Trehalose (Tre) is a non-reducing disaccharide found in many species, including bacteria, fungi, invertebrates, yeast, and even plants, where it acts as an osmoprotectant, energy source, or protein/membrane protector. Despite relatively small amounts in plants, Tre concentrations increase following exposure to abiotic stressors. Trehalose-6-phosphate, a precursor of Tre, has regulatory functions in sugar metabolism, crop production, and stress tolerance. Among the various abiotic stresses, temperature extremes (heat or cold stress) are anticipated to impact crop production worldwide due to ongoing climate changes. Applying small amounts of Tre can mitigate negative physiological, metabolic, and molecular responses triggered by temperature stress. Trehalose also interacts with other sugars, osmoprotectants, amino acids, and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation. Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance. Genome-wide studies of Tre-encoding genes suggest roles in plant growth, development, and stress tolerance. This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism, crosstalk, and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species. We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

Plant height (PH) is associated with lodging resistance and planting density, which is regulated by a complicated gene network. In this study, we identified a spontaneous dwarfing mutation in maize, m30, with decreased internode number and length but increased internode diameter. A candidate gene, ZmCYP90D1, which encodes a member of the cytochrome P450 family, was isolated by map-based cloning. ZmCYP90D1 was constitutively expressed and showed highest expression in basal internodes, and its protein was targeted to the nucleus. A G-to-A substitution was identified to be the causal mutation, which resulted in a truncated protein in m30. Loss of function of ZmCYP90D1 changed expression of hormone-responsive genes, in particular brassinosteroid (BR)-responsive genes which is mainly involved in cell cycle regulation and cell wall extension and modification in plants. The concentration of typhasterol (TY), a downstream intermediate of ZmCYP90D1 in the BR pathway, was reduced. A haplotype conferring dwarfing without reducing yield was identified. ZmCYP90D1 was inferred to influence plant height and stalk diameter via hormone-mediated cell division and cell growth via the BR pathway.

Gibberellic acid (GA), a ubiquitous phytohormone, has various effects on regulators of plant growth and development. GAs promote growth by overcoming growth restraint mediated by DELLA proteins (DELLAs). DELLAs, in the GRAS family of plant-specific nuclear proteins, are nuclear transcriptional regulators harboring a unique N-terminal GA perception region for binding the GA receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) and a C-terminal GRAS domain necessary for GA repression activity via interaction with multiple regulatory proteins. The N-terminal conserved region of DELLAs evolved to form a mode of GID1/DELLA-mediated GA signaling originating in bryophytes and ferns. Binding of GA to GID1 increases the affinity between DELLAs and a SCF E3 ubiquitin-ligase complex, thus promoting the eventual destruction of DELLAs by the 26S proteasome. DELLAs negatively regulate GA response by releasing transcription factors to directly activate downstream genes and indirectly regulate GA biosynthesis genes increasing GA responsiveness and feedback control by promoting GID1 transcription. GA communicates extensively with other plant hormones and uses crosstalk to regulate plant growth and development. In this review, we summarize current understanding of evolutionary DELLA-mediated gibberellin signaling and functional diversification of DELLA, focusing primarily on interactions of DELLAs with diverse phytohormones.

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.

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.

