Global crotonylatome and GWAS revealed a TaSRT1-TaPGK model regulating wheat cold tolerance through mediating pyruvate

Natural variation of CsUGT71A60 determines growth and cold tolerance via regulating cytokinin glycosylation in Camellia sinensis

Cold stress severely limits tea plant (Camellia sinensis) productivity, yet the molecular mechanisms underlying cold adaptation remain elusive. Here, we identified a cold-inducible glycosyltransferase, CsUGT71A60, through integrative genome-wide association studies (GWAS) and proteomic profiling. Natural variation in CsUGT71A60 was strongly associated with cold tolerance, as evidenced by linkage disequilibrium analysis of flanking SNPs. Functional characterization revealed that CsUGT71A60 specifically catalyses the glycosylation of cis-zeatin to form cis-zeatin 9-O-glucoside in vitro and in vivo. Overexpression of CsUGT71A60 in Arabidopsis enhanced cold tolerance and agronomic traits, including germination rate, tiller number and seed weight, while delaying flowering. Transient silencing of CsUGT71A60 in tea plants disrupted cis-zeatin homoeostasis, impairing antioxidant defences and osmotic regulation under cold stress. Mechanistically, the transcription factor ARR (TEA021099) directly binds to CRM elements in the CsUGT71A60 promoter, activating its expression to fine-tune cytokinin signalling. This study unveils a dual-function glycosyltransferase that orchestrates stress tolerance and developmental plasticity, offering a strategic target for breeding climate-tolerance crops without yield penalties.

GlSIRT1 deacetylates and activates pyruvate kinase to improve pyruvate content and enhance heat stress resistance in Ganoderma lucidum

Heat stress is a prevalent environmental stressor. Previous studies have shown that heat stress drives many cellular changes in Ganoderma lucidum. Interestingly, glycolysis is activated during heat stress, which could contribute to increased heat resistance. However, the molecular mechanisms underlying the enhanced heat resistance of G. lucidum following heat exposure are not yet fully understood. In this study, we explored the possibility that acetylation modification plays a significant role in responses to abiotic stress. After heat treatment, an enhanced interaction between the deacetylase GlSIRT1 and pyruvate kinase (PK) was observed, and the acetylation level of PK was decreased. Further studies revealed that GlSIRT1 increases PK activity through deacetylation, thereby increasing pyruvate content. Consistent with these findings, both PK activity and pyruvate content were reduced in GlSIRT1 knockdown strains, which exhibited greater sensitivity to heat stress compared to the wild-type (WT) strain. Collectively, our results reveal a novel molecular mechanism by which heat treatment increases pyruvate content.

Genetically encoding ε-N-methacryllysine into proteins in live cells

Lysine acylation is a ubiquitous post-translational modification (PTM) that plays pivotal roles in various cellular processes, such as transcription, metabolism, protein localization and folding. Thousands of lysine acylation sites have been identified based on advances in antibody enrichment strategies, highly sensitive analysis by mass spectrometry (MS), and bioinformatics. However, only 27 lysine methacrylation (Kmea) sites have been identified exclusively in histone proteins. It is hard to separate, purify and differentiate the Kmea modification from its structural isomer lysine crotonylation (Kcr) using general biochemical approaches. Here, we identify Kmea sites on a non-histone protein, Cyclophillin A (CypA). To investigate the functions of Kmea in CypA, we develop a general genetic code expansion approach to incorporate a non-canonical amino acid (ncAA) ε-N-Methacryllysine (MeaK) into target proteins and identify interacting proteins of methacrylated CypA using affinity-purification MS. We find that Kmea at CypA site 125 regulates cellular redox homeostasis, and HDAC1 is the regulator of Kmea on CypA. Moreover, we discover that genetically encode Kmea can be further methylated to ε-N-methyl-ε-N-methacrylation (Kmemea) in live cells.

Integration of multi-omics data accelerates molecular analysis of common wheat traits

Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we build a multi-omics atlas containing 132,570 transcripts, 44,473 proteins, 19,970 phosphoproteins, and 12,427 acetylproteins across wheat vegetative and reproductive phases. Using this atlas, we elucidate transcriptional regulation network, contributions of post-translational modification (PTM) and transcript level to protein abundance, and biased homoeolog expression and PTM in wheat. The genes/proteins related to wheat development and disease resistance are systematically analyzed, thus identifying phosphorylation and/or acetylation modifications for the seed proteins controlling wheat grain quality and the disease resistance-related genes. Lastly, a unique protein module TaHDA9-TaP5CS1, specifying de-acetylation of TaP5CS1 by TaHDA9, is discovered, which regulates wheat resistance to Fusarium crown rot via increasing proline content. Our atlas holds great promise for fast-tracking molecular biology and breeding studies in wheat and related crops.

