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8 recordsLinked to original sources
PubMed2026

Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.

Barley (Hordeum vulgare L.) is an important crop in the world, and its seed dormancy is primarily controlled by a mitogen-activated protein kinase kinase 3 (MKK3) gene. Although kinase activity of MKK3 and its roles in barley post-domestication have been widely studied, the pre-domestication evolution of MKK3 and the spread of nondormant alleles among global barley varieties remain largely unexplored. In this study, we analyzed MKK3 sequences in barley and its wild progenitor (Hordeum spontaneum K. Koch) and identified two polymorphic miniature inverted-repeat transposable elements (MITEs). Comparative analyses indicated that the insertions/excision of the MITEs predated the current estimates of barley domestication. Examination of the barley pangenomes coupled with droplet digital polymerase chain reaction revealed extensive copy number variation of MKK3 and suggested that transposons likely contributed to tandem amplification of the MKK3 gene on chromosome 5H. Additionally, approximately 1-Kb MKK3 sequences were found on chromosomes 1H and 6H. Further analysis indicated that these short MKK3 sequences were captured by a CACTA transposon that also contained fragments from four other expressed genes. The acquisition of MKK3 was estimated to be between 1.9 and 2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and identify three divergent MKK3 haplotype groups including a unique lineage predominant in Ethiopian germplasm. This study highlights the contribution of transposons to structural diversification and evolutionary differentiation of the MKK3 locus and provides helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting tolerant varieties under distinct natural conditions.

Hordeum↗
PubMed2026

From dormancy to germination: Transcriptome analysis reveals the potential involvement of heat shock proteins in gibberellin-induced seed dormancy release in Solanum torvum.

Solanum torvum, a superior vegetable grafting rootstock and medicinal Solanaceae plant, exhibits strong seed dormancy, which limits its commercial cultivation. Among various strategies explored to improve the germination rate of S. torvum, exogenous application of gibberellin (GA) has been shown to be effective. In this study, a GA concentration of 2.5 mM was established as the optimal for breaking dormancy in S. torvum seeds. Transcriptome analysis of dry, water-soaked, GA-soaked, and GA-induced germinated seeds was conducted to investigate the molecular mechanism of GA-mediated dormancy release. During the soaking period, GA application significantly induced transcriptome changes in processes including protein processing, translation, and peptide biosynthesis. Concurrently, GA treatment promoted plant hormone signal transduction, enhanced DNA-binding transcription factor activity, and activated monocarboxylic acid biosynthetic process, all of which facilitated seed water absorption. Furthermore, the differentially expressed genes (DEGs) induced by GA during soaking primarily functioned in signal transduction or activation. While most of these DEGs returned to their pre-treatment expression levels before subsequent recovery, a subset persisted until seed germination. During radicle protrusion, the persistent DEGs were associated with energy metabolism and cell structure establishment. Notably, heat shock protein (HSP) genes showed dynamic expression across all stages (soaking, germination, and radicle penetration). Furthermore, by adjusting germination conditions, temperature was confirmed to be a necessary but not sufficient condition for GA-induced S. torvum seed germination. However, functional validation (e.g., using HSP inhibitors or genetic approaches) is still required to confirm the causal role of HSPs. Collectively, these findings not only clarify the molecular basis of GA-regulated seed dormancy breaking in S. torvum but also provide practical guidance for optimizing its commercial propagation protocols.

Gibberellins↗
PubMed2026

ATX1-COMPASS-like complex participates in the bud dormancy release of tree peony by regulating H3K4me3 modification.