Global crop productivity faces a significant threat from climate change-induced drought stress (DS), which is vital for sustainable agriculture and global food security. Uncovering DS adaptation and tolerance mechanisms in crops is necessary to alleviate climate challenges. Innovative plant breeding demands revolutionary approaches to develop stress-smart plants. Metabolomics, a promising field in plant breeding, offers a predictive tool to identify metabolic markers associated with plant performance under DS, enabling accelerated crop improvement. Central to DS adaptation is metabolomics-driven metabolic regulation, which is critical for maintaining cell osmotic potential in crops. Recent innovations allow rapid mapping of specific metabolites to their genetic pathways, providing a valuable resource for plant scientists. Metabolomics-driven molecular breeding, integrating techniques such as mQTL and mGWAS, enhances our ability to discover key genetic elements linked to stress-responsive metabolites. This integration offers a beneficial platform for plant scientists, yielding significant insights into the complex metabolic networks underlying DS tolerance. Therefore, this review discusses (1) insights into metabolic regulation for DS adaptation, (2) the multifaceted role of metabolites in DS tolerance and nutritional/yield trait improvement, (3) the potential of single-cell metabolomics and imaging, (4) metabolomics-driven molecular breeding, and (5) the application of metabolic and genetic engineering for DS-tolerant crops. We finally propose that the metabolomics-driven approach positions drought-smart crops as key contributors to future food production, supporting the vital goal of achieving “zero hunger”.

Shade tolerance is essential for soybeans in inter/relay cropping systems. A genome-wide association study (GWAS) integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance. An improved GWAS procedure, restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers (GASM-RTM-GWAS), identified 140 genes and their alleles associated with shade-tolerance index (STI), 146 with relative pith cell length (RCL), and nine with both. Annotation of these genes by biological categories allowed the construction of a protein-protein interaction network by 187 genes, of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages. From the identified genes, three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network. Altogether, both STI and RCL gene systems worked for shade-tolerance with genes interacted each other, this confirmed that shade-tolerance is regulated by more than single group of interacted genes, involving multiple biological functions as a gene network.

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.

Transcription factors (TFs) play essential roles in transcriptional reprogramming during activation of plant immune responses to pathogens. OsSPL10 (SQUAMOSA promoter binding protein-like10) is an important TF regulating trichome development and salt tolerance in rice. Here we report that knockout of OsSPL10 reduces whereas its overexpression enhances rice resistance to blast disease. OsSPL10 positively regulates chitin-induced immune responses including reactive oxygen species (ROS) burst and callose deposition. We show that OsSPL10 physically associates with OsJAmyb, an important TF involved in jasmonic acid (JA) signaling, and positively regulates its protein stability. We then prove that OsJAmyb positively regulates resistance to blast. Our results reveal a molecular module consisting of OsSPL10 and OsJAmyb that positively regulates blast resistance.

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.

Foxtail millet (Setaria italica) is an important crop and an emerging model plant. Photoperiodic flowering is a key determinant of its production and geographic expansion. In this study, we found that SiPRR37 is responsible for the major quantitative trait locus (QTL) Heading date 2 (Hd2) identified in 680 foxtail millets using a genome-wide association study. Overexpression of SiPRR37 in foxtail millet significantly delayed the heading date under both natural long-day and short-day conditions. CRISPR/Cas9-induced Siprr37 mutants exhibited earlier flowering in long-day conditions but later flowering in short-day conditions. The critical day length (CDL) for the reversal of Siprr37’s function was around 14.3 h. Haplotype analysis revealed that accessions with the Tc1-Mariner transposon insertion in SiPRR37 (Hap 1) flowered significantly earlier at higher latitudes, and later at lower latitudes, indicating that natural variants of SiPRR37 exert dual functions in flowering regulation according to geographic latitude. The gradual, successive decrease in the frequency of Hap 2 from low to high latitudes, with the concurrent increase of Hap 1, demonstrates that these haplotypes have undergone artificial selection. Further F_ST analysis demonstrated that SiPRR37 has contributed to the ecological adaption of foxtail millet. Additionally, we reveal that OsPRR37 promotes flowering in rice, while GmPRR37 may only inhibit flowering in soybean. Further diurnal expression and transgenic analyses suggest that the dual function of SiPRR37 might depend on SiHd1. Our study uncovered the distinct functional reversal of SiPRR37 and functional diversification of PRR37 homologs in SD crops. These findings not only enrich knowledge about the regulation of photoperiodic flowering, but also contribute to genetic improvement of crops’ regional adaptability.

