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Plants have evolved a variety of mechanisms to synchronize flowering with their environment to optimize reproductive success. Many species flower in spring when the photoperiod increases and the ambient temperatures become warmer. Winter annuals and biennials have evolved repression mechanisms that prevent the transition to reproductive development in the fall. These repressive processes can be overcome by the prolonged cold of winter through a process known as vernalization. The memory of the past winter is sometimes stored by epigenetic chromatin remodeling processes that provide competence to flower, and plants usually require additional inductive signals to flower in spring. The requirement for vernalization is widespread within groups of plants adapted to temperate climates; however, the genetic and biochemical frameworks controlling the response are distinct in different groups of plants, suggesting independent evolutionary origins. Here, we compare and contrast the vernalization pathways in different families of plants.

[This corrects the article DOI: 10.1371/journal.pone.0203068.].

Background Winter wheat undergoes vernalization, a process activated by prolonged exposure to low temperatures. During this phase, flowering signals are generated and transported to the apical meristems, stimulating the transition to the inflorescence meristem while inhibiting tiller bud elongation. Although some vernalization genes have been identified, the key cis -regulatory elements and precise mechanisms governing this process in wheat remain largely unknown. Results In this study, we construct extensive epigenomic and transcriptomic profiling across multiple tissues—leaf, axillary bud, and shoot apex—during the vernalization of winter wheat. Epigenetic modifications play a crucial role in eliciting tissue-specific responses and sub-genome-divergent expressions during vernalization. Notably, we observe that H3K27me3 primarily regulates vernalization-induced genes and has limited influence on vernalization-repressed genes. The integration of these datasets enables the identification of 10,600 putative vernalization-related regulatory elements including distal accessible chromatin regions (ACRs) situated 30Kb upstream of VRN3 , contributing to the construction of a comprehensive regulatory network. Furthermore, we discover that TaSPL7/15, integral components of the aging-related flowering pathway, interact with the VRN1 promoter and VRN3 distal regulatory elements. These interactions finely regulate their expressions, consequently impacting the vernalization process and flowering. Conclusions Our study offers critical insights into wheat vernalization’s epigenomic dynamics and identifies the putative regulatory elements crucial for developing wheat germplasm with varied vernalization characteristics. It also establishes a vernalization-related transcriptional network, and uncovers that TaSPL7/15 from the aging pathway participates in vernalization by directly binding to the VRN1 promoter and VRN3 distal regulatory elements.

Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite direction of protein-coding genes often positively correlates with and is required for the expression of their cognate sense genes. We further characterized MAS , a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 ( MAF4) locus. MAS is induced by cold and indispensable for the activation of MAF4 transcription and suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes. Long non-coding RNAs regulate developmental transitions and stress responses in plants. Here Zhao et al. show that a non-coding antisense transcript MAS transcribed from the Arabidopsis MAF4 locus activates H3K4me3 deposition and MAF4 transcription to suppress precocious flowering.

Perception of seasonal cues is critical for reproductive success in many plants. Exposure to winter cold is a cue that can confer competence to flower in the spring via a process known as vernalization. In certain grasses, exposure to short days is another winter cue that can lead to a vernalized state. In Brachypodium distachyon, we find that natural variation for the ability of short days to confer competence to flower is due to allelic variation of the FLOWERING LOCUS T (FT1) paralog FT-like9 (FTL9). An active FTL9 allele is required for the acquisition of floral competence, demonstrating a novel role for a member of the FT family of genes. Loss of the short-day vernalization response appears to have arisen once in B. distachyon and spread through diverse lineages indicating that this loss has adaptive value, perhaps by delaying spring flowering until the danger of cold damage to flowers has subsided.

Background Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages ( Brassica rapa L. ssp. pekinensis ), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization. Results There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting ‘XBJ’ to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2 , CPRD49 , AAP8 , endoglucanase 10, BXLs , GATLs , and WRKYs . Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT ), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions. Conclusion The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.

Climate change and increasing pressure on water resources have renewed interest in autumn cultivation of sugar beet, a practice that benefits from seasonal precipitation and reduces dependence on irrigation. However, bolting remains a major limitation, substantially affecting yield stability and the economic viability of production. This study evaluated ten experimental sugar beet hybrids and two bolting-resistant control varieties across three environments over two cropping years (2022–2023 and 2023–2024). Randomized complete block design with four replications was implemented for agronomic evaluations. The vernalization–intensity model was used to estimate vernalization threshold (VT) and bolting sensitivity. Genotype BOL436 exhibited the highest VT (134 h) but also showed pronounced sensitivity to bolting. In contrast, genotypes BOL435 and BOL434, with similarly high VT values, displayed low bolting sensitivity and thus greater suitability for fluctuating winter conditions. Combined ANOVA revealed significant genotype and environment effects (P < 0.01) for all measured traits, while genotype–environment interaction (GEI) significantly influenced white sugar yield (WSY) and root yield (RY). Additive main effects and multiplicative interactions (AMMI) analysis indicated that the first two interaction principal components (IPCs) accounted for 75.20% of GEI variation in WSY, whereas IPC1 alone explained 57.60% for RY. WAASB-based stability analysis identified BOL375, BOL239, BOL376, and BOL068 as stable, high-performing genotypes for WSY, with BOL239, BOL375, BOL068, and BOL435 showing comparable superiority for RY. Results from the WAASBY index were consistent with these findings. Multi-trait stability index (MTSI) analysis further highlighted BOL434, BOL376, and BOL239 as the most stable genotypes across agronomic and qualitative traits. Overall, the results demonstrate that autumn cultivation, supported by robust modeling and stability analysis, can contribute to reduced irrigation needs, while the identified genotypes offer promising options for enhancing productivity and minimizing bolting risk in water-limited environments.