable. In this study, we developed a MaizeGerm50K array comprising 50,852 SNPs selected from the resequencing data of 1604 maize inbred lines and other markers. A genome-wide association study using a landrace panel genotyped with the array permitted mapping of several known genes. We also verified a candidate gene, RNA-binding motif protein 24-like 1 (ZmRBM24L1), delaying flowering through overexpression lines. Genomic selection for yield and agronomic traits showed high prediction accuracy. The MaizeGerm50K array is thus a valuable genomic tool for maize genetic studies and breeding.

Rice is a major crop susceptible to chilling stress. The identification of quantitative trait loci and genes for cold tolerance is crucial for the rice breeding. Of 30 quantitative-trait loci affecting seedling cold tolerance identified in a genome-wide association study of 540 rice accessions, OsbZIP72 was assigned as the causative gene for one, qCTS9.1. A single-nucleotide polymorphism in its promoter accounted for variation in expression between indica and japonica subspecies. The favorable haplotype of OsbZIP72 originated in wild rice and contributed to the expansion of japonica rice to colder habitats. OsbZIP72 positively regulates genes coding reactive oxygen species (ROS)-scavenging proteins and maintains intracellular ROS homeostasis. These findings not only enhanced our understanding of environmental adaptation but also provide novel genetic resources and potential targets for molecular design breeding for cold tolerance in rice.

Soybean (Glycine max) is an important and valuable crop, providing oil and proteins for both humans and animals. Seed weight is a key trait that determines soybean yields; however, the genes and mechanisms controlling seed weight remain poorly understood. Here, we used genome-wide association study (GWAS) and joint linkage mapping to identify a ubiquitin-specific protease, GmSW17.1, which regulates 100-seed weight in soybean. Two natural allelic variants of GmSW17.1 resulted in significantly different 100-seed weight, with GmSW17.1^T conferring heavier seeds. We used CRISPR/Cas9 technology to knock out GmSW17.1, resulting in lighter and smaller seeds; however, these mutants produced more seeds than the wild type, resulting in similar overall yields. Owing to the increased number of seeds, we determined that GmSW17.1 is highly transcribed in developing seeds, and its encoded protein physically interacts in the nucleus with GmSGF11, which plays a crucial role in the deubiquitinating pathway. Analysis of genomic sequences from more than 1714 soybean accessions suggested that the natural allele GmSW17.1^T was selected during the domestication and genetic improvement, resulting in its rapid expansion in cultivated soybean. These findings provide important insights into the role of GmSW17.1 in 100-seed weight and offer valuable clues for the molecular breeding of soybean.

Fusarium head blight (FHB) threatens wheat production worldwide. Utilization of FHB resistant varieties is the most effective solution for disease control. Owing to the limited sources of FHB resistance, mining of novel resistance genes is crucial. Here, we report an FHB resistance gene from a wild wheat relative species, Roegneria ciliaris and developed FHB resistant germplasm containing this gene. Wheat-R. ciliaris disomic addition line DA3S^c showed enhanced type II FHB resistance compared to its sister line 3S^c-Null without chromosome 3S^c, indicating that the resistance was contributed by the addition of 3S^c. The resistance gene on 3S^c was validated using F₂ and F_2:3 populations derived from the cross between DA3S^c and susceptible Aikang 58 (a susceptible cultivar), demonstrating that the lines with 3S^c had significantly enhanced FHB resistance compared to the individuals without 3S^c. This was the second resistance gene identified in R. ciliaris, designated FhbRc2. To transfer FhbRc2 to common wheat, we produced a double-monosomic chromosome population by crossing DA3S^c with the Chinese Spring nulli-tetrasomic line N3DT3B. Eight alien chromosome lines containing 3S^c were identified using genomic/fluorescence in situ hybridization and 3S^c-specific marker analysis. Only the lines carrying the long arm of 3S^c conferred FHB resistance, further locating FhbRc2 on 3S^cL. A compensating wheat-R. ciliaris Robertsonian translocation line T3DS·3S^cL harboring FhbRc2 is developed and provides a potential genetic resource in wheat breeding for enhanced FHB resistance.

Total spikelet number per spike (TSS) is a crucial yield component in wheat. Dissecting and characterizing major stable quantitative trait loci (QTL) associated with TSS can significantly enhance the genetic improvement of yield potential. In a previous study, we identified a stable major QTL for TSS, named QTss.cas-3D. In the present study, we conducted fine mapping of QTss.cas-3D, interval to approximately 6.35 Mb, ranging from 105.03 to 111.38 Mb, based on the IWGSC RefSeq v2.1. Through genome re-sequencing and gene function annotation, we identified TraesCS3D03G0308000 (TaFT-D2) as the candidate gene. Phenotypic evaluation with paired near-isogenic lines revealed that this locus predominantly increases kernel number per spike by enhancing TSS and fertile spikelet number per spike, without significantly affecting thousand-kernel weight or tiller number. The presence of the TaFT-D2 allele in the parent P3228, which is rare in nature populations, highlights its potential value. This study provides a valuable gene resource and functional marker for wheat molecular breeding aimed at improving TSS and establishes a foundation for gene functional analysis of TaFT-D2.

