Horticultural Plant Journal最新文献

{"title":"A graph pangenome annotation pipeline (PAP) enhances annotation completeness and variant-aware gene models in population-scale assemblies","authors":"Zhongqi Liu, Zhenya Liu, Guiqi Bi, Zain Ali, Ting Hou, Jiacui Li, Ruoyan Zhao, Wenrui Wang, Tianrong Fan, Yang Dong, Lianzhu Zhou, Qi Xu, Xiaodong Xu, Yanling Peng, Hua Xiao, Cheng Chen, Binxiong Su, Ezi Zhao, Yongfeng Zhou, Yanshuai Xu, Zhijun Dai","doi":"10.1016/j.hpj.2026.05.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.05.001","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"22 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148460311","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":"Cytokinin drives apple branching through the MdWUS2–MdSPL9–MdTCP regulatory module","authors":"Ming Tan, Haican Guo, Feng Ye, Xinran Zhao, Xiaomei Zhao, Zheng Yang, Jiuyang Li, Haoyu Ye, Jianzhu Shao, Ke Li, Zhibo Wang, Guofang Li","doi":"10.1016/j.hpj.2026.04.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.04.005","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"231 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148462143","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":"Advances in Lythraceae genomics: Ecological adaptation, growth and development, and genetic engineering","authors":"Qifang Lin, Ye Zhang, Tangchun Zheng, Cai Ming, Qixiang Zhang, Siren Lan, Zhongjian Liu, Huitang Pan","doi":"10.1016/j.hpj.2026.04.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.04.004","url":null,"abstract":"Plant genomics underpins a foundation for understanding evolution, gene regulation, and fundamental biological processes, subsequently supporting both the conservation and innovative utilization of plant germplasm resources. The Lythraceae family encompasses numerous species of economic and ecological significance, and are valued for their edible, medicinal, and ornamental properties. The family-wide distribution, spanning extreme intertidal zones, semi-deserts and tropical forests, positions Lythraceae as an exemplary model for investigating the genomic mechanisms underlying ecological adaptation. Recent advances in chromosome-level genomes, pan-genomics, genetic mapping, multi-omics integration, and large-scale phenotyping have greatly accelerated research in plant evolution and breeding. Nevertheless, despite the growing genomic and trait-focused studies in Lythraceae, a comprehensive conceptual synthesis linking evolutionary events, structural variation (SV), regulatory networks, and future research directions remain absent. In this review, we present an overview of genomic resources and introduce a unified framework linking whole-genome duplications, lineage-specific SVs, and their functional impacts on species diversification. We also synthesize recent advances in genome evolution, phylogenetic relationships, biotechnology, and molecular mechanisms controlling growth, development, and stress responses. In addition, we address challenges associated with genetic transformation of woody Lythraceae species and discuss strategies to enhance molecular breeding. This review provides a forward-looking perspective on Lythraceae genomics and identifies key scientific questions that will steer future research in evolutionary biology, functional genomics, and crop improvement.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"17 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148538341","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":"Characterization and comparison of three hydroxycinnamoyl acyltransferases involved in caffeoylquinic acids metabolism in Lonicera japonica Thunb","authors":"Liu He, Yufeng Li, Qi Yuan, Zhiying Sun, Xiaohui Pang, Hongmei Luo","doi":"10.1016/j.hpj.2025.12.022","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.12.022","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"39 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148383899","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":"Engineering drought resilience in plants: integrating multi-omics, machine learning, and single-cell technologies for future food security","authors":"Muhammad Umair Hassan, Waqas Mushtaq, Xinfeng Jiang, Abdul Rehman, Inzamam Ul Haq, Shifaa O. Alshammari, Tahani A.Y. Asseri, Qitao Su, Lixian Wang","doi":"10.1016/j.hpj.2026.03.014","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.03.014","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"36 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148383901","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 chromosome–level reference genome of European greenhouse cucumber provides insights into the regulation of fruit external traits","authors":"Yue Chen, Haifan Wen, Jian Pan, Hui Du, Juan Liu, Keyan Zhang, Weiwei Zhang, Huanle He, Run Cai, Junsong Pan, Gang Wang","doi":"10.1016/j.hpj.2026.02.