Abstract This research examines how the basic leucine zipper (bZIP) transcription factor (TF) influences drought stress responses in tree species, emphasizing its related regulatory pathways, and thus offering a theoretical framework for understanding drought response mechanisms regulated by the bZIP TF family. Specifically, we characterized the functional role of the S subfamily bZIP gene, PtrbZIP12, from Populus trichocarpa, by developing transgenic poplars that either overexpressed or knocked down of PtrbZIP12. The findings indicated that PtrbZIP12 markedly improved drought tolerance in transgenic plants by facilitating reactive oxygen species (ROS) scavenging, enhancing proline biosynthesis, and reducing plasma membrane peroxidation and cell death. To pinpoint PtrbZIP12’s downstream targets, RNA sequencing was performed, followed by chromatin immunoprecipitation-PCR (ChIP-PCR), yeast one-hybrid, and dual-luciferase assays. These analyses confirmed that PtrbZIP12 binds directly to the promoters of PtrDHN (Dehydrin) and PtrPOD (peroxidase), leading to the activation of their expression. Transgenic poplars overexpressing (OE) PtrDHN or PtrPOD were subsequently generated, and similar to PtrbZIP12, their OE conferred enhanced drought tolerance. Moreover, co-expression of PtrbZIP12 with PtrbZIP3 further elevated PtrDHN transcript levels, resulting in improved drought resilience in the PtrbZIP12 transgenic lines. Moreover, phosphorylation was identified as a key factor in boosting PtrbZIP12-mediated transcriptional regulation of PtrPOD and PtrDHN, underscoring the significance of post-translational modification in plant drought stress responses.

Abstract Global climate change and widespread unsustainable agricultural practices, increasingly impose both biotic and abiotic stresses on the production of horticultural plants. Lilies (Lilium spp.) are globally renowned ornamental plants, with some species also possessing medicinal, edible, and cosmetic value. However, their quality and yield are often negatively affected by various stresses. Conventional breeding methods are often inefficient due to the long juvenile phase, complex genetic background, and large genome size of lilies. While numerous emerging technologies provide opportunities for resistance breeding in lilies, their successful application relies on a thorough understanding of the resistance response mechanisms. This review systematically summarizes recent advances in lily stress resistance research, delineates the physiological and molecular response mechanisms of lilies under abiotic stresses (extreme temperature, drought, high salinity), biotic stresses (pathogens, pests), and continuous cropping obstacles. Furthermore, it discusses current challenges and limitations, and explores the potential applications of emerging technologies in improving the stress adaptability of lilies. These findings provide important insights for advancing stress resistance research and breeding stress-tolerant lily cultivars.

Abstract Soil salinization poses a serious threat to plant development and represents a major obstacle to the sustainable production of crops worldwide. Melatonin (MT) contributes prominently to plant tolerance against abiotic environments. However, the molecular basis of transcriptional regulation underlying melatonin accumulation in tomato under saline-alkali stress is still largely unknown. Herein, we identify SlNAC2, a NAC transcription factor in tomato induced by saline–alkali stress, which suppresses the key melatonin biosynthetic genes SlCOMT2 and SlSNAT, while activating SlCV, a gene linked to ROS accumulation and programmed cell death. These regulatory effects reduce MT levels and promote excessive ROS production, ultimately altering the plant’s tolerance to saline–alkali stress. Silencing of SlNAC2 through RNA interference method significantly improves saline-alkali tolerance in tomato, while its constitutive overexpression shows increased susceptibility to saline–alkali stress. Further evidence reveals that under saline-alkali conditions, SlNAC2 directly targets cis-elements of SlCOMT2 and SlSNAT promoters, suppressing their transcription and consequently reducing melatonin levels, whereas simultaneously binding to the SlCV promoter to activate its expression, ultimately leading to ROS accumulation. Moreover, comprehensive protein interaction analyses confirmed that SlNAC2 physically associates with SlDREB2, a DREB-type transcription factor involved in salt stress response. Through its interaction with SlNAC2, SlDREB2 partially attenuates its repression of SlCOMT2 and SlSNAT, thereby increasing melatonin accumulation and ROS scavenging, ultimately enhancing tomato’s resilience to saline–alkali stress conditions. Collectively, our findings reveal a SlNAC2–SlDREB2 regulatory module that finely tunes melatonin synthesis and ROS levels to regulate tomato’s response to saline–alkali stress, providing new strategies for developing stress-resilient tomato varieties.

Abstract Bacterial spot (BS) disease significantly impairs vigor, fruit quality, and yield in peach trees. However, research on this disease remains limited. In this study, peach leaves and fruits were inoculated with the pathogen isolated from infected leaves, triggering a robust accumulation of proanthocyanidins (PA) in both tissues. Further investigation revealed that pathogen inoculation promoted PA accumulation by upregulating PpMYB123, which transactivated the core PA biosynthetic genes PpANR and PpLAR. Notably, the E3 ubiquitin ligase PpPUB23 negatively regulated PpMYB123. However, its transcript levels were significantly suppressed following inoculation, thereby stabilizing PpMYB123 and enhancing PA production. PA conferred dual protection by scavenging excess reactive oxygen species (ROS) and suppressing pathogen growth. Our findings provide molecular evidence for PA-mediated defense against BS disease in peach.