The size and shape of rice grains influence their yield and commercial value. We investigated the role of OsDA1, a rice homolog of the Arabidopsis DA1 gene, in regulating grain size and shape. OsDA1 was highly expressed in young spikelets and glumes. Its overexpression led to enlarged seeds with increased width and decreased length/width ratio (LWR) and knocking out OsDA1 reduced grain width and increased grain length and LWR. A R310K point mutation in the DA1-like domain is a potential target for breeding for increased grain width and length. OsDA1 interacted with TCP gene-family proteins to regulate grain size and shape. Our findings deepen our understanding of the molecular mechanisms underlying grain size regulation and provide useful information for improving grain yield.

Some haplotypes of the sucrose synthase gene TaSus1 are associated with thousand-grain weight (TGW) in wheat (Triticum aestivum L.). However, no mutations have been identified within the gene to test this association. The effects of TaSus1 on grain number per spike (GNS) also are largely unknown. Our previous genome-wide association study identified TaSus-A1 as a candidate gene controlling fertile spikelet number per spike (FSN). In the present study, we generated two independent mutants for the three TaSus1 homoeologs by CRISPR/Cas9-mediated genome editing. The triple mutants displayed lower FSN, GNS, grain number per spikelet (GNST), and TGW than wild-type plants. In 306 hexaploid wheat accessions, two single-nucleotide polymorphisms in TaSus-A1 contributed differently to GNS. Introgression of the two alleles into a wheat genetic background confirmed their effects. The alleles differed in geographical distribution among the accessions.

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart, irrigated rice. Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations. A nonsynonymous mutation (C to T, from irrigated to upland rice) may have led to functional variation fixed by artificial selection, but the exact biological function in dryland adaptation is unclear. In this study, transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2, increasing ABA levels, root development, and drought tolerance in upland rice under dryland conditions. OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance. OsNCED2^T-NILs showed a denser root system and drought resistance, promoting the yield of rice under dryland conditions. OsNCED2^T may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted, water-saving rice.

Receptor-like cytoplasmic kinase OsBSK1-2 was reported to play an important role in regulation of response to rice blast, but the signaling pathway remained unknown. In this study, we identified OsMAPKKK18 and previously uncharacterized MAPKKKs OsMAPKKK16 and OsMAPKKK19 that interact with OsBSK1-2. Expression of all three MAPKKKs was induced by Magnaporthe oryzae infection, and all three induced cell death when transiently expressed in Nicotiana benthamiana leaves. Knockout of OsMAPKKK16 and OsMAPKKK18 compromised blast resistance and overexpression of OsMAPKKK19 increased blast resistance, indicating that all three MAPKKKs are involved in regulation of rice blast response. Furthermore, both OsMAPKKK16 and OsMAPKKK19 interacted with and phosphorylated OsMKK4 and OsMKK5, and chitin-induced MAPK activation was suppressed in osmapkkk16 and osbsk1-2 mutants. OsMAPKKK18 was earlier reported to interact with and phosphorylate OsMKK4 and affect chitin-induced MAPK activation, suggesting that OsBSK1-2 is involved in regulation of immunity through multiple MAPK signaling pathways. Unlike BSK1 in Arabidopsis, OsBSK1-2 was not involved in response to avirulent M. oryzae strains. Taken together, our results revealed important roles of OsMAPKKK16/18/19 and a OsBSK1-2-OsMAPKKK16/18/19-OsMKK4/5 module in regulating response to rice blast.

Precise timing of flowering in plants is critical for their growth and reproductive processes. One factor controlling flowering time is the cycle of light and darkness within a day, known as the photoperiod. Plants are classified into long-day, short-day, and day-neutral plants based on light requirements for floral initiation. Although the molecular mechanisms that govern this differentiation remain incompletely understood, studies have consistently shown that the circadian clock plays a central role in regulating photoperiod response across diverse plant species. However, there is a scarcity of reviews describing the regulatory network linking the circadian clock with photoperiodic flowering. This review summarizes that regulatory network, focusing on the distinct roles of clock genes in long-day and short-day plants. We also discuss the strategies of clock gene mutations contributing to geographic variation in long-day and short-day crops.

