Horticulture Research最新文献

{"title":"Multi-trait evaluation of a tomato MAGIC population identifies promising lines with improved nitrogen use efficiency (NUE)","authors":"Virginia Baraja-Fonseca, Daniel Gil-Villar, Jon Bančič, Begoña Renau-Morata, María Salud Justamante, Mariola Plazas, Pietro Gramazio, Santiago Vilanova, José Manuel Pérez-Pérez, Antonio Granell, Rosa Victoria Molina, Sergio G Nebauer, Jaime Prohens, Andrea Arrones","doi":"10.1093/hr/uhag428","DOIUrl":"https://doi.org/10.1093/hr/uhag428","url":null,"abstract":"Nitrogen-use efficiency (NUE) is a pivotal breeding target in tomato (Solanum lycopersicum L.) to sustain production under reduced N inputs. Here, we leveraged a recently developed tomato multi-parent advanced generation inter-cross (ToMAGIC) population to identify lines with superior performance under reduced N availability. The eight founders and a core subset of 118 ToMAGIC lines were characterized with 10,684 SNP markers and evaluated under optimal (opN, 15 mM) and suboptimal (subN, 8 mM) N supply in an experiment totalling 1,576 plants, generating 48,068 data points across 61 phenotypic variables. Under both N treatments, ToMAGIC lines exhibited transgressive segregation for most traits, confirming the value of this population as a reservoir of untapped variation. Notably, under subN conditions, harvest index (Hi) increased by 29-44%, suggesting adaptive resource redistribution toward reproductive sinks. Variance partitioning revealed that agronomic and NUE-related traits were largely under genetic control, with heritability estimates frequently above 0.80 and broadly conserved across N treatments. Multivariate trait analysis identified fruit yield N concentration (NUE component, CN,y), shoot biomass N content (NAb), and shoot growth-related traits as the main drivers of treatment differentiation. Finally, proxy traits were prioritized by integrating response magnitude, heritability, trait correlations, and treatment-discriminatory power into multi-trait selection indices. This strategy generated favorable predicted genetic gains, reaching 158% for high-performance lines and 170% for subN-adapted lines, and consistently identified lines 402, 428, 518, 800, and 816 as promising pre-breeding materials. Overall, this study supports ToMAGIC as a powerful resource for developing N-efficient cultivars suited for sustainable agriculture.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229939","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":"Population genomics of a rare and endangered semi-wild cucumber ( Cucumis sativus var. xishuangbannanensis ) reveals genetic architecture of seasonal flowering, fruit morphology, and carotenoid accumulation","authors":"Huixia Jia, Jiyan Zang, Jiangping Song, Tingting Zhang, Yumin Tan, Mengzhen Wang, Xiaohui Zhang, Wenlong Yang, Yanfei Yang, Yanhui Pang, Ruifeng Wang, Haiping Wang","doi":"10.1093/hr/uhag446","DOIUrl":"https://doi.org/10.1093/hr/uhag446","url":null,"abstract":"The Xishuangbanna cucumber (Cucumis sativus var. xishuangbannanensis, XIS) is a rare and endangered semi-wild variety endemic to Yunnan Province, China. It possesses orange-fleshed fruits, large fruit mass, excellent storage tolerance, and disease resistance, making it a valuable resource for cucumber genetic improvement. However, genetic basis underlying its key agronomic traits remains largely unexplored. Here, we present a telomere-to-telomere gapless genome assembly of the XIS (322.9 Mb). Whole-genome resequencing of 342 XIS accessions identified 1,482,096 SNPs, 267,632 INDELs, 19,475 SVs, and 5,739 CNVs. Comparative population genomics between stable and unstable seasonal flowering accessions identified 248 selected genes commonly detected by XP-CLR, FST, and πSFF/πUSFF, revealing an integrated regulatory network converging on photoperiod and circadian clock (e.g., CONSTANS-like), flowering time (FY, SPL4), and multiple hormone signaling pathways (ARF9, MYC2, AOS1, GSK3). Genome-wide association study identified 4,109 variants significantly associated with flower and fruit traits, yielding 2,709 candidate genes. Two major hotspots on chromosome 1 harboring FT and COP1 were associated with multiple flower traits. Additionally, a distinct auxin-related cluster comprising TMK4 and HDA8 was identified as a key regulator of fruit morphology. Quantification of 68 carotenoid compounds revealed high inter-accession variation, with β-carotene, β-cryptoxanthin, and (E/Z)-phytoene being predominant. These carotenoid compounds were associated with a set of candidate genes including core carotenoids pathway genes BCH1, DXS, PDS, PSY, and LCYB, multiple transcription factors, etc. This work provides insights into seasonal flowering, fruit morphology, and carotenoid accumulation, establishing foundation for conservation and utilization of XIS, enabling genomics-assisted breeding of cucumber varieties.