Bud dormancy release in woody plants is crucial for survival, regrowth, flowering, and fruiting. Tree peony (Paeonia suffruticosa), an important ornamental and economic plant, undergoes bud endodormancy in winter, and sufficient chilling duration and exogenous gibberellins (GAs) can effectively break the dormancy. However, the epigenetic regulation mechanism remains poorly understood. Here, immunoblotting revealed that H3K4me3, but not H3K4me1 or H3K4me2, was associated with chilling- and GA3-induced dormancy release. Chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNA-seq results revealed that H3K4me3 enriched near transcription start sites (TSS). H3K4me3 enrichment genes (HEGs) and differentially expressed genes (DEGs) were commonly enriched in KEGG pathways, such as plant hormone signal transduction and MAPK signaling. The expression patterns of these marker genes, such as EARLY BUD-BREAK 3 (PsEBB3), CYCLIND3.1 (PsCYCD3.1), CYCLIND3.3 (PsCYCD3.3), and β-1,3-glucanase 6 (PsBG6), were correlated with their H3K4me3 enrichment and were validated by chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR). Four COMPASS-like component homologs and one histone methyltransferase were screened; among them, PsWDR5a, PsRBL, PsASH2R, and PsATX1 were upregulated by prolonged chilling and GA3 treatments. Yeast two-hybrid (Y2H), yeast three-hybrid (Y3H), luciferase complementation (LCA), and co-immunoprecipitation (Co-IP) analyses revealed that PsRBL interacts with PsWDR5a and PsASH2R as a bridge. PsATX1 was confirmed as an H3K4me3 methyltransferase and interacted with PsWDR5a and PsRBL to form the PsATX1-COMPASS-like complex using Y2H, LCA, and Co-IP assays. Functional analyses showed that PsWDR5a, PsRBL, PsASH2R, and PsATX1 significantly promoted budburst by elevating genomic H3K4me3 levels. Our findings provide insights into the epigenetic regulation of dormancy transitions in woody perennials.

Histones↗
PubMed2025

Heat-Induced Secondary Dormancy Contributes to Local Adaptation in Arabidopsis thaliana.

Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimise the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavourable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analysing natural variations within 361 Arabidopsis thaliana accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favours plant survival in habitats exposed to harsh summers.

Arabidopsis↗
PubMed2025

ODR1, the key seed dormancy and germination regulator, promotes seed Proanthocyanidin biosynthesis via interaction with TTG1 and modulation of MBW complex activity.

Seed dormancy and germination are crucial for both plant survival and reproduction and for crop sowing and harvesting. Proanthocyanidins (PAs), one of the most abundant seed metabolites, play a role in enhancing dormancy and inhibiting germination. Multiple regulatory factors involved in PAs biosynthesis can alter seed dormancy or germination capacity. However, whether the dormancy or germination factors reciprocally influence the PAs biosynthesis is unclear. Here, we report that ODR1, a seed dormancy and germination key factor and a transcriptional (co-) repressor, can regulate seed PAs biosynthesis and act as a transcriptional co-activator. The odr1 mutant shows lighter seed coat color, decreased PAs contents, and reduced expression of PAs biosynthesis genes, which are restored in the ODR1 complementary lines. ODR1 interacts with TTG1 and forms a complex with TTG1/TT2/TT8 (three MBW complex components), enhancing their activation on promoters of PAs biosynthesis genes like DFR and ANS. Overexpressing TTG1 in the odr1-2 mutant rescues or even reverses PA-related phenotypes of odr1-2, confirming that ODR1-mediated regulation of PAs biosynthesis is dependent on TTG1. Moreover, three homologous copies of ODR1 in rapeseed were identified, and simultaneous knockout of them reduces the PAs contents. These results revealed the previously uncharacterized functions of ODR1 in PAs biosynthesis, suggested its conservation between Arabidopsis and rapeseed, and provided important gene resources for rapeseed variety improvement.

Proanthocyanidins↗
PubMed2025

Speed breeding: protocols, application and achievements.

One of the limiting factors in breeding and genetic research is the time required to develop pure lines. This is due, on the one hand, to the prolonged vegetative period of a single generation and, on the other hand, to the specifics of inbreeding, which typically requires 4-6 consecutive generations of self-pollination in plant material. Researchers have always sought approaches that enable the rapid development of homozygous plant lines. Consequently, methods such as greenhouse cultivation during the autumn-winter period, single-seed descent, shuttle breeding, embryo culture, and doubled haploid technology have been introduced into practice. All these methods have both advantages and limitations. One of the latest approaches facilitating a significant reduction in the vegetative period of plants is speed breeding (SB). This method is based on the application of factors that shorten the time from sowing to flowering, as well as techniques that accelerate the generative phase of development and overcome postharvest dormancy. This review provides a comprehensive list and characterization of all factors that influence the efficiency of speed breeding to varying degrees. Among the factors discussed that reduce the sowing-to-flowering period are photoperiod, light sources, spectral composition and light intensity, temperature, carbon dioxide levels, vernalization, mineral nutrition, substrate volume, mechanical shoot removal, and the use of plant growth regulators. To shorten the generative phase, the review summarizes the application of embryo culture and forced desiccation of immature seeds, along with methods to overcome postharvest dormancy. Additionally, applications of genetic approaches and genetic engineering for shortening generation time in speed breeding are described. The review also consolidates detailed protocols for approximately thirty crops. The high efficiency of speed breeding in reducing both the vegetative period per generation and the time required to develop pure lines has led to its increasing adoption in various research fields. This review highlights the application of speed breeding for hybridization and pure line development, introgression of target alleles, and genomic selection. A list of phenotypic traits exhibiting high correlation between controlled-environment and field conditions is provided.

