Horticultural Plant Journal最新文献

{"title":"ABA-induced PbrMYB8-PbrMYB169 module promotes lignin biosynthesis in corking disorder in pear fruit","authors":"Xiaoke Zhang, Shicheng Zou, Chenjie Yao, Yanfei Shan, Jianfa Cai, Cheng Li, Jun Wu","doi":"10.1016/j.hpj.2025.08.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.08.003","url":null,"abstract":"Pear fruit corking disorder is a non-infectious physiological condition that primarily occurs during the late developmental stages of pear and significantly impacts fruit quality and economic value in several major cultivars. As the underlying mechanism remains unclear, effective prevention strategies and genetic improvements continue to present major challenges. In this study, ‘Akizuki’ pear was used as experimental material, and the lignin content in cork-affected tissue was found to be significantly higher than in healthy tissue. Exogenous abscisic acid (ABA) treatment induced cork formation and promoted lignin biosynthesis, a major structural component, in both pear fruits and calli. Through integrated RNA-seq and expression analyses, we identified the ABA-responsive gene <ce:italic>PbrMYB8</ce:italic>, which was differentially expressed between healthy and diseased tissues and associated with lignin biosynthesis during corking disorder. Stable transformation of <ce:italic>PbrMYB8</ce:italic> into pear calli and <ce:italic>Arabidopsis</ce:italic> confirmed its role in promoting lignin biosynthesis. Notably, PbrMYB8 not only activated lignin biosynthesis genes independently but also interacted with PbrMYB169 to form a protein complex that co-regulated their expression. These findings improve our understanding of lignin biosynthesis in pear fruit corking disorder by identifying a key regulator and its interaction network and provide a theoretical foundation for future strategies aimed at improving pear fruit quality.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"24 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning applications advance plant genomics research","authors":"Wenyuan Fan, Zhongwei Guo, Xiang Wang, Lingkui Zhang, Yuanhang Liu, Chengcheng Cai, Kang Zhang, Feng Cheng","doi":"10.1016/j.hpj.2025.08.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.08.004","url":null,"abstract":"With the rapid development of high-throughput sequencing technologies and the accumulation of large-scale multi-omics data, deep learning (DL) has emerged as a powerful tool to solve complex biological problems, with particular promise in plant genomics. This review systematically examines the progress of DL applications in DNA, RNA, and protein sequence analysis, covering key tasks such as gene regulatory element identification, gene function annotation, and protein structure prediction, and highlighting how these DL applications illuminate research of plants, including horticultural plants. We evaluate the advantages of different neural network architectures and their applications in different biology studies, as well as the development of large language models (LLMs) in genomic modelling, such as the plant-specific models PDLLMs and AgroNT. We also briefly introduce the general workflow of the basic DL model for plant genomics study. While DL has significantly improved prediction accuracy in plant genomics, its broader application remains constrained by several challenges, including the limited availability of well-annotated data, computational capacity, innovative model architectures adapted to plant genomes, and model interpretability. Future advances will require interdisciplinary collaborations to develop DL applications for intelligent plant genomic research frameworks with broader applicability.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"131 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of PYL genes as core components of abscisic acid signaling in plant abiotic stress response","authors":"Rongrong Zhang, Shilei Luo, Long Li, Tingting Mu, Peng Wang, Guobin Zhang","doi":"10.1016/j.hpj.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.06.006","url":null,"abstract":"The PYL gene family, encoding core ABA receptors, plays a pivotal role in abiotic stress adaptation and growth regulation in horticultural crops. By binding ABA via its conserved structural domain, PYL proteins initiate signaling cascades through PP2C phosphatase inhibition, precisely modulating downstream ABA responses. This review systematically examines the functional diversification of PYL members and their stress-responsive expression patterns in horticultural species. PYL participates in physiological processes involved in ABA signal transduction regulation. These include stomatal movement, transcriptional regulation, and metabolic regulation, thereby enhancing tolerance to abiotic stresses encountered in horticultural production, such as drought, salinity, low temperature, and darkness. Furthermore, PYLs also regulate developmental traits such as seed germination and root structure, highlighting their dual role in stress resistance and growth and development. The genetic and regulatory complexity of the PYL family offers valuable targets for molecular breeding in horticulture. Future research should elucidate crop-specific PYL regulatory networks to advance precision breeding strategies for sustainable horticultural systems.