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field conditions. Here we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deep-sowing conditions by increasing shoot length. Expression of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing conditions. Levels of free abscisic acid (ABA) and jasmonates (JA) were higher in shoots of OsUGT75A mutants than in those of wild-type plants, and OsUGT75A mutants were more sensitive to ABA and JA treatments. Reduced shoot length was attributed to higher ABA INSENSITIVE 3 (OsABI3) expression and lower JASMONATE-ZIM domain protein (OsJAZ) expression in shoots. Shoot extension by OsUGT75A is achieved mainly by promotion of cell elongation. An elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice accessions. OsUGT75A acts to increase seedling emergence under deep-sowing conditions.

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.

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.

Drought stress limits agricultural productivity worldwide. Identifying and characterizing genetic components of drought stress-tolerance networks may improve crop resistance to drought stress. We show that the regulatory module formed by miR166 and its target gene, ATHB14-LIKE, functions in the regulation of drought tolerance in soybean (Glycine max). Drought stress represses the accumulation of miR166, leading to upregulation of its target genes. Optimal knockdown of miR166 in the stable transgenic line GmSTTM166 conferred drought tolerance without affecting yield. Expression of ABA signaling pathway genes was regulated by the miR166-mediated regulatory pathway, and ATHB14-LIKE directly activates some of these genes. There is a feedback regulation between ATHB14-LIKE and MIR166 genes, and ATHB14-LIKE inhibits MIR166 expression. These findings reveal that drought-triggered regulation of the miR166-mediated regulatory pathway increases plants drought resistance, providing new insights into drought stress regulatory network in soybean.

The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4-6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein-protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.

Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

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.

Nitrogen (N) fertilization is necessary for obtaining high rice yield. But excessive N fertilizer reduces rice plant N efficiency and causes negative effects such as environmental pollution. In this study, we assembled key genes involved in different nodes of N pathways to boost nitrate and ammonium uptake and assimilation, and to strengthen amino acid utilization to increase grain yield and nitrogen use efficiency (NUE) in rice. The combinations OsNPF8.9a × OsNR2, OsAMT1;2 × OsGS1;2 × OsAS1, and OsGS2 × OsAS2 × OsANT3 optimized nitrate assimilation, ammonium conversion, and N reutilization, respectively. In co-overexpressing rice lines obtained by co-transformation, the tiller number, biomass, and grain yield per plant of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of wild-type ZH11, the OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line, and the OsGS2 × OsAS2 × OsANT3-overexpressing line. The glutamine synthase activity, free amino acids, and nitrogen utilization efficiency (NUtE) of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of ZH11 and other lines that combined key genes. N influx efficiency was increased in the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line and OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line under a low ammonium and a low nitrate treatment, respectively. We propose that combining overexpression of OsAMT1;2, OsGS1;2, and OsAS1 is a promising breeding strategy for systematically increasing rice grain yield and NUE by focusing on key nodes in the N pathway.

Plant height and grain size are the most important factors determining rice yield. Here, in the rice mutant small plant and organ size1 (spos1) with reduced plant height and small grain, T-DNA insertion revealed that the mutant phenotype was caused by increased expression of of OsSAUR23 and OsRR9, which participate in auxin and cytokinin signal transduction, respectively. Knock out of OsSAUR23 increased rice grain size but did not change plant height. Double knock out of OsRR9 and its replicated gene OsRR10 also brought similar effects on rice as that of OsSAUR23 knock-out. Genetic analysis suggested that OsSAUR23 was a major recessive gene and OsRR9 was a minor dominant gene, which co-regulated the phenotype of spos1. Compared with wild type, auxin synthesis and signaling, cytokinin homeostasis and signaling, as well as GA, ABA and BR metabolism and signaling were regulated in seedlings of spos1. The increased concentrations of IAA and cytokinins in the mutant suggest hormonal co-regulation of rice organ size.