accelerated flowering↗
PubMed2026

The SPL-family transcription factor MpSPL3 orchestrates the proper regulation of vegetative and reproductive programs in Marchantia polymorpha.

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors that are widely distributed across the plant kingdom. In angiosperms, the multimember SPL family regulates various biological processes, including vegetative-to-reproductive phase transition, inflorescence architecture, and lateral organ development. In contrast, the liverwort Marchantia polymorpha genome encodes only four SPL genes, with functional studies available only for microRNA-targeted members, MpSPL1 and MpSPL2. MpSPL1 was shown to control the meristem dormancy to modulate the thallus architecture, whereas MpSPL2 was found to promote the transition from vegetative-to-reproductive phase. Here, we investigate the impact of the MpSPL3 gene on M. polymorpha development. We demonstrate that MpSPL3 influences coordination of the vegetative growth and the reproductive phase transition. Knockout of MpSPL3 leads to strong growth retardation with disordered thallus morphology, reduced gemma cup number, and, most strikingly, complete loss of gametangiophore formation. Interestingly, overexpression of MpSPL3.2, the shorter isoform, has no detectable morphological effect, whereas the overexpression of MpSPL3.1, the longer isoform encoding a protein with an additional 61-aa long fragment, results in a delay in timing and reduced efficiency of gametangiophore production. Moreover, all the observed developmental abnormalities might be a consequence of the altered expression of genes essential for proper vegetative development and responsible for germ cell specification in MpSPL3 knockout and overexpression plants. Altogether, our findings demonstrate that MpSPL3 is important in regulating gametophyte development and ensuring reproductive success in M. polymorpha.

Marchantia↗
PubMed2026

Long-term saline-alkaline selection rewires the growth-survival trade-off in Priestia megaterium.

Saline-alkaline soils impose persistent osmotic, ionic, pH, and nutrient stress on soil microorganisms, but the evolutionary routes by which beneficial bacteria adapt to such conditions remain poorly resolved. We performed adaptive laboratory evolution to examine the adaption of the plant growth-promoting rhizobacterium Priestia megaterium HA22 to long-term oligotrophic saline-alkaline selection. After 175 serial transfers, the evolved lineage proliferated stably at 40 g L-1 Na2SO4 at pH 10.0, whereas the wild-type strain failed to proliferate. Genome resequencing and allelic replacement revealed a 5-bp insertion in spo0A, the master sporulation regulator, as a major adaptive mutation. This mutation abolished sporulation; shortened the lag phase; and enhanced vegetative growth, nutrient uptake, and expression of tricarboxylic acid cycle and nitrogen metabolism gene under saline-alkaline stress. According to untargeted metabolomics, adaptation was accompanied by increased amino acid metabolism and aminoacyl-tRNA biosynthesis, with proline, isoleucine and pantothenic acid functionally promoting growth. A point mutation in ugpB enhanced glycerol-3-phosphate uptake, increased peptidoglycan and wall teichoic acid levels, and partially rescued the survival cost of the spo0A mutation. In greenhouse assays under combined saline-alkaline stress, the evolved strain increased soybean shoot dry weight and root dry weight by 56.08% and 27.02%, respectively. These results indicate that prolonged, predictable saline-alkaline selection can favor active growth rather than dormancy when compensatory cell envelope reinforcement buffers survival costs.

Adaptive laboratory evolution↗