Hormone perception and signaling pathways play a fundamental regulatory function in the physiological processes of plants. Cytokinins, plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well-established in model plant Arabidopsis. Several negative feedback mechanisms, tightly controlling the cytokinin signaling output, were described previously. Here, we identified a new feedback mechanism executed through an alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1 results from seventh intron retention, introducing a premature termination codon in the transcript. We show that CRE1 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. The CRE1 can bind the cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway facilitated by a decoy receptor, which can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. While a similar molecular mechanism is well-known in mammals, decoy receptors are rare in plants. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. The CRE1 represents a yet unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.

The WA-type CMS in rice is widely used in Asia for its stability and adaptability. Li Li's team found that the Rf20 gene enhances the fertility restoration of Rf4. It is recommended to introduce the H3 haplotype of the Rf20 gene into indica or Basmati rice, and high-temperature fertility issues in CMS-WA can be addressed through Rf20 gene editing.

As well as being a popular vegetable crop worldwide, waxy corn represents an important amylopectin source. However, little is known about the breeding history and flavor characteristics of this crop. In this study, comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines revealed that many metabolic pathways and genes exhibited characteristics of selection during the breeding history of waxy corn, contributing to the divergence between waxy and field corn. We show that waxy corn is not only altered in its glutinous property, but that sweetness, aroma, and palatability are all significantly affected. A substantial proportion (43%) of flavor-related metabolites have pleiotropic effects, impacting both flavor and yield characteristics and 27% of these metabolites are related to antagonistic outcomes on yield and flavor. Furthermore, we demonstrated, through multiple concrete examples, how yield and quality are coordinately or antagonistically regulated at the genetic level. In particular, we identified some sweet molecules such as DIMBOA and raffinose, that do not participate in the starch biosynthesis pathway, as potential targets for breeding a new type of "sweet-waxy" corn. Our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor, thereby collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.

Aromatic rice is globally favored for its distinctive scent, not only increasing nutritional value but also enhancing economic importance. However, apart from 2-acetyl-1-pyrroline (2-AP), the metabolic basis of aroma remains elusive, and the genetic underlying of the accumulation of fragrance metabolites are largely unknown. Here, we revealed 2-AP and fatty acid-derived volatile metabolites (FAVs) as key contributors to rice aroma by combining aroma rating with molecular docking. Using volatilome-based GWAS, we identified two regulatory genes that determine the natural variation of these fragrance metabolites. We demonstrated that OsWRKY19 not only enhances fragrance by negatively regulating OsBADH2 but also promotes agricultural traits in rice. Additionally, we revealed OsNAC021 that negatively regulates FAVs through the LOX pathway, and the knockout of it resulted in the over-accumulation of grain FAVs without a yield penalty. Our findings provide a compelling example of deciphering the genetic regulatory mechanisms underlying rice fragrance and pave the way for the creation of aromatic rice varieties.

Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco's CO fixation. Yet, hornwort Rubisco remains poorly characterized. Here we assemble the hornwort Anthoceros agrestis Rubisco (AaRubisco) using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates, prompting us to develop a new SynBio system with A. agrestis cognate chaperones. We successfully assembled AaRubisco and Rubisco from three other hornwort species. Unlike A. thaliana Rubisco, AaRubisco assembly is not dependent on RbcX or Raf2. Kinetic characterization reveals that hornwort Rubiscos exhibit a range of catalytic rates (3-10 s), but with similar affinity (∼30 μM) and specificity (∼70) for CO. In other words, hornwort Rubiscos do not comply with the long held canonical catalytic trade-off observed in other land plants, providing experimental support that Rubisco kinetics may be phylogenetically constrained. Unexpectedly, we observed a 50% increase in AaRubisco catalytic rates when RbcX was removed from our SynBio system, without any reduction in specificity. Structural biology, biochemistry and proteomic analysis suggest that subtle differences in Rubisco large subunit interactions, when RbcX is absent during biogenesis, increases the accessibility of active sites and catalytic turnover rate. This study uncovered a previously unknown Rubisco kinetic parameter space and provides a SynBio chassis to expand the survey of other Rubisco kinetics. Our discovery could thus reshape the approaches for engineering Rubisco with superior kinetics.

The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore Technologies (ONT), which offers ultra-long, real-time sequencing. Despite its promise, sequencing length and gap filling remain significant challenges. This study optimized DNA extraction and library preparation, achieving DNA lengths exceeding 485 kb; average N50 read lengths of 80.57 kb, reaching up to 440 kb; and maximum reads of 5.83 Mb. Importantly, we demonstrated that combining ultra-long sequencing and adaptive sampling can effectively fill gaps during assembly, evidenced by successfully filling the remaining gaps of a near-complete Arabidopsis genome assembly and resolving the sequence of an unknown telomeric region in watermelon genome. Collectively, our strategies improve the feasibility of complete T2T genomic assemblies across various plant species, enhancing genome-based research in diverse fields.