Abstract Oregano (Origanum vulgare) is a highly valued aromatic herb for culinary, medicinal, and ornamental purposes. Its commercial value is largely from its essential oil (EO), which is rich in key bioactive terpenoids, such as carvacrol and thymol. Greek oregano (O. vulgare subsp. hirtum) subspecies is particularly prized for its high EO content. In this study, we generated a high-quality genome assembly of Greek oregano to investigate its evolutionary trajectory and the genetic basis of terpenoid biosynthesis. The assembly spans 709.74 Mb and is anchored to 15 chromosomes, with a scaffold N50 of 46.36 Mb. Comparative genomic analysis revealed a whole-genome duplication (WGD) event, estimated at ~59.93 million years ago (Mya), which likely contributed to the diversification of terpenoid biosynthesis pathways within the Lamiaceae family. Using a rapid screening approach, we identified Greek oregano mutants with higher EO content. Integrated genomic and transcriptomic analysis of a high-EO mutant highlighted the importance of α-linolenic acid metabolism/jasmonic acid (JA) biosynthesis pathways in EO production. Exogenous JA treatment led to upregulation of key EO biosynthetic genes and higher EO content. Furthermore, a JA-inducible bHLH transcription factor, OvbHLH13, was identified as a central regulator of terpenoid biosynthesis. Through Y1H, transcriptional activation, and EMSA assays, we demonstrated that OvbHLH13 directly bound to and transactivated the promoter of OvSDR1, which encodes a critical enzyme in thymol and carvacrol production. Collectively, this genomic resource provides valuable insights into the genetic and regulatory network controlling terpenoid biosynthesis and establishes a critical genomic foundation for molecular breeding of Greek oregano.

Abstract Anthracnose, caused by Colletotrichum species, poses a significant threat to global tea (Camellia sinensis) production, yet its inducible resistance mechanisms remain largely uncharacterized. Through integrated transcriptomic and metabolomic analyses of the anthracnose-resistant cultivar ‘Zijuan’ and the susceptible cultivar ‘Longjing43’, we identified sakuranetin as a key phytoalexin in tea plants and elucidated a complete jasmonic acid (JA)-mediated defense pathway. Our functional characterization revealed that CsNOMT (Cha09g008790), a naringenin 7-O-methyltransferase, catalyzes sakuranetin biosynthesis with high substrate specificity. Following infection with Colletotrichum camelliae, sakuranetin accumulated exclusively in resistant cultivars, exhibiting superior antifungal activity compared to major tea catechins. Functional validation demonstrated that overexpression of CsNOMT enhanced both sakuranetin accumulation and disease resistance, while gene silencing compromised both traits. Mechanistically, we established that the JA-responsive transcription factor CsMYC2.1 directly activates CsNOMT transcription via G-box binding, establishing a novel JA-CsMYC2.1-CsNOMT-sakuranetin defense axis that distinguishes resistant from susceptible tea cultivars. This study represents the first comprehensive characterization of inducible phytoalexin-mediated immunity in tea, providing immediate applications for sustainable tea production. CsNOMT serves as a valuable functional marker for resistance breeding, while sakuranetin emerges as a promising natural biopesticide to reduce reliance on synthetic fungicides.

Abstract Crotalaria is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although Crotalaria pallida is widely distributed in tropical and subtropical regions, the degree of genetic diversity and the specific traits influenced by geographic dispersal remain unknown. We here report a high-quality genome assembly of C. pallida with 98.52% coverage which is assembled into 8 chromosomes. C. pallida is closely related to Lupinus angustifolius, with genetic divergence occurring approximately 42.5-57.4 million years ago (MYA). Re-sequencing of 236 C. pallida accessions revealed a genetic diversity decrease as C. pallida spread from Africa to America and Asia, and from Asia to China and finally to Hainan. Significant divergence was observed in seven traits between non-Hainan and Hainan accessions. Genome-wide association studies identified 73 loci for 18 agronomic traits, 25 of which overlapped with divergent sweeps between non-Hainan accessions and Hainan accessions. Furthermore, the dispersal of C. pallida in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes (CpPTR, CpMYB, CpRLPK, and CpNADK) associated with plant height. This study reveals the genetic basis of trait divergence driven by geographic dispersal and offers valuable resources for the strategic development of C. pallida breeding.

Abstract Kiwifruit (Actinidia spp.) is a globally significant horticultural crop, renowned for its exceptional nutritional value and high vitamin C content. The distinctive genetic features of this genus, including a dioecious sexual system (XY/XX) and a wide range of ploidy (2x–10x), have driven substantial genomic and phenotypic diversification, thereby constituting a valuable germplasm resource for systematic breeding. Recent advances in kiwifruit genomics are transforming the field and revolutionizing our understanding of its evolution, domestication, and the genetic mechanisms underlying agronomic traits. In this review, we highlight the key achievements in kiwifruit genome research over the past decades, chronologically spanning from the initial draft genome assembly to the recent super pan-genome construction. We further synthesize how multi-omics approaches have been leveraged for fine mapping, gene discovery, and the analysis of gene expression and metabolic pathways. Finally, we discuss future research directions and breeding strategies enabled by these genomic breakthroughs, particularly through the applications of genomic selection and gene editing in kiwifruit.