Metabolomics, a rapidly evolving field, has revolutionized horticultural crop research by enabling comprehensive analysis of metabolites that influence plant yield, growth, quality and nutritional value. The integration of web-based resources, including databases, computational tools and analytical platforms has significantly enhanced metabolomics studies by facilitating data processing, metabolite identification and pathway analysis. Moreover, the application of machine learning algorithms to these web resources has further optimized data interpretation, enabling more accurate prediction of metabolic profiles. Publicly available reference libraries and bioinformatic tools support precision of breeding, postharvest quality assessment and ultimately improving crop yield and sustainability. In this mini-review, we explore the current status of the diverse range of plant metabolomics databases in horticultural crops, highlighting the synergy between machine learning and traditional bioinformatics methods, their applications, challenges and future prospects in advancing plant science and agricultural innovation.

The plant hormone abscisic acid (ABA) regulates fruit growth, development, and ripening, playing a pivotal role in fruit quality during non-climacteric ripening. As a typical non-climacteric fruit, strawberries rely on ABA to promote ripening. However, the optimal concentration for ABA treatment and the mechanisms through which ABA signaling influences gene targets that determine key quality attributes, such as sugar-acid balance and coloration, remain poorly understood. This study examined the effects of exogenous ABA and its inhibitor nordihydroguaiaretic acid (NDGA) on white-stage 'Benihoppe' strawberries. Phenotypic observations and quality measurements were conducted. Results revealed that 0.2 mM ABA treatment most significantly increased soluble sugar content, anthocyanin levels, and the sugar-acid ratio while decreasing fruit firmness and organic acid concentrations. In contrast, NDGA treatment produced opposite effects. RNA-seq analysis further identified differentially expressed genes primarily involved in flavonoid biosynthesis and fructose-mannitol metabolism, suggesting alterations in carbon metabolism within the fruit. These findings elucidate the role of ABA signaling in shaping strawberry quality during fruit development and highlight key genes as potential targets, providing a theoretical basis for advancing strawberry breeding and farming practices.

MicroRNA164 (miR164) is a highly conserved miRNA that targets NAC transcription factors in plants. This study explores its role in regulating stress responses in petunia by generating MIR164 overexpression (MIR164-ox) and miR164 suppression (miR164-STTM) lines. Under heat stress, MIR164-ox lines exhibited enhanced tolerance, while miR164-STTM lines showed reduced tolerance with growth reduction in both shoots and roots. Conversely, under salinity stress, miR164-STTM lines displayed improved tolerance, while MIR164-ox lines were more sensitive, suggesting that miR164 may have a differential regulatory effect on heat and salinity stress responses. To further investigate the molecular mechanisms underlying these differential stress responses mediated by miR164, we conducted a bioinformatic analysis of the NAC transcription factor family in Petunia, the primary targets of miR164. A genome-wide analysis of the NAC gene family in Petunia identified 80 NAC genes in P. axillaris and 91 in P. inflata. Phylogenetic analysis revealed nine distinct clades, indicating both conserved and divergent functions of NAC proteins. Expression analysis of miR164-targeted NAC genes showed tissue- and stress-specific patterns. Protein–protein interaction (PPI) network and Gene Ontology (GO) enrichment analyses provided insights into the potential functions of NAC proteins in petunia, particularly in secondary cell wall biogenesis and xylem development. Real-time qRT-PCR analysis revealed differential expression of specific NAC genes in miR164 transgenic lines under heat and salinity stress, with NAC06 and NAC39/NAC54 showing the most pronounced changes, suggesting their potential involvement in heat and salinity stress responses, respectively. Taken together, our findings suggest that miR164 plays a crucial role in regulating NAC gene expression and stress responses in petunia, providing a foundation for further functional characterization of miR164-NAC regulatory modules in plant stress adaptation.