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.

The study of yield traits can reveal the genetic architecture of grain yield for improving maize production. In this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap (HPO) genes, which are genes prioritized in a genome-wide association study (GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic QTL. Seven SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield traits. Among the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.

A dynamic plant architecture is the basis of plant adaptation to changing environments. Although many genes regulating leaf rolling have been identified, genes directly associated with water homeostasis are largely unknown. Here, we isolated a rice mutant, dynamic leaf rolling 1 (dlr1), characterized by ‘leaf unfolding in the morning-leaf rolling at noon-leaf unfolding in the evening’ during a sunny day. Water content was decreased in rolled leaves and water sprayed on leaves caused reopening, indicating that in vivo water deficiency induced the leaf rolling. Map-based cloning and expression tests demonstrated that an A1400G single base mutation in Oryza sativa Polygalacturonase 1 (OsPG1)/PHOTO-SENSITIVE LEAF ROLLING 1 (PSL1) was responsible for the dynamic leaf rolling phenotype in the dlr1 mutant. OsPG1 encodes a polygalacturonase, one of the main enzymes that degrade demethylesterified homogalacturonans in plant cell walls. OsPG1 was constitutively expressed in various tissues and was enriched in stomata. Mutants of the OsPG1 gene exhibited defects in stomatal closure and decreased stomatal density, leading to reduced transpiration and excessive water loss under specific conditions, but had normal root development. Further analysis revealed that mutation of OsPG1 led to reduced pectinase activity in the leaves and increased demethylesterified homogalacturonans in guard cells. Our findings reveal a mechanism by which OsPG1 modulates water homeostasis to control dynamic leaf rolling, providing insights for plants to adapt to environmental variation.

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.

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.

In flowering plants, the inflorescence meristem (IM) provides founder cells to form successive floral meristems, which are precursors of fruits and seeds. The activity and developmental progression of IM are thus critical for yield production in seed crops. In some cereals, such as rice (Oryza sativa) and maize (Zea mays), the size of undifferentiated IM, which is located at the inflorescence apex, is positively associated with yield traits such as spikelet number. However, the relationship between IM size and yield-related spike traits remains unknown in the Triticeae tribe. Here we report that IM size has a negative correlation with yield traits in barley (Hordeum vulgare). Three FASCIATED EAR (FEA) orthologs, HvFEA2, HvFEA3, and HvFEA4, regulate IM size and spike morphogenesis and ultimately affect yield traits. Three HvFEAs genes are highly expressed in developing spikes, and all three loss-of-function mutants exhibit enlarged IM size, shortened spikes, and reduced spikelet number, which may lead to reduced grain yield. Natural variations identified in HvFEAs indicate selection events during barley domestication. We further reveal that HvFEA4, as a transcription factor, potentially targets multiple pathways during reproductive development, including transcriptional control, phytohormone signaling, and redox status. The roles of barley FEA genes in limiting IM size and promoting spikelet formation suggest the potential of increasing yield by manipulating IM activity.

Salinity impairs plant growth, limiting agricultural development. It is desirable to identify genes responding to salt stress and their mechanism of action. We identified a function of the Zea mays WRKY transcription factor, ZmWRKY104, in salt stress response. ZmWRKY104 was localized in the nucleus and showed transcriptional activation activity. Phenotypic and physiological analysis showed that overexpression of ZmWRKY104 in maize increased the tolerance of maize to salt stress and alleviated salt-induced increases in O₂^- accumulation, malondialdehyde (MDA) content, and percent of electrolyte leakage. Further investigation showed that ZmWRKY104 increased SOD activity by regulating ZmSOD4 expression. Yeast one-hybrid, electrophoretic mobility shift test, and chromatin immunoprecipitation-quantitative PCR assay showed that ZmWRKY104 bound directly to the promoter of ZmSOD4 by recognizing the W-box motif in vivo and in vitro. Phenotypic, physiological, and biochemical analysis showed that ZmSOD4 increased salt tolerance by alleviating salt-induced increases in O₂^- accumulation, MDA content, and percent of electrolyte leakage under salt stress. Taken together, our results indicate that ZmWRKY104 positively regulates ZmSOD4 expression to modulate salt-induced O₂^- accumulation, MDA content, and percent of electrolyte leakage, thus affecting salt stress response in maize.