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.02.004","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"343 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148357355","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":"Integrated multi-omics analyses elucidate bagging effects on apple fruit quality and regulatory mechanisms underlying flavonoid and sugar metabolism","authors":"Wen Tian, Lin Wang, Zichen Li, Yanming Sun, Dajiang Wang, Simiao Sun, Kun Wang, Zhao Liu, Hanxin Guo, Wei Shang, Yuan Gao","doi":"10.1016/j.hpj.2025.12.021","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.12.021","url":null,"abstract":"With the rise in comprehensive production costs, non-bagging cultivation has replaced bagging as the core direction for the sustainable development of the apple (<ce:italic>Malus</ce:italic> × <ce:italic>domestica</ce:italic>) industry. Thus, a systematic analysis of bagging cultivation is crucial for modern agricultural innovation. However, the metabolic changes in apple fruit quality induced by bagging and their underlying gene regulatory networks remain poorly explored. This study utilized ‘Fuji’ and ‘Ralls’ apples which are distinct in flavor and integrated transcriptomics, metabolomics, and physiological and biochemical analysis to investigate the effects of bagging on fruit quality and the regulatory mechanisms of flavonoid and sugar metabolism. The results showed that bagging significantly improved the appearance quality of apple fruits, as well as soluble solids, soluble sugars, respiration rate, and ethylene release rate. However, it reduced firmness, vitamin C, titratable acid and total phenols. Further analysis revealed variety-specific impacts. The increase in content of ‘Fuji’ soluble sugar relied on the synergistic rises in fructose, sucrose, glucose and sorbitol, while that of ‘Ralls’ mainly depended on fructose and sucrose accumulation. The reduced titratable acid and total phenols in both varieties were linked to lower levels of malic, quinic, citric, shikimic acids, and phenolic acids under bagging. The integrated transcriptomic and metabolomics analysis indicated that differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) of the flavonoid pathway in ‘Fuji’ were significantly upregulated, with higher expression levels than those in ‘Ralls’. In addition, through a comprehensive analysis of DAMs and DEGs of sugar metabolism, combined with co-expression networks, the regulatory mechanism of DEGs-DAMs mediated by differentially expressed transcription factors (DETFs) was revealed. These findings provide new insights into apple quality regulation and lay a theoretical foundation for high-quality industry development.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"36 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148357358","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":"AcLACs involved in lignin biosynthesis mediate sulfur-induced resistance to bacterial canker in kiwifruit","authors":"Zhaoyi Li, Xianhui Yin, Kun Guo, Youhua Long, Weizhen Wang, Umair Gul, Longjin Li, Kaijing Li","doi":"10.1016/j.hpj.2025.12.020","DOIUrl":"https://doi.org/10.1016/j.hpj.2025.12.020","url":null,"abstract":"Sulfur is an essential plant mineral, playing crucial roles in regulating plant growth and enhancing their disease resistance. Laccases are essential multicopper oxidases involved in lignin polymerization and plant immune responses. However, their function in sulfur-induced resistance (SIR) against <ce:italic>Pseudomonas syringae</ce:italic> pv. <ce:italic>actinidiae</ce:italic> in kiwifruit (<ce:italic>Actinidia chinensis</ce:italic> var. <ce:italic>chinensis</ce:italic>) remains largely unexplored. This study was aimed at identifying SIR-responsive laccase genes and elucidating their functions. The methods included sulfur treatment (S 1.5 kg · m<ce:sup loc=\"post\">-3</ce:sup>), transient and stable overexpression, lignin/ROS assays, defense enzyme activity measurements, hormone signaling analysis, subcellular localization, and RNA-seq. Three SIR-responsive <ce:italic>AcLAC</ce:italic> genes, <ce:italic>AcLAC1</ce:italic>, <ce:italic>AcLAC6</ce:italic>, and <ce:italic>AcLAC31</ce:italic>, were substantially upregulated by sulfur treatment. Transient overexpression of these genes promoted lignin deposition; increased reactive oxygen species (ROS) accumulation, and enhanced the activities of key defense enzymes, including peroxidase, phenylalanine ammonia-lyase, and superoxide dismutase. Furthermore, <ce:italic>AcLACs</ce:italic> were observed to coordinate plant immune responses through the regulation of salicylic acid and jasmonic acid signaling pathways. Among the three genes, <ce:italic>AcLAC1</ce:italic> conferred the strongest resistance, as evidenced by the lowest bacterial load and smallest lesion areas in inoculation assays. Stable overexpression of <ce:italic>AcLAC1</ce:italic> in <ce:italic>Nicotiana benthamiana</ce:italic> (OE4 line) significantly increased syringyl and guaiacyl lignin content, improving stem mechanical strength and enhancing resistance to <ce:italic>Ralstonia solanacearum</ce:italic>. Subcellular localization revealed that <ce:italic>AcLAC1</ce:italic> is located on the plasma membrane, whereas RNA-Seq analysis demonstrated its involvement in regulating phenylpropanoid biosynthesis. These findings indicate that <ce:italic>AcLAC1</ce:italic> plays a central role in sulfur-mediated defense by reinforcing lignification, modulating ROS homeostasis, and activating immune signaling. This study advances our understanding of SIR mechanisms and provides promising molecular targets for breeding disease-resistant kiwifruit cultivars.