The wild decaploid species Thinopyrum ponticum (Podp.) Barkworth & D.R. Dewey is an important source of genes against biotic and abiotic stresses affecting wheat. The wheat-Th. ponticum partial amphiploid AUS6770 shows resistance to multiple diseases, including stripe rust, stem rust, and powdery mildew. Mitotic chromosomes of AUS6770 were characterized by non-denaturing-fluorescence in situ hybridization (ND-FISH), and the individual Th. ponticum chromosomes 1Ae to 7Ae were karyotypically distinguished by Oligo-FISH painting using bulked oligo pools based on wheat-barley collinear regions. A novel stripe rust resistant line A155, derived from AUS6770, was found to have 44 chromosomes, including a pair of 2Ae chromosomes and a pair of 6B-6Ae translocations. To detect plants with transfer of resistance genes from A155 to wheat chromosomes, 1770 plants were developed from F₂-F₅ progenies of A155 crossed with the susceptible wheat cultivar MY11 and characterized with ND-FISH using multiple probes. A high frequency of transmission of chromosome 2Ae was observed, and 31 types of 2Ae chromosomal aberrations were identified using ND-FISH. Ten chromosomal bins on the 2Ae chromosome were determined from the deletion and translocation lines based on genome-based PCR markers. In combination with the evaluation of disease resistance, the gene(s) for stripe rust resistance was located on the FL0.79-1.00 of 2AeS and covers the corresponding region of 0-58.26 Mb in the reference genome of Th. elongatum. The newly identified wheat-Th. ponticum 2Ae translocation lines can be exploited as potential germplasm in wheat breeding for stripe rust resistance.

Pod size is a key agronomic trait that influences peanut yield greatly. However, our understanding of the mechanisms underlying pod size is limited. In this study, we employed a segregating population derived from a cross between the small-pod line ND_S and the large-pod line ND_L to map quantitative trait loci (QTL) associated with pod size. Initial mapping performed using bulk segregant analysis revealed a candidate interval on chromosome A05 referred to as qPSW05. We refined this interval to a 256.9 kb genomic region using newly developed molecular markers. Through sequence and expression analyses, we identified the candidate gene AhXE45GC, which encodes an AN1 zinc finger protein. We discovered a 33-bp insertion in the intron of AhXE45GC in ND_S. Accessions that lack this insertion, such as ND_L, had significantly larger pods than those with the insertion, including ND_S. To facilitate marker-assisted selection for peanut pod size, we developed a molecular marker associated with this polymorphism. This marker could provide a valuable genetic resource for breeding high-yielding peanut varieties.

Maize stalk lignin and cellulose contents are linked to lodging resistance, disease resistance, feed quality and ethanol conversion efficiency. After the six-leaf stage of maize (V6), these constituents are biosynthesized and accumulated under the control of related enzymes and genes. However, the key enzymes, critical MYB transcription factors, and their dynamic alterations pattern under natural field circumstances are still unknown. Hence, we selected five cultivars with significant differences in lignocellulose content and lodging resistance as testing materials, performed field experiments for two years, and investigated the dynamics of lignin and cellulose content, related enzyme concentrations, and gene expression levels in the 3^rd and 5^th internodes above the ground after V6. The results showed that lignin and cellulose content increased after V6, stabilizing during the silking stage. This study identified COMT (caffeic acid 3-O-methyltransferase), TAL (tyrosine ammonia-lyase) and PAL (phenylalanine ammonia-lyase) as the key enzymes of lignin biosynthesis, while ZmCOMT, ZmCesA10 and ZmCesA8 were identified as essential genes. ZmMYB8, ZmMYB31 and ZmMYB39 were involved in regulating the expression of genes related to lignin synthesis, with ZmMYB31 potentially acting as a key negative regulator, while ZmMYB39 and ZmMYB8 acting as positive regulators. The study also found that around 14 d after V6 was a critical stage for regulating lignocellulose synthesis in the 3^rd to 5^th basal internode. This provides a theoretical foundation for developing regulatory techniques and breeding new cultivars to enhance lodging and disease resistance as well as the utility of maize stalks.