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"72 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of grape root to determine the regulatory network response to melatonin","authors":"Lili Xu, Wenmao Yang, Hongyang Guo, Chengyin Liu, Aoxing Chen, Syed Aftab Ahmad, Xianpu Wang","doi":"10.1016/j.hpj.2025.04.018","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.04.018","url":null,"abstract":"A root system, which serves as the cornerstone of a plant, is the organ system that initially perceives alterations in soil nutrient concentrations and water conditions. Plant hormones constitute highly significant determinants of root growth and development. To explore the response patterns of ‘Sapphire’, ‘Black Emperor’ and ‘Autumn Crisp’ grape (<ce:italic>Vitis vinifera</ce:italic> L.) roots to melatonin (MT), grape roots were treated with different concentrations of melatonin respectively. The results revealed that the effects of different MT concentrations were similar to those of different auxin concentrations within the range of 0.1, 0.3, and 0.5 mg·L<ce:sup loc=\"post\">−1</ce:sup> for IBA and IAA, which promoted root growth at low concentrations but inhibited root growth at high concentrations. Furthermore, compared with the control, 10 μmol·L<ce:sup loc=\"post\">−1</ce:sup> MT significantly promoted root growth and development by interacting with various endogenous hormones and signaling molecules and with phenols and anthocyanins in grape roots. RNA<ce:bold>–</ce:bold>seq analysis revealed that a total of 1,419 differentially expressed genes (DEGs) identified after MT treatment were enriched in 20 biological processes associated with secondary metabolism, including the biosynthesis of phenylpropanoids, nitrogen metabolism, plant hormone signal transduction, and galactose metabolism. In particular, 11 genes were significantly enriched in the resveratrol metabolic pathway, with 10 being upregulated from 2.93<ce:bold>–</ce:bold> to 9.19<ce:bold>–</ce:bold>fold compared with those in the control. Overall, these results suggested that MT promoted the growth and development of grape roots by regulating the levels of hormones and signaling molecules. Our findings revealed a novel role for MT in root growth and development, suggesting that several transcription-related metabolic pathways could be involved in hormone signaling. This study provided valuable information on root growth and development for the breeding of grape varieties.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"28 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the role of VcCOMT38 as a specific O-methyltransferase for enhancing lignin biosynthesis: Insights from blueberry and cross-species analysis","authors":"Yushan Liu, Ruiyi Fan, Li Chen, Jiabo Pei, Yu Deng, Kun Dong, Liangsheng Wang","doi":"10.1016/j.hpj.2025.02.022","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.02.022","url":null,"abstract":"Lignin is a significant secondary metabolite produced through the phenylpropanoid pathway. As a vital component of the plant cell wall, lignin affects various fruit characteristics, including size, seed quantity, and firmness. In this study, we conducted comprehensive identification and phylogenetic analysis of 265 Caffeic acid <ce:italic>O</ce:italic>-methyltransferase (COMT) genes across ten different plant species, including <ce:italic>Vaccinium corymbosum</ce:italic> and four other <ce:italic>Vaccinium</ce:italic> species. The results reveal that <ce:italic>VcCOMT38</ce:italic> is a promising structural gene for the biosynthesis of lignin in blueberry. An <ce:italic>in vitro</ce:italic> enzymatic assay of VcCOMT38 demonstrated that it is a special enzyme in the lignin biosynthesis pathway and prefers to use caffeic acid as a substrate over 5-hydroxyferulic acid. Transient overexpression and silencing of <ce:italic>VcCOMT38</ce:italic> in <ce:italic>Vaccinium corymbosum</ce:italic> ‘Northland’ fruits demonstrated that <ce:italic>VcCOMT38</ce:italic> participates in lignin biosynthesis and contributes to both an increased number of immature seeds and enhanced fruit firmness. The heterogeneous overexpression of <ce:italic>VcCOMT38</ce:italic> in <ce:italic>Nicotiana benthamiana</ce:italic> revealed that this gene could increase the lignin content and the syringyl/guaiacyl (S/G) ratio, which determines the maximum monomer yield during lignin depolymerization. These results highlight <ce:italic>VcCOMT38</ce:italic> as a crucial gene in lignin biosynthesis and its potential for improving lignin production in industry through genetically modified woody plants.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"52 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Loss of CsPOD7 triggers ROS-induced metabolic collapse and male sterility in cucumber","authors":"Sen Li, Yuming Dong, Xi Zhao, Li Shan, Lin Yang, Menghang An, Yingqi Shi, Tiantian Pei, Muhammad Ahmad, Yifan Xu, Yibing Zhao, Hao Xue, Xinyue Ma, Xingwang Liu, Huazhong Ren","doi":"10.1016/j.hpj.2025.07.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.07.005","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"23 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and functional characterization of anaphase-promoting complex/cyclosome subunits in tomato","authors":"Ge Wang, Peng Zhang, Yingying Wang, Xuemei Zhang, Di Ma, Genzhong Liu, Zhilong Bao, Fangfang Ma","doi":"10.1016/j.hpj.2025.06.