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"145 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148357477","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":"Fulvic acid alleviates apple replant disease by promoting nitrogen uptake and regulating rhizosphere soil microbial communities","authors":"Yawen Gao, Mei Wang, Li Xiang, Qingfeng Chang, Keke Zhang, Weixiao Tang, Gang Zhao, Xuesen Chen, Chengmiao Yin, Zhiquan Mao","doi":"10.1016/j.hpj.2026.01.008","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.01.008","url":null,"abstract":"Apple replant disease (ARD) poses a significant threat to the health and sustainable development of the apple industry. Chemical fumigation, as the most effective method, is limited due to residual pollution mitigation and other problems. It is crucial to find green and pollution-free prevention and control measures to replace chemical fumigation. Fulvic acid (FA) demonstrates considerable potential in promoting plant growth, resisting soil pathogen infection, and improving soil quality. In this study, we conducted a pot experiment to compare the changes in photosynthetic capacity, reactive oxygen species (ROS) scavenging capacity, <ce:sup loc=\"pre\">15</ce:sup>N uptake and utilization efficiency, and the abundance and community composition of soil bacteria and fungi in replanted apple rootstocks (<ce:italic>Malus hupehensis</ce:italic> Rehd.) after exogenous application of different concentrations of FA, and explored the biocontrol effect of FA on ARD. We found that application of FA at 2 g·L<ce:sup loc=\"post\">-1</ce:sup> effectively mitigated replanting-induced ROS accumulation by enhancing photosynthesis and increasing the activities of defense enzymes in <ce:italic>M. hupehensis</ce:italic> Rehd. seedling roots. Furthermore, FA supplementation improved <ce:sup loc=\"pre\">15</ce:sup>N absorption and utilization by enhancing nitrogen-metabolizing enzyme activities in roots. Notably, significant changes were observed in the community structure of both soil bacteria and fungi, along with a substantial increase in bacterial and fungal abundance compared with treatments without FA addition. Additionally, FA supplementation significantly increased soil enzyme activities. Mantel test results indicated positive correlations between soil properties (except for pH), growth indices, <ce:sup loc=\"pre\">15</ce:sup>N uptake rate, and utilization efficiency. Spearman correlation analysis further revealed relationships of these factors with bacterial/fungal community composition, suggesting that microbial community composition plays a pivotal role in mediating changes within the replant soil environment, thereby affecting plant growth and nutrient uptake and utilization. In conclusion, FA can effectively alleviate ARD by promoting plant nitrogen uptake and optimizing soil microbial community structure.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"132 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148312903","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":"VvHB04/19 delays grape berry ripening via a multi-pathway network and inhibits softening by repressing VvPG5","authors":"Ruiqiang Chao, Linjia Luo, Qiqi Wu, Xicheng Wang, Ehsan Sadeghnezhad, Haitao Chen, Lianshuang Liang, Yuxuan Song, Deshuai Xia, Yan Zhong, Chen Wang","doi":"10.1016/j.hpj.2026.03.010","DOIUrl":"https://doi.org/10.1016/j.hpj.2026.03.010","url":null,"abstract":"Grape (<ce:italic>Vitis vinifera</ce:italic> L.), a fruit crop of global importance, have their quality and market value predominantly determined by the ripening process. Homeobox (HB) transcription factors are known to modulate plant growth and development, hormone signaling, and stress responses; however, their specific roles in fruit ripening remain largely unexplored. Here, a comprehensive analysis identified 56 VvHB genes within the grape genome, distributed across 18 chromosomes. Promoter cis-element analysis revealed a significant enrichment of motifs related to plant hormones and development. Among the VvHBs, transcript levels of <ce:italic>VvHB04</ce:italic> and <ce:italic>VvHB19</ce:italic> declined progressively during grape berry ripening. The transient overexpression of either <ce:italic>VvHB04</ce:italic> or <ce:italic>VvHB19</ce:italic> in grape berries significantly delayed the ripening process. This delay was concomitant with the down-regulation of key genes involved in ethylene biosynthesis (<ce:italic>VvACO1</ce:italic>, <ce:italic>VvACO2</ce:italic>, <ce:italic>VvACS2</ce:italic>, <ce:italic>VvACS4</ce:italic>) and cell wall modification (<ce:italic>VvPG5</ce:italic>, <ce:italic>VvPG11</ce:italic>, <ce:italic>VvPME19</ce:italic>). Consistent with this, the corresponding transient overexpression in tomato fruit also repressed the expression of maturation-related genes. Furthermore, yeast one-hybrid, luciferase reporter, and electrophoretic mobility shift assays (EMSA) demonstrated that both VvHB04 and VvHB19 directly bind to and repressed the promoter of <ce:italic>VvPG5</ce:italic>, a critical gene responsible for ripening-related softening. Collectively, our results establish a regulatory network in which <ce:italic>VvHB04</ce:italic> and <ce:italic>VvHB19</ce:italic> function as transcriptional repressors to delay berry ripening by modulating multiple ripening pathways. This study highlights <ce:italic>VvHB04</ce:italic> and <ce:italic>VvHB19</ce:italic> as potential targets for biotechnological or breeding strategies aimed at fine-tuning ripening timing, thereby improving fruit quality and extending shelf-life in grapes and other fleshy fruits.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"37 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148313161","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}