Genome-wide association study revealed candidate genes associated with leaf size in alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial leguminous forages globally, known for its high yield and quality. Leaf size plays a crucial role in influencing its photosynthetic capacity, forage yield, and quality. Therefore, understanding the genetic factors regulating leaf size is of great importance for breeding new alfalfa varieties with improved yield and quality. In this study, we performed a genome-wide association study on four leaf size-related traits in 176 alfalfa germplasm resources to identify candidate genes associated with leaf size.

RESULTS

Phenotypic analysis revealed varying degrees of variation among the four traits, with coefficients of variation ranging from 3.43 to 36.84%. The broad sense heritability of these traits was found to be between 38.30% and 53.23%. Correlation analysis showed a significant positive correlation among the four traits (P < 0.01). The GWAS identified 39 SNPs associated with leaf size, distributed across eight chromosomes, of which 9 SNPs were linked to multiple traits. Haplotype analysis further confirmed that the number of superior alleles in each material was positively correlated with leaf area. Finally, we identified five genes near these 39 significant SNPs that are associated with leaf size or development.

CONCLUSION

Our findings provide new molecular markers for marker-assisted selection in alfalfa breeding programs. Moreover, this study provides a solid foundation for subsequent functional verification and genetic improvement in alfalfa.

Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

The advancement of multi-omics tools has revolutionized the study of complex biological systems, providing comprehensive insights into the molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify and characterize biological elements that contribute to phenotypic traits. This review delves into recent progress in applying multi-omics approaches to elucidate the genetic, epigenetic, and metabolic networks associated with key traits in plants. We emphasize the potential of these integrative strategies to enhance crop improvement, optimize agricultural practices, and promote sustainable environmental management. Furthermore, we explore future prospects in the field, underscoring the importance of cutting-edge technological advancements and the need for interdisciplinary collaboration to address ongoing challenges. By bridging various omics platforms, this review aims to provide a holistic framework for advancing research in plant biology and agriculture.

Unraveling the Molecular Mechanisms of Blueberry Root Drought Tolerance Through Yeast Functional Screening and Metabolomic Profiling

Blueberry plants are among the most important fruit-bearing shrubs, but they have shallow, hairless roots that are not conducive to water and nutrient uptake, especially under drought conditions. Therefore, the mechanism underlying blueberry root drought tolerance should be clarified. Hence, we established a yeast expression library comprising blueberry genes associated with root responses to drought stress. High-throughput sequencing technology enabled the identification of 1475 genes potentially related to drought tolerance. A subsequent KEGG enrichment analysis revealed 77 key genes associated with six pathways: carbon and energy metabolism, biosynthesis of secondary metabolites, nucleotide and amino acid metabolism, genetic information processing, signal transduction, and material transport and catabolism. Metabolomic profiling of drought-tolerant yeast strains under drought conditions detected 1749 differentially abundant metabolites (DAMs), including several up-regulated metabolites (organic acids, amino acids and derivatives, alkaloids, and phenylpropanoids). An integrative analysis indicated that genes encoding several enzymes, including GALM, PK, PGLS, and PIP5K, modulate key carbon metabolism-related metabolites, including D-glucose 6-phosphate and β-D-fructose 6-phosphate. Additionally, genes encoding FDPS and CCR were implicated in terpenoid and phenylalanine biosynthesis, which affected metabolite contents (e.g., farnesylcysteine and tyrosine). Furthermore, genes for GST and GLT1, along with eight DAMs, including L-γ-glutamylcysteine and L-ornithine, contributed to amino acid metabolism, while genes encoding NDPK and APRT were linked to purine metabolism, thereby affecting certain metabolites (e.g., inosine and 3',5'-cyclic GMP). Overall, the yeast functional screening system used in this study effectively identified genes and metabolites influencing blueberry root drought tolerance, offering new insights into the associated molecular mechanisms.

Genome-Wide Development of InDel-SSRs and Association Analysis of Important Agronomic Traits of Taro (Colocasia esculenta) in China

Taro (Colocasia esculenta (L.) Schott) is a tropical tuber crop whose underground corms are used as an important staple food. However, due to a lack of molecular markers, the genetic diversity, germplasm identification, and molecular breeding of taro are greatly limited. In this study, high-density InDel-SSR molecular markers covering the whole genome were developed based on the resequencing data of taro core germplasm. A total of 1,805,634 InDel-SSR loci were identified, and 219 highly polymorphic markers with an average polymorphism information content PIC value of 0.428 were screened. Furthermore, a genetic diversity analysis of 121 taro germplasm resources was conducted based on 219 markers, dividing the resources into three groups. In addition, an association analysis showed that, of the multiple InDel-SSR markers, g13.52 and g12.82 were significantly associated with leaf area and average cormel weight, respectively; the candidate genes CeARF17 (EVM0014444) and CeGA20ox (EVM0001890) were related to cormel expansion; and we excavated the candidate genes CeXXT2 (EVM0016820) and CeLOG1 (EVM0017064), which regulate leaf development. The InDel-SSRs and candidate genes identified in this study are expected to provide important support for genetically improving and breeding new varieties of taro.

