Yong Xiang

SUMMARY: ABA‐INSENSITIVE 5 (ABI5) is a key transcriptional regulator mediating abscisic acid (ABA)–induced suppression of seed germination. However, the downstream regulatory network through which ABI5 exerts its function remains incompletely understood. Here, by integrating ChIP‐seq and RNA‐seq analyses, we identify RAF12 , a member of the B2 Raf‐like kinase subfamily, as a direct transcriptional target of ABI5. ABI5 binds to the RAF12 promoter and activates its expression. Loss‐of‐function raf12 mutants exhibit reduced sensitivity to ABA during seed germination, suggesting a negative regulatory role for RAF12 in this process. Conversely, RAF12 interacts with and phosphorylates ABI5, thereby enhancing its transcriptional activity. Further analysis showed that RAF12 regulates its own kinase activity through autophosphorylation. Mutations at its phosphorylation sites significantly weaken its ability to enhance ABI5's transcriptional activity. Together, these findings uncover a positive feedback loop wherein ABI5 transcriptionally activates RAF12 , which in turn reinforces ABI5 activity through phosphorylation. This module may function in parallel with the canonical SnRK2s‐ABI5‐mediated ABA signaling cascade, offering new mechanistic insights into the fine‐tuning of ABA responses during seed germination.

Seed dormancy and germination are crucial processes affecting the propagation and survival of plant populations. These phenomena are precisely regulated through a complex interplay between internal signals, such as plant hormones and environmental cues including light, temperature, moisture, and nutrient availability. Dormancy release and germination initiation are distinct, yet closely associated, processes involving complex transcriptional, translational, and epigenetic changes mediated by intricate regulatory mechanisms. This review comprehensively summarizes the complex regulatory networks governing seed dormancy and germination across different plant species. By integrating physiological, genetic, and molecular biology perspectives, the latest advances in the research on mechanisms regulating seed dormancy and germination are discussed, providing valuable insights for improving seed quality through biotechnology-based breeding strategies and establishing a solid foundation for future research in this field.

To optimize offspring seed survival in fluctuating environments, seed plants have evolved two key adaptive strategies, seed dormancy under favorable conditions and germination arrest under stress, to control germination timing. The phytohormone abscisic acid acts as a master regulator in both processes, exerting precise control over its endogenous levels and signaling to fine-tune this seed-seedling transition. Previously, we identified ODR1 as a key seed dormancy regulator: it negatively modulates seed dormancy by suppressing ABA accumulation during seed development via inhibiting bHLH57-dependent transcriptional activation of the ABA biosynthesis genes NCED6/9. However, whether ODR1 also modulates seed germination under stress conditions remains unknown. Here, we showed that loss of ODR1 function arrested seed germination under osmotic stress, while specific overexpression of ODR1 in odr1 mutant seeds rescued this osmotic germination arrest. Osmotic stress induced and maintained high ODR1 expression, but this induction was reduced in the ABA biosynthesis-deficient mutant nced6/9 and ABA signaling mutants abi3-1, abi4-t, and abi5-8, indicating ABA dependence of ODR1 induction. In odr1 mutants, 8 out of 12 key ABA biosynthesis genes were significantly upregulated. ChIP-seq data analysis revealed an ODR1 binding peak in the promoter of the ABA biosynthesis gene ABA1. Specific overexpression of ODR1 in odr1 mutant seeds notably rescued the upregulated ABA1 expression, confirming the repression of ABA1 by ODR1. Furthermore, ABA content was significantly increased in germinating seeds of odr1 mutant, and exogenous application of fluridone, an ABA biosynthesis inhibitor, effectively rescued their germination arrest, linking the phenotype to excessive ABA accumulation. These results reveal a novel role of ODR1 in osmotic stress-induced germination arrest: ODR1 is induced by osmotic stress via an ABA-dependent pathway and in turn limits ABA accumulation via repressing the expression of ABA biosynthesis genes, thereby alleviating germination arrest under stress. Together, we demonstrate that ODR1 coordinates germination timing via ABA-dependent negative feedback regulation of ABA biosynthesis during both dormancy establishment and osmotic stress responses. This mechanism addresses the critical question of how plants fine-tune ABA signaling to balance survival and germination in variable environments.

