Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer–promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.

Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N₂ fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N₂ fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high nitrogen inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high nitrogen transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high nitrogen.

The banana (Musa spp.) peel undergoes rapid softening during ripening, leading to finger drop and a shortened shelf life. The regulatory mechanism behind this process remains to be elucidated. In this study, we confirmed the role of peel softening in banana finger drop and uncovered the underlying transcriptional regulatory network. Cell wall-related (CWR) genes were substantially upregulated in both the peel and finger drop zone during ethylene-induced ripening. Transcriptome analysis and genome-wide profiling of chromatin accessibility and transcription factor (TF) binding revealed that two key regulators of fruit ripening, Musa acuminata NAC-like, Activated by apetala3/Pistillata1 (MaNAP1) and MaMADS1, regulate CWR genes by directly binding to their promoters or by targeting other ripening-related TFs to form a hierarchical regulatory network. Notably, MaNAP1 and MaMADS1 were directly targeted by ETHYLENE INSENSITIVE3 (MaEIN3), and MaNAP1 and MaMADS1 associated with tissue-specific histone modifications, enabling them to integrate MaEIN3-mediated ethylene signaling and undergo epigenetic regulation. Overexpression of MaNAP1, MaMADS1 or other identified regulatory TFs upregulated CWR genes and promoted peel softening. Our findings unveil a MaNAP1-MaMADS1-centered regulatory cascade governing banana peel softening and finger drop, offering potential targets for enhancing banana texture and shelf life.

Inconsistent nitrogen application rates across global croplands necessitate the adaptation of different genetic alleles to optimize nitrogen-use efficiency (NUE) in agriculture. In rice (Oryza sativa L.), different TEOSINTE BRANCHED 1, CYCLOIDEA AND PROLIFERATING CELL FACTOR 19 (OsTCP19) alleles contribute to the geographical adaptation to soil fertility. The nitrogen-sensitive allele OsTCP19-H is predominantly found in low-nitrogen regions due to its superior tillering and yield accumulation capabilities. Conversely, the nitrogen-insensitive allele OsTCP19-L is more common in nitrogen-sufficient regions, though the precise factors affecting this distribution remain unknown. Here, we report that high-nitrogen levels lead to lodging in an OsTCP19-dependent manner. Overexpression of this gene modifies plant architecture, enhancing lodging resistance in rice. Importantly, fine-tuning OsTCP19 expression can confer lodging resistance without a yield penalty. This is particularly important as it alleviates yield loss from lodging under high-nitrogen conditions and, intriguingly, can result in a substantial increase in plot yield when combined with dense planting strategies. Furthermore, the distinct nitrogen sensitivity of different OsTCP19 alleles allows for substantial improvement in grain yield and NUE under certain nitrogen conditions. Thus, our findings suggest that genetic manipulation of a single gene, OsTCP19, could allow flexible adaptation to diverse planting scenarios, maximizing genetic benefits based on local nitrogen availability.

Banana (Musa spp.) fruit peel browning during cold storage results in significant postharvest losses; however, the molecular mechanisms linking antioxidant metabolism and transcriptional regulation remain unclear. Here, we demonstrate that exogenous ascorbic acid alleviates chilling-induced browning by suppressing the WRKY-AAO regulatory module through histone H3K18 lactylation (H3K18la)-mediated chromatin remodeling. DNase-seq analyses revealed that cold stress induces chromatin accessibility at the promoters of WRKY transcription factor genes (MaWRKY11/18/40/50/60). DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid confirmed these WRKYs can bind to W-box motifs in the ascorbate oxidase (MaAAO1) promoter. This activation triggered ascorbic acid depletion and reactive oxygen species accumulation, accelerating peel browning. Conversely, ascorbic acid treatment reduced H3K18la levels at MaWRKY genes, diminishing their accessibility and lowering the expression of MaWRKY target genes. Transient overexpression assays confirmed that MaAAO1 drives peel browning, while ascorbic acid disrupts this cascade by coupling redox signaling to lactylation-dependent chromatin silencing. Our study unveils a redox-sensitive epigenetic switch wherein exogenous ascorbic acid mitigates chilling injury by repressing oxidative pathways via histone lactylation, offering strategies for preserving tropical fruit quality.

Green Revolution rice varieties deliver high yields but require excessive nitrogen (N) fertilizer and show diminished N responsiveness, severely reducing nitrogen-use efficiency (NUE). To dissect the molecular basis of low N sensitivity in modern cultivars, we conducted a genome-wide association study (GWAS) for biomass response to N (BRN), a trait tightly linked to N sensitivity, using a diverse rice germplasm panel. We identified BRN1 as a key regulator of N-dependent biomass accumulation that regulates NLP3, a master transcription factor governing nitrate signaling. Under elevated N supply, the strigolactone signaling repressor D53 accumulates substantially and interacts with BRN1 to repress NLP3 transcription, thereby reducing rice N response. Notably, the high-response BRN1^H allele encodes a more stable protein that alleviates D53-mediated suppression. Introgression of this allele into modern cultivars significantly enhanced N sensitivity and grain yield under both low and high N conditions. Our findings establish a D53-BRN1-NLP3 regulatory module controlling rice NUE, providing a target for rice breeding to sustain high productivity with improved resource sustainability.