Rice grain yield is determined by three major “visible” morphological traits: grain weight, grain number per panicle, and effective tiller number, which are affected by a series of “invisible” physiological factors including nutrient use efficiency and photosynthetic efficiency. In the past few decades, substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation, laying a solid foundation for improving rice yield by molecular breeding. This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency. It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

Mitochondrial protein translation that is essential for aerobic energy production includes four essential steps of the mitochondrial ribosome cycle, namely, initiation, elongation, termination of the polypeptide, and ribosome recycling. Translation termination initiates when a stop codon enters the A site of the mitochondrial ribosome where it is recognized by a dedicated peptide release factor (RF). However, RFs and mechanisms involved in translation in plant mitochondria, especially in monocotyledons, remain largely unknown. Here, we identified a crumpled kernel (crk5 allele) mutant, with significantly decreased kernel size, 100-kernel weight, and an embryo-lethal phenotype. The Crk5 allele was isolated using map-based cloning and found to encode a mitochondrial localization RF2a. As it is an ortholog of Arabidopsis mitochondrial RF2a, we named the gene ZmmtRF2a. ZmmtRF2a is missing the 5th-7th exons in the crk5 resulting in deletion of domains containing motifs GGQ and SPF that are essential for release activity of RF, mitochondrial ribosome binding, and stop codon recognition. Western blot and qRT-PCR analyses indicate that the crk5 mutation results in abnormal mitochondrion structure and function. Intriguingly, we observed a feedback loop in the crk5 with up-regulated transcript levels detected for several mitochondrial ribosome and mitochondrial-related components, in particular mitochondrial complexes CI, CIV, and a ribosome assembly related PPR. Together, our data support a crucial role for ZmmtRF2a in regulation of mitochondrial structure and function in maize.

Plants adaptively change their cell wall composition and structure during their growth, development, and interactions with environmental stresses. Dirigent proteins (DIRs) contribute to environmental adaptations by dynamically reorganizing the cell wall and/or by generating defense compounds. A maize DIR, ZmDRR206, was previously reported to play a dominant role in regulation of storage nutrient accumulation in endosperm during maize kernel development. Here we show that ZmDRR206 mediates maize seedling growth and disease resistance by coordinately regulating biosynthesis of cell wall components for cell-wall integrity (CWI) maintenance. Expression of ZmDRR206 was induced in maize seedlings upon pathogen infection. ZmDRR206 overexpression in maize resulted in reduced seedling growth and photosynthetic activity but increased disease resistance and drought tolerance, revealing a tradeoff between growth and defense. Consistently, ZmDRR206 overexpression reduced the contents of primary metabolites and down-regulated genes involved in photosynthesis, while increasing the contents of major cell wall components, defense phytohormones, and defense metabolites, and up-regulated genes involved in defense and cell-wall biosynthesis in seedlings. ZmDRR206-overexpressing seedlings were resistant to cell-wall stress imposed by isoxaben, and ZmDRR206 physically interacted with ZmCesA10, which is a cellulose synthase unit. Our findings suggest a mechanism by which ZmDRR206 coordinately regulates biosynthesis of cell-wall components for CWI maintenance during maize seedling growth, and might be exploited for breeding strong disease resistance in maize.

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.