SUMMARY: Pentatricopeptide repeat (PPR) proteins are key regulators of organelle RNA metabolism in plants, yet their precise mechanisms in chloroplast RNA processing remain unclear. Here, we identify WPR, a unique P‐type PPR protein in rice ( Oryza sativa L.), as a critical factor in chloroplast RNA splicing and editing. A ~112‐kb chromosomal inversion upstream of WPR causes an albino panicle rachis phenotype ( wpr mutant), while complete loss of WPR function leads to seedling lethality. WPR deficiency disrupts the splicing of multiple group II introns (atpF, ndhA, ndhB, petB, rpl2, and rps12) and impairs RNA editing in transcripts such as ndhA, ndhB, ndhG, rps14, and ycf3. Electrophoretic mobility shift assay (EMSA) data confirm that WPR directly binds to precursor mRNAs of atpF, ndhA, petB, rpl2, and rps12. Strikingly, WPR interacts with both RNA editing factors (MORF1, MORF8b) and the splicing factor CAF2, but not with other PPR proteins targeting the same transcripts. Unlike most PPR proteins, WPR contains only six PPR repeats, which is the fewest among all functionally characterized rice PPR proteins. With few informative repeats, WPR likely possesses a broad, low‐specificity RNA‐binding activity. Moreover, WPR may act on chloroplast RNA maturation by recruiting MORFs and CAF2 rather than other PPR proteins, highlighting a novel regulatory mode in which P‐type PPR protein may act as an RNA‐binding scaffold to integrate diverse RNA‐processing machineries. This study advances the understanding of PPR protein diversity and provides new insights into the molecular mechanisms of chloroplast RNA processing in rice.

Seed dormancy and germination is regulated by internal hormones and exogenous environment cues. Ethylene is one of the hormones that break seed dormancy and induce seed germination. Our previous study showed that N-degron pathway gene, proteolysis6 (PRT6) was involved in dormancy release by ethylene, the defection of which exhibiting ethylene-insensitivity in Arabidopsis thaliana. In the present study, through screening an ethyl methyl sulfonate-mutagenized (EMS) population of prt6−1, we isolated a recessive mutant that acted as a suppressor of prt6 that rescued its insensitivity to ethylene as well as a phenotype of shorter silique length. Further bulk segregant analysis on F2 population identified a premature termination located in the third exon of LONGIFOLIA1 (LNG1), previously reported in the regulation of longitudinal cell elongation. Mutation of LNG1 in prt6−1 background by CRISPR-Cas9 confirmed that LNG1 was epistatic to PRT6 in seed responsiveness to ethylene. Our finding proposed the pleiotropic effect of LNG1 in seed dormancy breakage by ethylene via PRT6, providing novel functional component at the downstream of the coordinated PRT6 and ethylene signaling pathway.

SUMMARY: 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.

Single-stranded DNA-binding proteins (SSBs) play essential roles in the replication, recombination and repair processes of organellar DNA molecules. In Arabidopsis thaliana, SSBs are encoded by a small family of two genes (SSB1 and SSB2). However, the functional divergence of these two SSB copies in plants remains largely unknown, and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete. In this study, phylogenetic, gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants. Based on accurate long-read sequencing results, ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA (mtDNA) and plastid DNA (ptDNA), accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes. Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.

Seed dormancy, an important adaptive trait that governs germination timing, is endogenously controlled by phytohormones and genetic factors. DELAY OF GERMINATION 1 (DOG1) is the vital genetic regulator of dormancy, significantly affecting the expression of numerous ABA and GA metabolic genes. However, whether DOG1 could influence the expression of other phytohormone-related genes is still unknown. Here, we comprehensively investigated all well-documented hormone-related genes which might be affected in dog1–2 dry or imbibed seeds by using whole-transcriptome sequencing (RNA-seq). We found that DOG1 could systematically control the expression of phytohormone-related genes. An evident decrease was observed in the endogenous signal intensity of abscisic acid (ABA) and indole-3-acetic acid (IAA), while a dramatic increase appeared in that of gibberellins (GA), brassinosteroids (BR), and cytokinin (CK) in the dog1–2 background, which may contribute considerably to its dormancy-deficient phenotype. Collectively, our data highlight the role of DOG1 in balancing the expression of phytohormone-related genes and provide inspirational evidence that DOG1 may integrate the phytohormones network to control seed dormancy.

Pre‐harvest sprouting (PHS), which reduces grain yield and quality, is controlled by seed dormancy genes. Because few dormancy‐related genes have been cloned, the genetic basis of seed dormancy in rice (Oryza sativa L.) remains unclear. Here, we performed a genome‐wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice. Our findings suggest that Seed Dormancy4 (Sdr4), a central modulator of seed dormancy, integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level. Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions. Furthermore, like the semi‐dwarf 1 (SD1) and Rc loci, Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice. The distribution frequency of the Sdr4‐n allele in different locations in Asia is negatively associated with local annual temperature and precipitation. Finally, we developed functional molecular markers for Sdr4, SD1, and Rc for use in molecular breeding. Our results provide clues about the molecular basis of Sdr4‐regulated seed dormancy. Moreover, these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance, yield, and quality in modern rice varieties.