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229935","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":"Machine learning reveals potato powdery scab resistance genes","authors":"Dai Zhang, Jingyan Liu, Baokun Zheng, Xin Zhang, Caishu Yue, Di Lu, Ran Qiang, Qian Li, Yang Pan, Dongmei Zhao, Haibin Jiang, Jianfei Xu, Jiehua Zhu, Zhihui Yang","doi":"10.1093/hr/uhag441","DOIUrl":"https://doi.org/10.1093/hr/uhag441","url":null,"abstract":"Powdery scab, caused by the soil-borne pathogen Spongospora subterranea f. sp. subterranea, is a destructive potato disease causing substantial yield losses and reduced marketability. However, tuber-specific resistance mechanisms remain poorly understood, largely due to phenotyping bottlenecks and the dynamic infection process. Here, we developed an integrated AI-omics pipeline combining deep-learning-based image analysis with machine-learning-driven transcriptomic modelling to dissect the genetic architecture of resistance. Automated disease quantification across 12 cultivars over a 118-day growth cycle revealed tuber initiation and expansion as the two critical infection windows. Integration of high-resolution phenotypic data with transcriptomic profiling and a consensus machine-learning framework prioritized 292 high-confidence candidate genes. Functional categorisation identified lignin biosynthesis as a core defence hub, with seven lignin-associated genes, including the rate-limiting enzyme CCR and three MYB transcription factors, consistently selected across complementary algorithms. Cross-dataset validation confirmed the directional robustness of the resistance signature (68.8% concordance). Virus-induced gene silencing of St4CL1 and StCCoAOMT1 compromised resistance and reduced lignin accumulation, functionally validating the pathway’s contribution to tuber defence. Beyond lignin, our pipeline ranked several poorly characterised genes, including EDNR2GH7 and DIV3B, as high-priority candidates, pointing to additional novel resistance components. This integrative framework enables objective, high-throughput resistance screening, eliminates observer bias, and provides a broadly applicable blueprint for accelerating molecular breeding in other crop–pathogen systems constrained by conventional phenotyping.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"9 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229940","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":"mRNA splicing links surface immunity to NLR activation: implications for horticultural disease resistance","authors":"Jian Meng,Shaoling Zhang,Xiaosan Huang","doi":"10.1093/hr/uhag431","DOIUrl":"https://doi.org/10.1093/hr/uhag431","url":null,"abstract":"","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"26 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149209278","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":"Reframing Citrus Iron Deficiency Chlorosis as a Whole-Tree Iron Homeostasis Disorder","authors":"Tianchi Jiang, Wan Zhou, Yiming Ma, Patrick Brown, Lingli Lu","doi":"10.1093/hr/uhag436","DOIUrl":"https://doi.org/10.1093/hr/uhag436","url":null,"abstract":"Iron deficiency chlorosis is a recurrent nutritional disorder that limits citrus growth, productivity and fruit quality, especially in calcareous, saline-alkaline and bicarbonate-rich orchards. Although it is often attributed to poor iron bioavailability in the rhizosphere, its persistence and recurrence cannot be explained by soil chemistry or root uptake alone. Citrus trees are perennial evergreen fruit crops with concurrent sinks, including roots, mature leaves, young flushes, flowers and developing fruits; therefore, iron nutrition depends on rootstock genotype, vascular transport, phloem remobilization, leaf-level iron bioavailability and seasonal source-sink allocation. Here, we reframe citrus iron deficiency chlorosis as a systemic disorder of whole-tree iron homeostasis. We synthesize citrus-specific evidence and broader plant iron-homeostasis concepts to connect rhizosphere iron mobilization, Strategy I root responses, rootstock-mediated acquisition, long-distance transport, the leaf iron paradox, reproductive sink allocation, management strategies and emerging multi-omics approaches. We emphasize that total iron concentration alone is insufficient for diagnosis because iron may be spatially misallocated, chemically immobilized or physiologically unavailable even when bulk levels appear adequate. We further propose a bottleneck-oriented diagnostic workflow linking symptom timing, soil and irrigation constraints, active iron status, root acquisition capacity, vascular transport, spatial localization and confounding stresses to targeted management. This framework provides a crop-specific roadmap for identifying dominant homeostasis bottlenecks, improving iron-efficient rootstock selection and designing precision strategies for recurrent citrus chlorosis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"10 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187923","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":"Grafting-associated chilling tolerance in grapevine involves VvERF113-regulated stilbene biosynthesis and changes in chromatin accessibility","authors":"Bin Han, Yanyan Zheng, Jingjing Li, Xuanyu Chen, Minmin Li, Zain Ali, Wenyuan Wang, Yonggang Yin, Shuli Han, Changjiang Liu, Nan Jia, Xinyu Wang, Pingyin Guan, Yan Sun, Yang Liu","doi":"10.1093/hr/uhag433","DOIUrl":"https://doi.org/10.1093/hr/uhag433","url":null,"abstract":"Grapevine (Vitis vinifera L.) is highly sensitive to low temperature, yet the molecular basis by which rootstocks improve scion chilling tolerance