Chrysanthemum (Chrysanthemum ×  morifolium Ramat.) is a widely cultivated ornamental species, among which green-flowered cultivar representing rarity and distinctiveness. However, the underlying mechanisms governing the formation and regulation of green color remain poorly understood. In this study, exposure to high-intensity light resulted in the loss of green coloration in green chrysanthemum, while low-intensity light preserved it during flower opening in chrysanthemum ‘Lv Dingdang’. A R1-type MYB transcription factor, CmREVEILLE2 (CmRVE2), was identified through transcriptomic analysis of flowers subjected to different light intensities (3,000 Lux for low light, LL; 6,000 Lux for moderate light, ML; and 12,000 Lux for high light, HL). CmRVE2 expression was significantly upregulated under HL conditions, while its expression was lower under LL compared to ML. Additionally, CmRVE2 was upregulated by abscisic acid (ABA) and downregulated by gibberellin (GA). Virus-induced gene silencing (VIGS) of CmRVE2 led to a marked increase in chlorophyll content and the upregulation of chlorophyll biosynthesis-related genes, while CmRVE2 overexpression resulted in the opposite trend. Yeast one-hybrid, electrophoretic mobility shift assays (EMSA), and transient activation assays demonstrated that CmRVE2 directly bound to the promoter of CHLI1, a gene encodes magnesium chelatase I subunit in chlorophyll biosynthesis. Furthermore, CmRVE2 repressed the expression of MAGNESIUM-PROTOPORPHYRIN IX MONOMETHYL ESTER OXIDATIVE CYCLASE1 (CRD1) and PROTOCHLOROPHYLLIDE OXIDOREDUCTASE1 (PORA1), thereby inhibiting chlorophyll synthesis. These findings provide new insights into how CmRVE2 mediates light signaling to negatively regulate chlorophyll biosynthesis in chrysanthemum flowers.

Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), represents a significant threat to the global citrus industry. LATERAL ORGAN BOUNDARIES 1 (LOB1) has been identified as a key gene involved in the development of citrus canker in susceptible varieties. However, the role and molecular mechanisms of LOB1 in disease-resistant varieties, such as Kumquat (Fortunella spp.), remain poorly understood. In this study, transgenic kumquat plants with either Citrus sinensis LOB1 (CsLOB1) overexpression or RNAi-mediated silencing were obtained to investigate the function and molecular basis of LOB1 in kumquat resistance to Xcc. Overexpression of CsLOB1 in kumquats resulted in dwarf phenotype with reduced leaf size, increased branching, and numerous pustule-like bulges resembling citrus canker. Microscopic analysis revealed that these bulges were due to the excessive proliferation of mesophyll cells, along with spongy cell enlargement and palisade cell shortening. Resistance assays showed that CsLOB1 overexpression promoted kumquat susceptibility to Xcc, while the resistance remained stable in the RNAi lines. RNA-seq analysis revealed that CsLOB1 significantly upregulated immune response-related genes in kumquat. Furthermore, CsLOB1 was shown to regulate kumquat immunity through modulation of indole- 3-acetic acid-amido synthetase 3.17 (GH3.17), elongation factor tu receptor (EFR), mitogen-activated protein kinase kinase 5 (MKK5) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1). Taken together, these findings demonstrate that CsLOB1 not only promotes citrus canker development by altering cellular states and hormone signaling but also activates immune responses in kumquat. Our work offers insights into harnessing LOB1 in the breeding of canker-resistant varieties in citrus.

Late blight, caused by Phytophthora infestans, is one of the most devastative global plant threats. Pyramiding multiple resistance genes (R genes) was initially considered as a promising strategy for breeding broad-spectrum late blight-resistance potato varieties. However, stacking multiple R genes may induce detrimental effects on plant health. Fine-tuning the expression of R genes is critical for their effective stacking in potato breeding. This study confirms that low-level expression of individual potato late blight resistance genes like RB, R8, and Vnt1.1, controlled by the CaMV 35S promoter, does not trigger cell death (CD). However, co-expression of these genes in Nicotiana benthamiana leaves induces CD. Plant upstream open reading frames (uORFs) attenuate the translation of the downstream main ORF. We demonstrates that N. benthamiana open reading frame (NbuORF) and Solanumtuberosum L. open reading frame (StuORF) completely suppress green fluorescent protein (GFP) translation, whereas Arabidopsisthaliana open reading frames (AtuORFs) only partially inhibit GFP translation in N. benthamiana leaves. Simultaneous expression of AtuORFs or StuORF and RB, under the control of either pathogen-inducible potato vetispiradiene synthase gene 3 (PVS3) promoter or the 35S promoter, leads to inhibition of CD. Transgenic potatoes with 35S::RB exhibit superior late blight resistance compared to PVS3::RB transgenic lines. Plants expressing 35S::StuORF-RB show increased resistance, although slightly lower than that of 35S::RB transgenic plants. However, 35S::AtuORFs-RB and PVS3::AtuORFs-RB transgenic potatoes are susceptible to P. infestans, suggesting that AtuORFs and StuORF suppress RB translation in these plants. These findings highlight the potential of different promoter and uORF combinations for finely tuning R gene expression, which may optimize the balance between plant resistance and normal growth.

