Celery (Apium graveolens) is a globally cultivated vegetable renowned for its health-promoting and nutraceutical benefits. Exploring its genomic and metabolic diversity can help to facilitate breeding selection. Here, by integrating genomic and metabolomic analyses of 305 globally representative accessions, we reveal pronounced east-west population structure that parallels geographical distribution and varietal differentiation, with three major variety groups showing distinct domestication trajectories. We identify key loci associated with domestication-related traits, including petiole morphology and bolting time. Metabolite profiling uncovers divergence among populations: var. dulce, predominantly consumed raw in Western culinary traditions, exhibits marked reductions in bitter coumarins and alkaloids-a metabolic signature consistent with fresh-eating preferences. Metabolite GWAS map 335,692 loci for 1552 metabolites. We develop genomic prediction models for metabolite abundance to aid breeding. Collectively, our study reveals the genomic and metabolic landscape of celery domestication, and provides hypotheses regarding how cultural practices, alongside regional environmental factors, may have jointly shaped current diversity.

Turnip mosaic virus (TuMV), an important member of the Potyvirus genus, exhibits broad host adaptability with increased prevalence under moderate drought and elevated temperature conditions. While our previous research identified eukaryotic translation initiation factor 2Bβ (eIF2Bβ) as a critical resistance determinant against TuMV in mustard (Brassica juncea), the mechanistic interplay between environmental factors and viral pathogenesis remains poorly understood. Here, we demonstrated that drought facilitates TuMV infection in an abscisic acid (ABA)-dependent manner in B. juncea. Integrated coexpression analysis revealed the functional relevance between ABA signaling and eukaryotic translation initiation pathways. We showed that ABA-responsive element-binding factor 4 (ABF4) directly binds to the eIF2Bβ promoter and activates its expression and that ABF4 overexpression significantly enhances TuMV accumulation in wild-type plants. Notably, eIF2Bβ knockout lines exhibited significantly reduced viral accumulation even when ABF4 was overexpressed, establishing that functional eIF2Bβ is required to mediate ABF4-dependent viral infection. These findings elucidate a new ABA-eIF2Bβ regulatory module that links drought responses with plant-virus interactions, providing mechanistic insights into the role of environmental factors in modulating pathogen susceptibility.

The bulbil, originating in the leaf axil of Lilium lancifolium, functions as a vital reproductive organ for bulbous propagation. The mechanism of bulbil formation, however, is still unclear. In this study, we conducted histological, transcriptomic, and gene function analyses on leaf axil samples throughout bulbil formation. Histological analysis revealed that the bulbils arose from the axillary meristem and bulbil formation undergoes a two-step process: initiation and development. During the bulbil initiation stage, RNA-seq analysis revealed that the differentially expressed genes (DEGs) were primarily enriched in phytohormone-related pathways, especially auxin. Through virus-induced gene silencing (VIGS), the individual silencing phenotypes of nine genes derived from four hormones imply that decreased auxin and ethylene signaling, paired with increased cytokinin and gibberellin, may contribute to bulbil initiation. Among the numerous differentially expressed transcription factors, LlMYB119 may play a role as a candidate gene in auxin-regulated bulbil initiation, as confirmed by quantitative real-time PCR (qRT-PCR) and VIGS. During bulbil development, DEGs showed significant enrichment in carbohydrate metabolism, as well as phytohormone signal transduction. Silencing seven specific genes involved in auxin and ethylene signaling, cytokinin and gibberellin biosynthesis, as well as carbohydrate metabolism, resulted in inhibition of axillary organ development. In summary, this study offers a rich pool of candidate genes, enhancing our understanding of the regulatory mechanism underlying bulbil initiation and development, and holding significant commercial potential for the advancement of new reproductive organs in L. lancifolium.

Mungbean is an important legume and protein source, but its productivity is severely limited by the mungbean yellow mosaic India virus (MYMIV), and no MYMIV resistance gene has been cloned and functionally validated in mungbean. This study conducted extensive phenotypic variation research on the resistance of a newly developed mungbean multiparent advanced-generation intercross (MAGIC) population. Through an integrated genome-wide association study (GWAS), transcriptome analysis, and induced expression analysis, the candidate gene for MYMIV resistance was identified as VrADH, encoding alcohol dehydrogenase. Haplotype analysis revealed natural variation in VrADH, with VrADH Hap1 being the elite haplotype that has undergone selection in regions severely affected by MYMIV. Functional validation demonstrated that VrADH significantly enhanced resistance by limiting excessive reactive oxygen species accumulation and reducing viral proliferation. Collectively, our results indicate that VrADH can contribute to MYMIV resistance, providing a valuable genetic resource for future molecular breeding and resistance improvement in mungbean.