Bioactive compounds play an increasingly prominent role in breeding functional and nutritive fruit crops such as citrus. However, the genomic and metabolic bases for the selection and differentiation underlying bioactive compound variations in citrus remain poorly understood. In this study, we constructed a species-level variation atlas of genomes and metabolomes using 299 citrus accessions. A total of 19 829 significant SNPs were targeted to 653 annotated metabolites, among which multiple significant signals were identified for secondary metabolites, especially flavonoids. Significant differential accumulation of bioactive compounds in the phenylpropane pathway, mainly flavonoids and coumarins, was unveiled across ancestral citrus species during differentiation, which is likely associated with the divergent haplotype distribution and/or expression profiles of relevant genes, including p-coumaroyl coenzyme A 2'-hydroxylases, flavone synthases, cytochrome P450 enzymes, prenyltransferases, and uridine diphosphate glycosyltransferases. Moreover, we systematically evaluated the beneficial bioactivities such as the antioxidant and anticancer capacities of 219 citrus varieties, and identified robust associations between distinct bioactivities and specific metabolites. Collectively, these findings provide citrus breeding options for enrichment of beneficial flavonoids and avoidance of potential risk of coumarins. Our study will accelerate the application of genomic and metabolic engineering strategies in developing modern healthy citrus cultivars.

Heat stress poses a significant threat to grain yield. Our previous study identified TT1, which encodes an α2 subunit of the 26S proteasome, as a critical regulator for rice heat tolerance, representing the first cloned QTL for crop heat tolerance. However, the mechanisms mediated by TT1 still remained elusive. In this study, we unveil SUMO-conjugating enzyme 1 (SCE1), which interacts with TT1 and acts as a downstream component of TT1, engaging in the TT1-mediated 26S proteasome degradation. SCE1 functions as a negative regulator of heat tolerance and can be linked to ubiquitination modification. Additionally, we observed that sHSPs such as Hsp24.1 and Hsp40 can undergo SUMOylation mediated by SCE1, leading to increased accumulation of sHSPs in the absence of SCE1. Furthermore, we propose that the global SUMOylation modulated by SCE1 serves as a crucial signal in response to heat stress, and the rapid decline in elevated SUMOylation is considered a positive effect to enhance heat tolerance due to the loss of SCE1 gene function. Reducing protein levels of SCE1 significantly enhanced grain yield under high-temperature stress by improving seed-setting rate and rice grain filling capacity. Our results uncover the critical role of SCE1 in TT1-mediated heat tolerance pathway, regulating the abundance of sHSP proteins and SUMOylation, and ultimately impacting rice heat tolerance. These findings underscore the significant potential of the TT1-SCE1 module in improving the heat tolerance of crops.

Leaf senescence plays a critical role in a plant's overall reproductive success due to its involvement in nutrient remobilization and allocation. However, our current understanding of the molecular mechanisms controlling leaf senescence remains limited. In this study, we demonstrate that the receptor-like kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) functions as a negative regulator of leaf senescence. We report that the SERINE-RICH ENDOGENOUS PEPTIDE 12, previously known to physically interact with MIK2, competes with SCOOP10 to control MIK2-dependent senescence regulatory mechanisms. We observed that increased expression of SCOOP10 or the application of exogenous SCOOP10 peptides accelerated leaf senescence in a MIK2-dependent manner. Conversely, SCOOP12 acted as a suppressor of MIK2-dependent senescence regulation. We also found that SCOOP12 enhanced while SCOOP10 diminished MIK2 phosphorylation. Thus, the SCOOP12-MIK2 module might function antagonistically on SCOOP10-MIK2 signaling at late senescing stages, allowing for fine-tuned modulation of the leaf senescence process. Our research sheds light on the complex mechanisms underlying leaf senescence and provides valuable insights into the interplay between receptors, peptides, and the regulation of plant senescence.

The plasticity of stem cells in response to environmental change is critical for multicellular organisms. Here, we show that MYB3R-like directly activates the key plant stem cell regulator WUSCHEL (WUS) by recruiting the methyltransferase ROOT INITIATION DEFECTIVE 2 (RID2), which functions in m7G methylation at the 5' cap of WUS mRNA to protect it from degradation. We demonstrated that protein-folding genes are repressed by WUS to maintain precise protein synthesis in stem cells by preventing the reuse of misfolded proteins. However, upon heat stress, the MYB3R-like/RID2 module is repressed to reduce WUS transcripts via the decapping of nascent WUS mRNA. This releases the inhibition of protein folding capacity in stem cells and protects plant stem cells from heat-shock by eliminating misfolded protein aggregation. Our results reveal a tradeoff strategy in plants by reducing the accuracy of protein synthesis in exchange for the survival of stem cells at high temperatures.

Pattern recognition receptors (PRRs) are integral to plant immunity, functioning as the first line of defense against pathogens. Among these, receptor kinases (RKs) play a critical role in recognizing external signals and initiating immune responses. Recent studies by Li et al. (2024) have identified the G-type lectin receptor kinase ZmLecRK1 in maize as essential for resistance to Pythium aphanidermatum and other fungal pathogens. A key finding is that a resistant variant of ZmLecRK1, which carries an alanine at position 404, has emerged in maize, while the ancestral form, with a serine at this position, is conserved across most grasses. This amino acid substitution significantly influences the interaction with the co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1 (BAK1), enhancing immune complex formation and subsequent defense signaling. This work underscores the importance of genetic variation in enhancing disease resistance, offering potential strategies for crop improvement through targeted genetic modification.