The SQUAMOUS PROMOTER BINDING PROTEIN-LIKE (SPL) gene family encodes plant-specific transcription factors that regulate diverse physiological processes, including growth, flowering, and stress responses. A total of 32 PaSPL genes were identified and characterized in the genome of Platanus × acerifolia, an ancient hexaploid species widely cultivated as a street tree. The PaSPL genes were classified into nine distinct groups based on their phylogenetic relationship. Gene structure examination revealed considerable variation in intron number and length among groups. Cis-regulatory element analysis indicated that the promoter regions of PaSPLs are enriched with light-responsive elements. Expression profiling across different tissues and developmental stages demonstrated that the PaSPL genes harboring a site targeted by microRNA156 exhibited stage-specific expression patterns, while those in the Groups II, III, V, and IX displayed tissue-specific expression. Notably, several PaSPL genes exhibited dynamic expression during floral transition, implicating their role in flowering regulation. Among them, PaSPL8a, a Group III member, was differentially expressed in flowerless germplasm resources. Functional characterization demonstrated that PaSPL8a overexpression in Arabidopsis thaliana accelerated flowering and upregulated key flowering regulators. These findings provide mechanistic insights into the function of PaSPLs in P. × acerifolia and establish PaSPL8a as a positive regulator of flowering.

The golden camellia, a highly valued ornamental plant, belongs to the Chrysantha section, the sole group in the Camellia genus that produces yellow flowers. The cultivation and broader application of this unique species have been significantly hindered by the scarcity of golden camellia and the limited knowledge of the molecular mechanisms governing yellow flower development. To investigate the dynamics of metabolite accumulation and gene expression during the yellow flower formation of C. perpetua, a continuously flowering golden camellia, a comprehensive metabolomic and transcriptomic analysis was performed across five distinct developmental stages. This analysis identified 1,160 metabolites, with flavonoids constituting the largest proportion at 21.6%. Comparative transcriptomic profiling indicated that differentially expressed genes (DEGs) associated with photosynthesis were predominantly active during the early stages of flower development, while DEGs involved in the flavonoid biosynthesis pathway showed a marked increase as the flowers matured. The integrated metabolomic and transcriptomic data highlighted the pivotal regulatory role of the flavonoid biosynthesis pathway in the formation of yellow flowers in C. perpetua, identifying 50 key genes and 17 crucial metabolites and mapping their interaction networks. Furthermore, weighted gene co-expression network analysis pinpointed several hub genes, such as flavonol synthase, which are likely critical to flavonoid production due to their elevated expression levels, particularly in the early bud and yellowing phases. This study provides valuable insights into the molecular pathways that underlie yellow flower development in golden camellia species.

In vitro slow-growth storage has long played an important role in maintaining valuable horticultural materials. It is particularly applicable to the conservation of virus-free materials recovered from meristem culture or shoot-tip cryotherapy. In this study, the apple cultivar ‘Yanfu-6’ and the rootstock genotype ‘Qingzhen-1’ obtained from a virus disinfection program were compared during the establishment of in vitro slow-growth storage programs. At room temperature (25℃), combining with 4.5% sucrose or 0.5% mannitol, extended the conservation period of ‘Yanfu-6’ and ‘Qingzhen-1’to 5 and 9 months, respectively. Decreasing the temperature to 12℃ led to further reduced shoot growth, extending the conservation period to 9 months for ‘Yanfu-6’, while more than 80% of ‘Qingzhen-1’ shoots could be recovered after one year of storage. Similarly, high rooting and acclimatization success levels were obtained for ‘Qingzhen-1’ after one-year storage at 12℃, as well as for the plants that underwent monthly subcultures, but not for ‘Yanfu-6’. The inability to root in ‘Yanfu-6’ was overcome by micrografting onto rootstock ‘Qingzhen-1’, which resulted in a rooting percentage of 83% and an acclimatization success of 77%. In the analysis of genetic stability by next-generation sequencing, reduced levels of single nucleotide polymorphism (SNPs) and insertions and deletions (InDels) were detected in ‘Qingzhen-1’ shoots recovered after one-year storage at 12℃, as compared with shoots that underwent regular subcultures. These results highlight the use of in vitro slow-growth program assisted with micrografting for the conservation of valuable horticultural species.