Drought stress poses a severe and growing threat to global crop production due to climate change. Brassica juncea is an important vegetable and oil crop with high potential for cultivation in arid and semi-arid regions, yet its genetic mechanisms underlying drought resilience remain poorly understood. Here, we evaluated the phenotypes of geographically diverse B. juncea accessions under drought stress and identified a candidate gene BjuB.HAM1 via genome-wide association study (GWAS) approach, a plant-specific GRAS-family transcription factor, as a key negative regulator of drought tolerance. We discovered two structural variations (SVs) within BjuB.HAM1 that significantly impair drought tolerance in B. juncea. Using heterologous expression of BjuB.HAM1 in Arabidopsis thaliana, combined with downstream gene validation, we demonstrated that this gene inhibits the expression of AtUGT76C2, a cytokinin glycosyltransferase, and reduces drought tolerance by binding to its GT cis-elements in the promoter. Collectively, these findings uncover a new insight into the functional gene module of drought resistance, and provide valuable genetic targets for drought resistance breeding in Brassica juncea.

Plant mitochondria possess a genome that not only encodes genes essential for respiration and energy production but also influences important traits such as cytoplasmic male sterility (CMS). However, the manipulation of mitochondrial DNA (mtDNA) has long been challenging. Recent breakthroughs in protein-based editing tools, beginning with Transcription Activator-Like Effector Nucleases (TALENs) and extending to TALEN gene-drive mutagenesis (TALEN-GDM) and, most recently, TALE-based base editors, have helped overcome some of these barriers. Nevertheless, mitochondrial transformation remains a significant limitation. Promising developments in this field come from nanotechnology and peptide engineering. In this review, we systematically compare these emerging tools, with a focus on the mechanisms responsible for their distinct editing outcomes and inheritance patterns, while critically examining current limitations and proposing potential strategies to overcome them. We assess persistent challenges in plant mitochondrial transformation. Furthermore, we detail how mitochondrial genome editing is advancing research on cytoplasmic male sterility, which has the potential to facilitate crop breeding. Finally, we outline how CRISPR is expected to enrich the editing toolbox and discuss potential uses of mitochondrial genome engineering to expand our understanding of mitochondrial biology and provide novel opportunities for crop improvement.

Waterlogging is a major abiotic stress that severely constrains plant growth and development. While studies on waterlogging tolerance have predominantly focused on wetland plants, the molecular adaptation mechanisms in xerophytes remain largely unexplored. Watermelon (Citrullus lanatus), a typical xerophyte, is highly susceptible to waterlogging and thus represents a valuable system for dissecting waterlogging adaptation in upland plants. We performed a genome-wide association study on waterlogging-induced shoot elongation using a diverse panel of 122 watermelon accessions and identified ClPrx53, which encodes a class III peroxidase, as a positive regulator of shoot elongation under waterlogging - a key component of the escape response. A causative G-to-T single-nucleotide polymorphism (SNP) in the promoter of ClPrx53 enhances its transcriptional activity and underlies natural variation in waterlogging tolerance. We further demonstrate that this SNP confers waterlogging-inducible expression of ClPrx53 and modulates the binding affinity of the DELLA protein ClGAI-LIKE to its promoter, thereby linking GA signaling to peroxidase-mediated reactive oxygen species homeostasis and shoot elongation under stress. Our work delineates a DELLA-ClPrx53 regulatory module that fine-tunes the waterlogging escape response in an upland crop, providing a precise molecular target for breeding climate-resilient crops.