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.06.004","url":null,"abstract":"The anaphase-promoting complex/cyclosome (APC/C), a multiunit-E3 ligase, governs both mitotic and non-mitotic pathways by interacting with ubiquitinated proteins. However, developmental functions of APC/C subunits in tomato have been rarely studied. Here, we identified a total of nine APC/C subunits in tomato genome and established their functions in leaf and fruit development via VIGS gene silencing technology. Protein interactions between subunits revealed that tomato ‘Heinz 1706’ had a slightly different APC/C structure from other systems, in which APC8 and APC10 had the most interactions. Silencing APC/C subunits in tomato led to smaller plants with significantly reduced plant height, biomass, leaf area, flower size and fruit size. Cytological analyses confirmed that silencing APC/C subunits repressed both cell division and expansion in tomato leaves and fruits. Both flow cytometric and mitotic index analyses verified the positive role of APC/C in regulating M phase of cell cycle, which led to increased DNA contents in cells of silencing plants. APC1, APC2, APC4, APC11 and CDC27a had more impacts on the floral organ development than other subunits. Silencing APC/C subunits reduced the pollen viability due to unbalanced meiotic division. APC4 and APC6 were important for the fruit maturation while APC1, APC4 and APC10 modulated the fruit shape. Taken together, our findings illustrate that APC/C is essential for tomato development through the modulation of mitotic and meiotic division, and different subunits may have distinct or more profound impacts on the certain tissue development than others.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"24 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AcPI and AcAP3 coordinately regulate sepal-petal formation in pineapple","authors":"Jing Wu, Wei Zhang, Ya Wu, Jingyao Xie, Tao Xie, Wen Yi, Ziqin Zhong, Yan Leng, Junhu He, Ze Peng, Chengjie Chen, Yehua He, Aiping Luan","doi":"10.1016/j.hpj.2025.03.014","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.03.014","url":null,"abstract":"Sepals and petals form the peels of pineapple fruits, which influence the size of cavities below the surface of the fruits (so-called “fruit eye”) and subsequently the fruit quality and edible rate. In this study, to investigate the underlying mechanisms controlling septal-petal formation in pineapple, we utilized a mutant of variety ‘Yulinglong’ with petaloid sepals for comparative analyses with the wild type. Phenotypic and microscopic observations confirmed the either partially or completely petalized structure of the sepals of the mutant. Comparative gene expression analysis identified two MADS-box family members <ce:italic>AcPI</ce:italic> and <ce:italic>AcAP3</ce:italic> that are potentially associated with the petaloid sepals. Heterologous overexpression experiments in <ce:italic>Arabidopsis</ce:italic> and tobacco validated their functions in controlling the identity and organogenesis of sepals/petals, as well as confirmed their role in transforming sepals to petals. Protein–protein interaction experiments and gene expression profiling suggested that AcPI and AcAP3 may coordinately determine floral organogenesis in pineapple flower bud primordia differentiation. The results provide important insights into the molecular regulation of floral organ identity and peel structure formation in pineapple, which may be harnessed to improve fruit quality and edible rate for pineapple.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"129 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The near-complete genome of Lycium ruthenicum shed light on the genetic mechanism of the fruit color differentiation","authors":"Yunlong Liang, Shiming Li, Yun Li, Yanyan Jiang, Jinglei Hu, Guanghui Fan, Dong Cao, Baolong Liu","doi":"10.1016/j.hpj.2025.06.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.06.003","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brassica diversity through the lens of polyploidy: Genomic evolution, introgression, and homoeologous exchange","authors":"Tianpeng Wang, Aalt D.J. van Dijk, Xu Cai, Jian Wu, Guusje Bonnema, Xiaowu Wang","doi":"10.1016/j.hpj.2025.08.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.08.002","url":null,"abstract":"Polyploidy, or whole-genome duplication, is an important evolutionary process that has shaped the genomes and traits of many plants, including numerous important crops. The <ce:italic>Brassica</ce:italic> genus, which includes diverse vegetables and oilseeds, is a key model system for studying how polyploidy affects plant diversification and domestication. This review summarizes the current understanding of how multiple rounds of ancient and more recent polyploidization events laid the foundation for the wide diversity seen in <ce:italic>Brassica</ce:italic>. We discuss the key outcomes through which polyploidy facilitates the accumulation of genetic variation, including genomic buffering that enables mutation retention. Furthermore, we explore the significant roles of interspecies and interploidy introgression in introducing external genetic novelty. We highlight homoeologous exchange (HE) as a critical mechanism unique to allopolyploids, driving substantial genomic rearrangements including presence-absence variations and gene dosage alterations that directly contribute to significant phenotypic innovation and adaptation in <ce:italic>Brassica</ce:italic>. Together, these polyploidy-associated processes have led to the extensive range of genomic variations that shaped great morphological diversification in the domestication of <ce:italic>Brassica</ce:italic>. By integrating insights from genomics, genetics, and evolutionary biology, this review shows how polyploidy has been central to <ce:italic>Brassica</ce:italic>'s success and agricultural value. We also suggest future research areas to better understand polyploid evolution and improve crop breeding.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"26 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}