remains poorly understood. Here, we show that the cold-tolerant rootstock CR3 markedly enhances chilling tolerance in the grape cultivar ‘Miguang’. Integrated ATAC-seq and RNA-seq analyses revealed that grafted plants underwent broader chilling-induced changes in chromatin accessibility than self-rooted plants, particularly in genomic regions associated with stress responses and secondary metabolism. Among these pathways, stilbene biosynthesis was strongly activated in grafted plants, accompanied by increased expression of VvSTS genes and higher accumulation of stilbene compounds. Exogenous resveratrol treatment further alleviated chilling-induced damage, supporting a protective role for stilbenes in grapevine chilling adaptation. We further identified the ethylene-responsive transcription factor VvERF113 as a direct repressor of VvSTS expression. Overexpression of VvERF113 suppressed stilbene accumulation and reduced chilling tolerance, whereas RNA interference of VvERF113 promoted stilbene biosynthesis and enhanced chilling tolerance. Together, these findings indicate that repression of VvERF113 in grafted plants may contribute to the enhanced activation of the stilbene pathway associated with CR3 grafting, thereby improving grapevine chilling tolerance, and provide a mechanistic framework for enhancing cold resistance through scion-rootstock interactions.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187920","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":"Generating popcorn-like fragrant Chinese cabbage via CRISPR/Cas9-mediated\u0000 BraBADH2\u0000 gene editing","authors":"Yunxiao Wei,Xiaojing Zeng,Lingyan Xu,Fei Li,Hui Zhang,Qiannan Zhang,Shifan Zhang,Rifei Sun,Rui Zhang,Jianjun Zhao,Shujiang Zhang,Guoliang Li","doi":"10.1093/hr/uhag437","DOIUrl":"https://doi.org/10.1093/hr/uhag437","url":null,"abstract":"","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"14 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149209279","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":"Population structure and genetic mapping of important agronomic traits in\u0000 Perilla frutescens","authors":"Xu Li,Duan Wu,Wei Zhang,He Wen,Zhiwei Shang,Qi Shen","doi":"10.1093/hr/uhag413","DOIUrl":"https://doi.org/10.1093/hr/uhag413","url":null,"abstract":"","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149209280","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":"Potassium sulfate modulates FabHLH18-like expression by a dual mechanism to regulate sugar and anthocyanin accumulation in strawberries","authors":"Zihui Zhang, Shanna Yi, Wenjie Yu, Yan Wang, Zhihong Zhang, He Li","doi":"10.1093/hr/uhag439","DOIUrl":"https://doi.org/10.1093/hr/uhag439","url":null,"abstract":"Sugar and anthocyanin contents are key indicators of both the intrinsic and extrinsic qualities of fruits. Application of potassium fertilizers can significantly improve fruit quality in crops; however, the specific molecular regulatory mechanisms underlying this effect remain unclear. In this study, treatment with potassium sulfate significantly improved strawberry fruit quality, while FabHLH18-like was significantly upregulated. Stable and transient transformation of FabHLH18-like in cultivated strawberry ‘Yanli’ both demonstrated that it can increase the sugar and anthocyanin contents. Meanwhile, transient transformation of FaINV and FaANS in cultivated strawberry ‘Yanli’ demonstrated that FaINV can convert sucrose into glucose and fructose, while FaANS can increase anthocyanin synthesis in fruits. Furthermore, the FabHLH18-like protein binds to the promoters of FaINV and FaANS, thereby promoting their expression. FaMYB6-like induced FaHLH18-like-mediated activation of FaINV to increase sugar contents in strawberry fruits; FaWRKY57 and FabHLH18-like synergistically regulated FaANS expression to jointly promote anthocyanin accumulation in strawberry fruits. Furthermore, under potassium sulfate treatment, FaChip expression decreased, weakening its effect in ubiquitinating and degrading FabHLH18-like; simultaneously, the potassium transporter FaPOT3 was continuously transported into fruits following potassium sulfate treatment, thereby enhancing the promotional effect of FabHLH18-like on sugar and anthocyanin contents in strawberry fruits. Our findings are the first to reveal the regulatory pathway through which potassium fertilizers improve strawberry fruit quality by inducing the upregulation of FabHLH18-like, providing molecular targets for enhancing crop fruit quality while offering a theoretical and scientific basis for using potassium fertilizers.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"48 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187927","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":"Establishment of a maternal haploid induction system in petunia via CRISPR/Cas9-mediated editing of\u0000 PhDMP8/9","authors":"Guoqi Xu,Yu Ma,Lanyu Cao,Jiaojiao Wang,Chenxin Li,Yuxin Yan,Yingjia Zeng,Jiafa Wang,Shujuan Tian,Li Yuan,Man Liu","doi":"10.1093/hr/uhag414","DOIUrl":"https://doi.org/10.1093/hr/uhag414","url":null,"abstract":"","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"236 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210417","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}