As a key agronomic trait, leaf color is closely linked to plant photosynthetic efficiency. In this study, we investigated the genetic mechanisms of leaf color variation in sponge gourd using an F2 population generated from two phenotypically distinct parents. Through bulked segregant analysis (BSA), a 4.89 Mb candidate region related to leaf color was mapped on chromosome 8. Further combination of resequencing and fine mapping analysis identified a non-synonymous SNP variation in the exon of the EXECUTER 1 (EX1). We verified its function through homologous gene mutation in Arabidopsis thaliana, revealing its role in leaf color variation and its significant impact on photosynthetic performance. Furthermore, a functional molecular marker developed based on this SNP showed strict co-segregation with the leaf color phenotypes in the F2 population. This study provides vital insights into the molecular basis of leaf color trait in sponge gourd and establishes a solid foundation for marker-assisted breeding targeting enhanced photosynthetic traits.

Non-Mendelian transmission of mitochondria has been well established across most eukaryotes, however the genetic mechanism that governs this uniparental inheritance remains unclear. Plants in the genus Cucumis, specifically melon and cucumber, exhibit paternal transmission of the mitochondrial (mt) DNA, making them excellent models for exploring the molecular mechanisms underlying mitochondrial transmission. Here, we develop a toolkit to screen for mutants in mitochondrial inheritance (mti), and use fine mapping to successfully identify a mitochondrially targeted endonuclease gene (MTI1) controlling mitochondrial transmission. Knockout of MTI1 results in a shift from paternal to bi-parental inheritance of the mtDNA, confirming the crucial role of MTI1 in uniparental inheritance of mitochondria. Moreover, we demonstrate that MTI1 exhibits robust endonuclease activity both in vitro and in vivo, specifically expresses in mitochondria of the fertilized ovule within 24 h of pollination. Collectively, this study reveals that a nuclear-encoded but mitochondria-targeted gene plays a causative role in governing the non-Mendelian mitochondrial inheritance, revolutionizing our knowledge about mitochondrial DNA transmission.

Lilies are globally cultivated ornamental flowers and an economic crop, whose flower bud initiation is regulated by a complex interplay of intrinsic factors and external environmental conditions; however, this mechanism remains largely unknown. In the present study, RNA sequencing (RNA-seq) coupled with histological and gene functional data were employed to reveal the differences in flower bud initiation between various lily cultivars. The results exhibited that the floral buds of the O-series 'Brasilia' and 'Hachi' differentiated quickly, the LA -series 'Purple Marble' and the OA-series 'Hotel California' were slower some differentially expressed genes (DEGS) involved in pathways such as photoperiod, gibberellin, age, vernalization, autonomous, and temperature were identified. A flowering transition-related gene, FCA, was identified, and the effectiveness of the virus-induced gene silencing (VIGS) system was validated. The results showed the expression of LtFCA was successfully knocked down using the VIGS system, leading to compromised flower bud initiation in silenced lily plants. This observation underscores a potential correlation between the expression patterns of flowering regulatory genes and the distinct species within the lily series. In conclusion, this research provides a basis for understanding the regulatory mechanisms of flower bud transition in lilies.

The homeodomain leucine zipper protein ClLMI1 plays a crucial role in the development of lobed leaf morphology in watermelon by influencing the auxin distribution. Lobed leaf is a critical phenotypic trait that influences light penetration and resultant canopy photosynthesis for potential productivity, which plays an important role in horizontal growing crops like watermelon. However, molecular mechanisms underlying the genetic variations of lobed leaves in watermelon remain poorly understood. In this study, we identified ClLMI1 encoding homeodomain leucine zipper protein as the causal gene for lobed leaf formation via BSA-Seq and subsequent fine mapping approaches. A splice-site SNP in an intron caused a 24 bp deletion in ClLMI1 coding region, leading to a deletion of eight amino acids in the leucine zipper domain of the mutant protein cllmi1 for lobe-free leaf phenotype. Additionally, CRISPR/Cas9-mediated knockout of ClLMI1 in watermelon validated its essential role in lobed leaf formation. Expression analysis revealed that ClLMI1 expression peaks at the tips of lobes, consistent with auxin accumulation patterns. Exogenous application of auxin and the auxin polar transport inhibitor N-1-naphthylphthalamic acid (NPA) inhibited lobes development in lobed leaf watermelon. Integrative yeast one-hybrid (Y1H) assay, electrophoresis mobility shift assay (EMSA) and dual-luciferase assay demonstrated that ClLMI1 can directly bind to the promoters of ClPIN1 and ClCUC2, activating their transcriptions to mediate auxin gradient distribution along leaf margin. Collectively, our findings elucidate ClLMI1 as a key regulator of leaf morphogenesis in watermelon and enhance the understanding of the regulatory mechanism of plant lobed leaf formation, facilitating the improvement of canopy photosynthesis by molecular design breeding in economically important watermelon crop.