Recent advances of CRISPR-based genome editing for enhancing staple crops

An increasing population, climate change, and diminishing natural resources present severe threats to global food security, with traditional breeding and genetic engineering methods often falling short in addressing these rapidly evolving challenges. CRISPR/Cas systems have emerged as revolutionary tools for precise genetic modifications in crops, offering significant advancements in resilience, yield, and nutritional value, particularly in staple crops like rice and maize. This review highlights the transformative potential of CRISPR/Cas technology, emphasizing recent innovations such as prime and base editing, and the development of novel CRISPR-associated proteins, which have significantly improved the specificity, efficiency, and scope of genome editing in agriculture. These advancements enable targeted genetic modifications that enhance tolerance to abiotic stresses as well as biotic stresses. Additionally, CRISPR/Cas plays a crucial role in improving crop yield and quality by enhancing photosynthetic efficiency, nutrient uptake, and resistance to lodging, while also improving taste, texture, shelf life, and nutritional content through biofortification. Despite challenges such as off-target effects, the need for more efficient delivery methods, and ethical and regulatory concerns, the review underscores the importance of CRISPR/Cas in addressing global food security and sustainability challenges. It calls for continued research and integration of CRISPR with other emerging technologies like nanotechnology, synthetic biology, and machine learning to fully realize its potential in developing resilient, productive, and sustainable agricultural systems.

The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes

Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112 000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra 'Protein list analysis' tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.

The crotonylated and succinylated proteins of jujube involved in phytoplasma-stress responses

BACKGROUND

Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear.

RESULTS

Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity.

CONCLUSIONS

This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.

Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding

Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.

PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants

BACKGROUND

Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological experiments is often time-consuming, expensive, and only a fraction of crotonylated peptides can be identified. This reality highlights the need for efficient and rapid prediction of Kcr sites through computational methods. Currently, several machine learning models exist for predicting Kcr sites in humans, yet models tailored for plants are rare. Furthermore, no downloadable Kcr site predictors or datasets have been developed specifically for plants. To address this gap, it is imperative to integrate existing Kcr sites detected in plant experiments and establish a dedicated computational model for plants.

RESULTS

Most plant Kcr sites are located on non-histones. In this study, we collected non-histone Kcr sites from five plants, including wheat, tabacum, rice, peanut, and papaya. We then conducted a comprehensive analysis of the amino acid distribution surrounding these sites. To develop a predictive model for plant non-histone Kcr sites, we combined a convolutional neural network (CNN), a bidirectional long short-term memory network (BiLSTM), and attention mechanism to build a deep learning model called PlantNh-Kcr. On both five-fold cross-validation and independent tests, PlantNh-Kcr outperformed multiple conventional machine learning models and other deep learning models. Furthermore, we conducted an analysis of species-specific effect on the PlantNh-Kcr model and found that a general model trained using data from multiple species outperforms species-specific models.

CONCLUSION

PlantNh-Kcr represents a valuable tool for predicting plant non-histone Kcr sites. We expect that this model will aid in addressing key challenges and tasks in the study of plant crotonylation sites.

How Antioxidants, Osmoregulation, Genes and Metabolites Regulate the Late Seeding Tolerance of Rapeseeds (Brassica napus L.) during Wintering

Rapeseed seeding dates are largely delayed under the rice-rape rotation system, but how rapeseeds adapt to the delayed environment remains unclear. Here, five seeding dates (20 October, 30 October, 10 November, 20 November and 30 November, T1 to T5) were set and the dynamic differences between two late-seeding-tolerant (LST) and two late-seeding-sensitive (LSS) rapeseed cultivars were investigated in a field experiment. The growth was significantly repressed and the foldchange (LST/LSS) of yield increased from 1.50-T1 to 2.64-T5 with the delay in seeding. Both LST cultivars showed higher plant coverage than the LSS cultivars according to visible/hyperspectral imaging and the vegetation index acquired from an unmanned aerial vehicle. Fluorescence imaging, DAB and NBT staining showed that the LSS cultivars suffered more stress damage than the LST cultivars. Antioxidant enzymes (SOD, POD, CAT, APX) and osmoregulation substances (proline, soluble sugar, soluble protein) were decreased with the delay in seeding, while the LST cultivar levels were higher than those of the LSS cultivars. A comparative analysis of transcriptomes and metabolomes showed that 55 pathways involving 123 differentially expressed genes (DEGs) and 107 differentially accumulated metabolites (DAMs) participated in late seeding tolerance regulation, while 39 pathways involving 60 DEGs and 68 DAMs were related to sensitivity. Levanbiose, α-isopropylmalate, s-ribosyl-L-homocysteine, lauroyl-CoA and argino-succinate were differentially accumulated in both cultivars, while genes including isocitrate dehydrogenase, pyruvate kinase, phosphoenolpyruvate carboxykinase and newgene_7532 were also largely regulated. This study revealed the dynamic regulation mechanisms of rapeseeds on late seeding conditions, which showed considerable potential for the genetic improvement of rapeseed.