Drought stress at the booting stage causes severe floret degeneration and a decrease in grain number. Polyamines are involved in wheat floret development under drought stress, but the underlying physiological mechanisms are unclear. This study showed that drought-induced accumulation of reactive oxygen species led to wheat spikelet cell apoptosis and floret degeneration. Drought induced stomatal closure to reduce photosynthesis, then inhibited the activities of sucrose phosphate synthase, sucrose synthetase (cleavage direction) and ADP-glucose pyrophosphorylase in spikes and leaves, and soluble vacuolar invertase and cell wall invertase in spikes, thus providing a poor nutrient base for floret development. Exogenous spermidine application increased antioxidant enzyme activities and polyamine metabolism, promoted starch and sucrose metabolism, amino acid utilization and increased the levels of glycolytic and tricarboxylic acid cycle intermediates to mitigate oxidative damage and maintain energy homeostasis in the spike, thereby reducing floret degeneration and increasing grain number.

Light is one of the most important environmental factors for plant growth and development. In relay cropping systems, crop layouts influence light distribution, affecting light use efficiency (LUE). However, the response of light interception, light conversion, and LUE for relay maize and relay soybean to different crop layouts remains unclear. We aimed to quantify the effect of crop layout on intraspecific and interspecific competition, light interception, light conversion, LUE, and land productivity between relay maize and relay soybean. We conducted a field experiment for four consecutive years from 2017 to 2020 in Sichuan province, China, comparing different crop layouts (bandwidth 2.0?m, row ratio 2:2; bandwidth 2.4?m, row ratio 2:3; bandwidth 2.8?m, row ratio 2:4), with sole maize and sole soybean as controls. The results showed that relay maize in the 2.0 m bandwidth layout had the largest leaf area index and plant biomass, the lowest intraspecific competitive intensity and the highest aggressiveness. Compared to a bandwidth of 2.0 m, a bandwidth of 2.8 m significantly decreased relay maize leaf area index by 11% and plant biomass by 24%, while a 2.4 m bandwidth caused roughly half these reductions. The 2.0 m bandwidth layout also significantly improved crop light interception and LUE compared to sole maize. The light interception, light interception rate, light conversion rate and LUE in relay maize all decreased significantly with increasing bandwidth, but they increased in relay soybean. The increased light transmittance to the lower and middle canopy with increasing bandwidth did not compensate for the loss of relay maize yield caused by increased intraspecific competition. However, it enhanced the yield of relay soybeans. Increasing the bandwidth by 80 cm increased the relay maize intraspecific competition by 580%, and reduced maize yield by 33%, light interception by 12%, and LUE by 18%. In contrast, the relay soybean intraspecific competition was reduced by 64%, and the soybean yield was increased by 26%, light interception by 32% and LUE by 46%. Relay cropping systems with a 2.0 m bandwidth optimize the trade-off between light transmittance and intraspecific competition of relay crops. These systems achieve the highest LUE, group yield and economic benefits, making them a recommended crop layout for the southwest regions of China. Our study offers valuable insights for developing strip relay cropping systems that maximize light utilization and contributes to the theoretical understanding of efficient sunlight use in relay cropping practices.

This study quantified climate effects on wheat yield heterogeneity in the North China Plain from 1960 to 2020, by integrating the Agricultural Production Systems sIMulator, Optimal Parameters-based Geographical Detector model, and Ensemble Empirical Mode Decomposition model. The factors dominating yield heterogeneity varied by growth stage. For sowing to anthesis, anthesis to maturation, and the entire growth season, minimum temperature, radiation, and vapor pressure deficit has the greatest effect on yield heterogeneity. Interannual periodic oscillations govern the long-term evolution of climate effects on yield heterogeneity from 1960 to 2020.

We have developed a dual base editor, rA&GBE, by fusing adenine and glycosylase base editors. It can induce up to eight types of mutations in T₀-generation rice, including single-base conversion, simultaneous multiple-base conversions, and InDels, using a single guide RNA. A-to-G and C-to-G/T conversions occur simultaneously on the same DNA strand. The rA&GBE system may prove useful for crop improvement and in planta direct evolution.

Amylose content, the key determinant of rice eating and cooking quality, is regulated primarily by the Waxy (Wx) gene. We adjusted the amylose content and transparency of semi-glutinous japonica rice carrying the Wx^mp allele by genome editing of upstream open reading frame 6 (uORF6) of Wx.

Accurate prediction of future rice yield needs the precise estimations of rice yield response to climate change factors, of which the most important one is the increasing carbon dioxide (CO₂) concentrations. Estimates of CO₂ fertilization effect (CFE) on rice, however, still had large uncertainties. Therefore, using the rice planting areas in East China as the study area, we firstly compared the rice yields and CFE predicted by four state-of-the-art crop models, and found that the CFE predicted by these models had significant differences. We then quantified the CFE on rice yield using the field-controlled experiment conducted at Danyang site at Jiangsu province. Using CFE measurements from a field experiment as benchmark, we have developed an experiment-model integration approach aiming to reduce this variation. This study thus highlights the large CFE uncertainties of current crop models and provides us with a method to reduce this uncertainty, which is beneficial for the accurate prediction of future global rice yield in the context of climate change.