The emerging technology of inhibiting polyphenol oxidase (PPO) is crucial for preventing enzymatic browning in food. This study aimed to investigate the effects of 4.5 kJ/m2 ultraviolet (UV)-C radiation and 0.02 mg/mL L-cysteine (L-cys) treatment on the enzyme activity, physico-chemical properties, thermal properties, structure, and molecular microstructure of PPO. UV-C/L-cys decreased PPO activity and had the highest aggregation index and turbidity of PPO. UV-C/L-cys further reduced the denaturation temperature point and increased the denaturation enthalpy of PPO. UV-C/L-cys turned the α-helix to random coil of PPO and destroyed the tertiary structure. This combined treatment aggregated the microstructure of PPO, which led to covering the active center of the enzyme, leading to its inactivation. Molecular docking simulation confirmed that L-cys bound to PPO through hydrogen bonding and ionic contact. This study established a foundation for the application of UV-C radiation and L-cys treatment to control food browning.

Lobed leaves play a critical role in enhancing the productivity of sprawling crops like zucchini by improving light capture and boosting photosynthesis. However, the genetic basis in zucchini remains largely unknown. Here, we developed an F2 population from a cross between the entire-leaf cultivar ‘LR’ and the deeply lobed cultivar ‘Xi’. Genetic analysis showed that the non-lobed trait is dominant, with the F2 segregation ratios (~9 entire:6 shallowly lobed:1 deeply lobed) indicating digenic inheritance. Using bulked segregant analysis sequencing (BSA-seq) and kompetitive allele-specific PCR (KASP) marker analysis, we identified a major effect locus at a 79.8 kb interval on chromosome 10. Within in this interval, gene expression profiling and annotation indicated CpARF6, encoding an auxin response factor, to be the prime candidate gene. Sequencing analysis revealed five nonsynonymous mutations in this gene, including a critical serine-to-leucine substitution at position 335 within the auxin response domain, which is likely a loss function mutation. Our findings establish CpARF6 as a critical regulator of lobed leaf formation in zucchini, providing valuable insights for both leaf development studies and zucchini breeding.

Lily bulbils originate from the leaf axils of the middle and upper stems of lilies and play an important role in the reproduction of triploid Lilium lancifolium. The development process of lily bulbils results from cell division and expansion, but the roles of plant hormones and carbohydrate metabolism remains unclear. In this study, we treated L. lancifolium with exogenous indole-3-acetic acid (IAA) and the auxin polar transport inhibitor N-1-naphthylphthalamic acid (NPA) and analyzed morphology, transcriptomics, and gene function during bulbil development. The IAA treatment increased the bulbil diameter and total weight per plant, promoting bulbil development. By constructing an association network of characters and modules, we found that bulbil diameter was significantly negatively correlated with the black module genes and positively correlated with the yellow module genes, which are related to plant hormone and carbohydrate metabolism. We identified key genes in the bulblet system due to bulbil and bulblet development similarities. Silencing the LlSAUR36 and LlIAA10 genes in the auxin signaling pathway inhibited bulblet development. In the carbohydrate metabolism pathway, we identified two key genes using silencing methods, LlTPS1 and LlCSLC5, resulting in phenotypes similar to LlSAUR36 and LlIAA10, which inhibited bulbil development. In conclusion, auxin signaling engages in the bulbil development of L. lancifolium by regulating key carbohydrate metabolism genes. This study provides a molecular basis for developing lily bulbils and offers useful clues for the future development of new lily bulbil production methods.

Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research. Lilies are perennial plants with ornamental flowers and large genomes. The authors assemble genomes of two Liliales species, analyze lily phylogeny, flower and stem development (bulbs in lilies, rhizomes in flame lilies), bulb growth transitions, and colchicine biosynthesis.

Outside Front Cover: The cover image is based on the article Identification and Characterization of Innate Immunity in Actinidia melanandra in Response to Pseudomonas syringae pv. actinidiae by Jay Jayaraman et al., https://doi.org/10.1111/pce.15189.