Pathogenesis-related proteins (PRs) are essential for plant defense against both biotic and abiotic stresses. However, knowledge regarding PRs in pears remains limited. In this study, 637 PRs, classified into 16 families, were identified in Pyrus bretschneideri. Phylogenetic, sequence similarity, and secondary structure analyses enabled the classification of several PRs with conserved sequences, including PR-11, PR-8, PR-15, and PR-16. Genomic analysis revealed that the expansion of most PR families resulted from recent whole-genome duplication (WGD) events, occurring approximately 30–45 million years ago (Mya). Various gene duplication mechanisms have collectively contributed to the proliferation of PR families, with purifying selection indicated by the low Ka/Ks ratios. Examination of apoplastic fluid composition showed that only a subset of PRs was present in the apoplast. Transcriptomic data from Pyrus infected with Erwinia amylovora and Colletotrichum fructicola revealed the expression profiles of PR genes post-infection, underscoring the complexity of PR regulation. This study elucidates the evolutionary expansion, regulation, and functional roles of PRs in disease resistance, highlighting certain PRs as reliable markers of pear disease resistance. These findings offer valuable insights for future functional analyses and breeding strategies to enhance pear resistance to pathogens.

Model organisms have been instrumental in advancing discoveries in plant biology. Tomato (Solanum lycopersicum) is distinguished as a prominent model system due to its well-characterized genetics and economic significance as a crop. Micro-Tom (MT), an ornamental dwarf tomato variety, was adopted by the tomato research community as a model plant due to its short stature, fast life cycle, ease of genetic transformation, and ample genomic resources. Over the last 30 years, the use of MT has illuminated various facets of plant development, including the control of growth habit, glandular trichomes, leaf anatomy, and the formation of arbuscular mycorrhizal symbioses. We briefly summarize these contributions and point to further potential advances in the future.

Horticultural crops yield considerable economic benefits, vital for supply stability and income enhancement. Plant breeders' rights (PBR) form a foundation, offering breeders essential safeguards to secure benefits and sustain breeding efforts. Therefore, comprehending the status and challenges in horticultural crop variety protection is vital for advancing horticulture. These crops encompass five primary categories: ornamental plants, fruit trees, vegetables, tea, and edible fungi. This article reviews the distinctness, uniformity, and stability (DUS) testing guidelines and progress in molecular identification research for Chinese horticultural crops from 1999 to 2022. Additionally, it statistically analyzes data from the Chinese Ministry of Agriculture and Rural Affairs and the Forestry Knowledge Service System on PBR applications and grants for all horticultural crop breeders. This review aims to provide a comprehensive understanding of the current state of horticultural crop variety protection in China. By thoroughly analyzing the existing status and challenges, the article seeks to enhance the international standing of plant variety protection in Chinese horticulture.

Lily (Lilium spp.) is popular for its colorful flowers and exquisite scents. Nonetheless, high temperatures often severely reduce its yield production and quality. The implementation of biotechnological approaches to manipulate the expression of key heat-resistant genes is an effective way to improve the thermotolerance of plants. Here, we isolated a gene encoding for a multi-protein bridging factor 1c (MBF1c) from L. longiflorum 'White Heaven' (LlMBF1c), which was highly similar to MBF1c from Elaeis guineensis (EgMBF1c). LlMBF1c harbors conserved MBF1 and helix-turn-helix (HTH) domains. Moreover, the expression of LlMBF1c and its promoter activity were enhanced under high-temperature conditions. Further analysis indicated that LlMBF1c is a transcriptional repressor in both yeast and Nicotiana benthamiana. Its protein was located in the nucleus and cytoplasm of N. benthamiana leaf cells. Overexpression of LlMBF1c in lily and Arabidopsis resulted in enhanced thermotolerance in these plants. By contrast, silencing LlMBF1c reduced the thermotolerance of lily. Our results identified an important candidate gene that can be utilized to develop thermotolerant lily germplasm.

It is essential to find environment-friendly agrochemicals to cope with the problems of nutrient imbalance, fruit quality decline, and physiological disorders during apple fruit production, which is beneficial for improving the quality and yield of apple. A natural extract from Paecilomyces variotii (ZNC), an endophytic fungus, has been used widely to enhance crop performance. However, an understanding of the mechanism underlying ZNC-triggered growth and alleviation of nutrient deficiency-associated symptoms in apples remains elusive. Here, the photosynthesis, leaf growth, and fruit quality were enhanced by adding ZNC. In addition, ZNC relieved nutrient deficiency-related symptoms promoted the differentiation of root morphology and vitality, and reduced the accumulation of osmoprotectants and reactive oxygen species, thereby promoting growth under normal and nutrient-deficient conditions. Finally, genome-wide RNA sequencing reveals the ZNC-regulated mechanisms involved in hormone and metal ion pathways. Our study reveals the role of ZNC in promoting growth and improving the quality of apple, providing a new direction for reducing the use of chemical fertilizers and pesticides.