Accurate variant genotyping is crucial for genomics-assisted breeding but remains highly challenging in many crop genomes. Varigraph, a pangenome graph-based variant genotyping algorithm, outperforms existing tools in genotyping both small variants and structural variants in plant genomes. It can handle large or complex pangenome graphs and genomes of autopolyploids such as rice, maize, and potato with high precision. Source link

Global lysine acetylomics reveal that the dark-to-light transition involves widespread protein lysine deacetylation in Arabidopsis seedlings. The far-red light photoreceptor phyA undergoes lysine deacetylation at K65, facilitating its ubiquitination and degradation, which is essential for its role in light signal transduction. The lysine deacetylase HDT2 deacetylates phyA in the nucleus to promote its ubiquitination and degradation in photomorphogenesis. Source link

This review examines the conserved and unique composition of plant chromatin remodeling complexes, highlighting their crucial roles in epigenetic regulation, stress adaptation, and plant development. It summarizes their specialized mechanisms, including interactions with histone modifications, DNA methylation, and transcription factors, while emphasizing their contributions to gene transcription regulation. The review advances our understanding of how chromatin remodelers coordinate plant responses to developmental signals and environmental stimuli. Source link

The rapid development of barley genomics research in recent years has greatly enhanced our understanding of the molecular regulatory mechanisms underlying the complex characters (Jiang et al., 2025). However, a huge challenge has also been posed for researchers to deal with the dramatically increasing amount of multi-omics data. Here, we developed BarleyOmics, a comprehensive platform of barley multi-omics database for genomic research and molecular breeding. We firstly integrated all the barley multi-omics data obtained from public databases and/or generated from our own research projects and then conducted unified analysis as well as quality control. Source link

In response to low-oxygen stress, plants undergo a metabolic switch from aerobic to anaerobic respiration. In this study, Zhao et al. identified Arabidopsis IQD22 as a crucial regulator that modulates the calcium-dependent formation of CaM2-ADH1 and CPK12-RAP2.12 complexes, thereby controlling the hypoxia-induced metabolic reprogramming through the activation of anaerobic respiration. Source link

Fungal extracellular vesicles (EVs) deliver virulence effectors, including RsNP8 and RsSerp, into host plant cells during infection. These EV-associated proteins enter through clathrin-mediated endocytosis, with RsNP8 targeting chloroplasts to suppress plant immunity by inhibiting ROS bursts. These results establish a new framework for cross-kingdom effector delivery by eukaryotic pathogens. Source link

This study identifies an RFEL1-NPR3 module that regulates wheat resistance against biotrophic fungal pathogens. RFEL1 is an E3 ligase that ubiquitinates TaNPR3 and promotes its degradation via the 26S proteasome. Overexpressing RFEL1 or knocking out TaNPR3 confers resistance against yellow rust, powdery mildew, and leaf rust diseases, highlighting the potential of the RFEL1-NPR3 module for the development of broad-spectrum resistance against biotrophic fungal pathogens in crops. Source link

The cysteine-rich receptor-like kinase OsCRK14 positively regulates drought resistance in rice by activating an OsRLCK57–MAPK signaling cascade. The activation of MAPK cascade subsequently stabilizes the transcription factor OsbZIP66 to enhance the expression of drought-response genes. Natural variations in the OsCRK14 promoter affect its binding by OsMYB72, influencing drought-resistance variability among rice varieties. These discoveries provides both mechanistic insights and genetic resources for breeding drought-resistant rice. Source link