Global climate change has rendered drought stress an increasing threat to sustainable crop production. Melon (Cucumis melo) crop is widely cultivated worldwide, and has been classified into two subspecies C. melo ssp. melo and C. melo ssp. agrestis with greater drought tolerance variation. However, the genetic basis for the difference in drought resilience between two subspecies ecotypes remains unclear. In this study, we constructed an F8 recombinant inbred lines (RILs) population generated by crossing drought-tolerant C. melo ssp. melo with drought-sensitive C. melo ssp. agrestis and identified a CmPPR4 gene that encoded a pentatricopeptide repeat (PPR) protein highly associated with drought tolerance. A single nucleotide polymorphism (SNP) variation in CmPPR4 resulted in a nonsynonymous mutation, leading to reduced drought resilience in C. melo ssp. agrestis. The geographical distribution of CmPPR4 genotypes among 297 melon accessions closely parallels global annual precipitation patterns. Furthermore, the diminished drought tolerant capacity in RNA silencing seedlings and enhanced drought tolerance in overexpression lines further confirmed CmPPR4 as a crucial regulator of drought tolerance in melon. Collectively, our findings provide new insights into the crucial role of CmPPR4 in regulating drought tolerance of melon ecotypes, promoting molecular breeding of water-saving and drought-resilient melon cultivars.

Domestication not only modulates the genetic characteristics of crops but also reconfigures their associated microbial communities, which subsequently impact plant health, disease resistance, and ecological adaptability. In our study, we explore the disparities in microbial communities, metabolic profiles, and fruit quality between the domesticated watermelon cultivar Citrullus lanatus var. vulgaris (M1511-3) and its wild progenitor, Citrullus mucosospermus (PI595203). Our findings reveal that domestication profoundly reshapes microbial composition: Citrullus lanatus var. vulgaris (M1511-3) is predominantly colonized by Sphingomonas species, which facilitate fruit development and enhance sweetness, whereas Citrullus mucosospermus (PI595203) sustains a more diverse microbial community, encompassing Gammaproteobacteria, Bacilli, and Actinomycetia, which confer increased ecological resilience and disease resistance. These microbial discrepancies are reflected in divergent metabolic profiles: Citrullus mucosospermus (PI595203) exhibits enhanced nucleotide and D-amino acid metabolism, indicative of superior stress adaptation, whereas Citrullus lanatus var. vulgaris (M1511-3) demonstrates optimized carbohydrate, lipid, and amino acid metabolism, underpinning its superior fruit quality. Furthermore, the microbial community of Citrullus lanatus var. vulgaris (M1511-3) exhibits augmented redox and carbohydrate-binding capacities, while Citrullus mucosospermus (PI595203) displays a broader enzymatic repertoire, promoting more efficient carbohydrate utilization and enhanced environmental adaptability. Remarkably, Citrullus mucosospermus (PI595203) harbors approximately 40 antibiotic resistance genes, underscoring its ability to withstand pathogen-induced stress. In contrast, Citrullus lanatus var. vulgaris (M1511-3) leverages optimized metabolic pathways to enhance fruit quality. These findings emphasize the pivotal role of microbial interactions in shaping plant traits and suggest the potential of introducing beneficial microbes, such as Sphingomonas, to enhance crop resilience and quality.

Fruit length (FL) is an important economical trait that affects fruit yield and appearance. Pumpkin (Cucurbita moschata Duch) contains a wealth genetic variation in fruit length. However, the natural variation underlying differences in pumpkin fruit length remains unclear. In this study, we constructed a F2 segregate population using KG1 producing long fruit and MBF producing short fruit as parents to identify the candidate gene for fruit length. By bulked segregant analysis (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) approach of fine mapping, we obtained a 50.77 kb candidate region on chromosome 14 associated with the fruit length. Then, based on sequence variation, gene expression and promoter activity analyses, we identified a candidate gene (CmoFL1) encoding E3 ubiquitin ligase in this region may account for the variation of fruit length. One SNP variation in promoter of CmoFL1 changed the GT1CONSENSUS, and DUAL-LUC assay revealed that this variation significantly affected the promoter activity of CmoFL1. RNA-seq analysis indicated that CmoFL1 might associated with the cell division process and negatively regulate fruit length. Collectively, our work identifies an important allelic affecting fruit length, and provides a target gene manipulating fruit length in future pumpkin breeding.